diff --git a/.github/workflows/debug_checks.yml b/.github/workflows/debug_checks.yml
index a4da80bc5..468547737 100644
--- a/.github/workflows/debug_checks.yml
+++ b/.github/workflows/debug_checks.yml
@@ -18,7 +18,7 @@ jobs:
       - uses: mpi4py/setup-mpi@v1
         with:
           mpi: 'openmpi'
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
           arch: x64
diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index b563a2f0d..405ffcb9e 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -14,10 +14,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-          arch: x64
       - uses: julia-actions/cache@v1
       - name: Test examples
         run: |
diff --git a/.github/workflows/longtest.yml b/.github/workflows/longtest.yml
index 9acc1f36b..80b9a9677 100644
--- a/.github/workflows/longtest.yml
+++ b/.github/workflows/longtest.yml
@@ -19,10 +19,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-          arch: x64
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
         with:
diff --git a/.github/workflows/parallel_test.yml b/.github/workflows/parallel_test.yml
index 30416a0f5..88fd99e63 100644
--- a/.github/workflows/parallel_test.yml
+++ b/.github/workflows/parallel_test.yml
@@ -17,7 +17,7 @@ jobs:
       - uses: mpi4py/setup-mpi@v1
         with:
           mpi: 'openmpi'
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
           arch: x64
@@ -49,14 +49,14 @@ jobs:
       - uses: mpi4py/setup-mpi@v1
         with:
           mpi: 'openmpi'
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-          arch: x64
       - uses: julia-actions/cache@v1
       - run: |
+          MPILIBPATH=$(find /opt/homebrew/Cellar/open-mpi/ -name libmpi.dylib)
           touch Project.toml
-          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_system_binary()'
+          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_system_binary(library_names="/opt/homebrew/Cellar/open-mpi/5.0.3/lib/libmpi.dylib")'
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["NCDatasets", "Random", "SpecialFunctions", "Test"]); Pkg.develop(path="moment_kinetics/")'
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.precompile()'
           # Need to use openmpi so that the following arguments work:
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ccaca9dc0..edb0bffa2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,10 +18,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-          arch: x64
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
         with:
diff --git a/.gitignore b/.gitignore
index 4d3aedd9f..a6eaf3e33 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,3 +26,4 @@ makie_postproc.so
 plots_postproc.so
 precompile-temp
 post_processing_input.toml
+.DS_Store
diff --git a/docs/src/external_sources_notes.md b/docs/src/external_sources_notes.md
index f805d1552..bdaadeffc 100644
--- a/docs/src/external_sources_notes.md
+++ b/docs/src/external_sources_notes.md
@@ -14,8 +14,8 @@ S_n &= A_n(r,z) \frac{1}{(\pi)^{3/2} (2 T_{\mathrm{source},n} / m_n)^{3/2}} \exp
 or in 1V simulations that do not include $v_\perp$, $v_\zeta$, $v_r$ dimensions
 ```math
 \begin{align}
-S_i &= A_i(r,z) \frac{1}{sqrt{\pi} \sqrt{2 T_{\mathrm{source},i} / m_i}} \exp\left( -\frac{v_\perp^2}{T_{\mathrm{source},i}} \right) \\
-S_n &= A_n(r,z) \frac{1}{sqrt{\pi} \sqrt{2 T_{\mathrm{source},n} / m_n}} \exp\left( -\frac{v_z^2}{T_{\mathrm{source},n}} \right)
+S_i &= A_i(r,z) \frac{1}{\sqrt{\pi} \sqrt{2 T_{\mathrm{source},i} / m_i}} \exp\left( -\frac{v_\perp^2}{T_{\mathrm{source},i}} \right) \\
+S_n &= A_n(r,z) \frac{1}{\sqrt{\pi} \sqrt{2 T_{\mathrm{source},n} / m_n}} \exp\left( -\frac{v_z^2}{T_{\mathrm{source},n}} \right)
 \end{align}
 ```
 
diff --git a/docs/src/moment_kinetic_equations.md b/docs/src/moment_kinetic_equations.md
index c21735b04..5f5f81a40 100644
--- a/docs/src/moment_kinetic_equations.md
+++ b/docs/src/moment_kinetic_equations.md
@@ -1018,7 +1018,7 @@ and for neutrals where several of the ionization terms cancel
   & \qquad-\frac{w_{\|,n}}{2}\frac{1}{p_{\|,n}}\left(-\frac{\partial q_{\|,n}}{\partial z}
   - R_{in}\left(n_{i}p_{\|,n} - n_{n}p_{\|,i}
   - n_{n}n_{i}\left(u_{n} - u_{i}\right)^{2}\right)
-  + \int dv_\parallel S_{n} + u_{n}^2\int dv_\parallel v_\parallel^2 S_{n}
+  + \int dv_\parallel v_\parallel^2 S_{n} + u_{n}^2\int dv_\parallel S_{n}
   + v_{\mathrm{th},n}w_{\|,n}\frac{\partial p_{\|,n}}{\partial z}\right) \\
   & \qquad\left. + \frac{w_{\parallel,n}}{2}\frac{1}{n_{n}}\int dv_\parallel S_{n}
   + \frac{w_{\|,n}^{2}}{2}\frac{v_{\mathrm{th},n}}{n_{n}}\frac{\partial n_{n}}{\partial z}\right]\frac{\partial g_{n}}{\partial w_{\|,n}} \\
diff --git a/examples/fokker-planck-1D2V/fokker-planck-1D2V-even_nz-shorttest-nstep200.toml b/examples/fokker-planck-1D2V/fokker-planck-1D2V-even_nz-shorttest-nstep200.toml
index 1b8758f47..eb7d60b18 100644
--- a/examples/fokker-planck-1D2V/fokker-planck-1D2V-even_nz-shorttest-nstep200.toml
+++ b/examples/fokker-planck-1D2V/fokker-planck-1D2V-even_nz-shorttest-nstep200.toml
@@ -86,7 +86,7 @@ vperp_discretization = "gausslegendre_pseudospectral"
 #vzeta_bc = "periodic"
 #vzeta_discretization = "chebyshev_pseudospectral"
 
-#[numerical_dissipation]
+#[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.0
 #vperp_dissipation_coefficient = 0.0
 #z_dissipation_coefficient = 0.1
diff --git a/examples/geometry/1D-mirror.toml b/examples/geometry/1D-mirror.toml
index 66c36fd5b..eb484f49d 100644
--- a/examples/geometry/1D-mirror.toml
+++ b/examples/geometry/1D-mirror.toml
@@ -71,7 +71,7 @@ vz_L = 18.0
 vz_bc = "both_zero"
 vz_discretization = "chebyshev_pseudospectral"
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
 vperp_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
 force_minimum_pdf_value = 0.0
diff --git a/examples/gk-ions/2D-periodic-gk.toml b/examples/gk-ions/2D-periodic-gk.toml
index df3f04e7d..36a8eacb3 100644
--- a/examples/gk-ions/2D-periodic-gk.toml
+++ b/examples/gk-ions/2D-periodic-gk.toml
@@ -73,15 +73,19 @@ vz_L = 18.0
 vz_bc = "both_zero"
 vz_discretization = "chebyshev_pseudospectral"
 
-[numerical_dissipation]
-vpa_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
-vperp_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
-#r_disspipation_coefficient = 1.0e-3
-#force_minimum_pdf_value = 0.0
-
 [geometry]
 #option="1D-mirror"
 DeltaB=0.0
 option="constant-helical"
 pitch=0.1
 rhostar= 0.1
+
+[ion_numerical_dissipation]
+vpa_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
+vperp_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
+#r_disspipation_coefficient = 1.0e-3
+#force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+moment_dissipation_coefficient = 0.0001
+vz_dissipation_coefficient = 0.01
\ No newline at end of file
diff --git a/examples/numerical-dissipation/num-diss-relaxation.toml b/examples/numerical-dissipation/num-diss-relaxation.toml
index e196c2e84..6fb8b0086 100644
--- a/examples/numerical-dissipation/num-diss-relaxation.toml
+++ b/examples/numerical-dissipation/num-diss-relaxation.toml
@@ -58,7 +58,7 @@ nwrite = 2000
 nwrite_dfns = 2000
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.1
 vperp_dissipation_coefficient = 0.1
 z_dissipation_coefficient = -1.0
diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3-init.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3-init.toml
index 9a0e2120d..5efe4c239 100644
--- a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3-init.toml
+++ b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3-init.toml
@@ -81,8 +81,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3.toml
index 7b74635ff..4436f7f8d 100644
--- a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3.toml
+++ b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3.toml
@@ -81,8 +81,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete104.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete104.toml
index 2719cc899..2843b91f8 100644
--- a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete104.toml
+++ b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete104.toml
@@ -87,8 +87,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete43.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete43.toml
index ac78baeb3..82c8e1ff1 100644
--- a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete43.toml
+++ b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete43.toml
@@ -87,8 +87,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete64.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete64.toml
index 3c9c289dc..8753de127 100644
--- a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete64.toml
+++ b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete64.toml
@@ -88,7 +88,7 @@ source_strength = 2.0
 source_T = 2.0
 
 [numerical_dissipation]
-#vpa_dissipation_coefficient = 1.0e-1
-#vpa_dissipation_coefficient = 1.0e-2
-#vpa_dissipation_coefficient = 1.0e-3
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
diff --git a/examples/wall-bc/wall-bc_cheb.toml b/examples/wall-bc/wall-bc_cheb.toml
index cd0dce518..4a076b110 100644
--- a/examples/wall-bc/wall-bc_cheb.toml
+++ b/examples/wall-bc/wall-bc_cheb.toml
@@ -65,6 +65,10 @@ dt = 1.0e-5
 nwrite = 1000
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
+force_minimum_pdf_value = 0.0
\ No newline at end of file
diff --git a/examples/wall-bc/wall-bc_cheb_split1.toml b/examples/wall-bc/wall-bc_cheb_split1.toml
index e995fd5f1..4c57ebf48 100644
--- a/examples/wall-bc/wall-bc_cheb_split1.toml
+++ b/examples/wall-bc/wall-bc_cheb_split1.toml
@@ -66,6 +66,10 @@ dt = 1.0e-5
 nwrite = 1000
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
+force_minimum_pdf_value = 0.0
\ No newline at end of file
diff --git a/examples/wall-bc/wall-bc_cheb_split2.toml b/examples/wall-bc/wall-bc_cheb_split2.toml
index 32ca888ff..53f29f0ac 100644
--- a/examples/wall-bc/wall-bc_cheb_split2.toml
+++ b/examples/wall-bc/wall-bc_cheb_split2.toml
@@ -66,6 +66,10 @@ dt = 1.0e-5
 nwrite = 1000
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
+force_minimum_pdf_value = 0.0
\ No newline at end of file
diff --git a/examples/wall-bc/wall-bc_cheb_split3.toml b/examples/wall-bc/wall-bc_cheb_split3.toml
index b400adb5a..3db98a2da 100644
--- a/examples/wall-bc/wall-bc_cheb_split3.toml
+++ b/examples/wall-bc/wall-bc_cheb_split3.toml
@@ -66,6 +66,10 @@ dt = 1.0e-5
 nwrite = 1000
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-3 #1.0e-2 #1.0e-1
+force_minimum_pdf_value = 0.0
\ No newline at end of file
diff --git a/examples/wall-bc/wall-bc_no-neutrals.toml b/examples/wall-bc/wall-bc_no-neutrals.toml
index 267247630..ce5da5ba8 100644
--- a/examples/wall-bc/wall-bc_no-neutrals.toml
+++ b/examples/wall-bc/wall-bc_no-neutrals.toml
@@ -77,7 +77,7 @@ z_width = 0.125
 source_strength = 8.0
 source_T = 1.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
diff --git a/examples/wall-bc/wall-bc_no-neutrals_split1.toml b/examples/wall-bc/wall-bc_no-neutrals_split1.toml
index 1350ba3dc..cae94a045 100644
--- a/examples/wall-bc/wall-bc_no-neutrals_split1.toml
+++ b/examples/wall-bc/wall-bc_no-neutrals_split1.toml
@@ -77,7 +77,7 @@ z_width = 0.125
 source_strength = 8.0
 source_T = 1.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
diff --git a/examples/wall-bc/wall-bc_no-neutrals_split2.toml b/examples/wall-bc/wall-bc_no-neutrals_split2.toml
index fb63806b1..ce74ec368 100644
--- a/examples/wall-bc/wall-bc_no-neutrals_split2.toml
+++ b/examples/wall-bc/wall-bc_no-neutrals_split2.toml
@@ -77,7 +77,7 @@ z_width = 0.125
 source_strength = 8.0
 source_T = 1.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
diff --git a/examples/wall-bc/wall-bc_no-neutrals_split3.toml b/examples/wall-bc/wall-bc_no-neutrals_split3.toml
index bb1b29b69..23316e611 100644
--- a/examples/wall-bc/wall-bc_no-neutrals_split3.toml
+++ b/examples/wall-bc/wall-bc_no-neutrals_split3.toml
@@ -77,7 +77,7 @@ z_width = 0.125
 source_strength = 8.0
 source_T = 1.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
diff --git a/examples/wall-bc/wall-bc_volumerecycle.toml b/examples/wall-bc/wall-bc_volumerecycle.toml
index bd1d59cc3..1cbf7f1b2 100644
--- a/examples/wall-bc/wall-bc_volumerecycle.toml
+++ b/examples/wall-bc/wall-bc_volumerecycle.toml
@@ -84,12 +84,18 @@ active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 #force_minimum_pdf_value = 0.0
 
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
+
 [krook_collisions]
 use_krook = true
 frequency_option = "reference_parameters"
\ No newline at end of file
diff --git a/examples/wall-bc/wall-bc_volumerecycle_split1.toml b/examples/wall-bc/wall-bc_volumerecycle_split1.toml
index c81531273..442ce033d 100644
--- a/examples/wall-bc/wall-bc_volumerecycle_split1.toml
+++ b/examples/wall-bc/wall-bc_volumerecycle_split1.toml
@@ -84,12 +84,18 @@ active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 #force_minimum_pdf_value = 0.0
 
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+#force_minimum_pdf_value = 0.0
+
 [krook_collisions]
 use_krook = true
 frequency_option = "reference_parameters"
\ No newline at end of file
diff --git a/examples/wall-bc/wall-bc_volumerecycle_split2.toml b/examples/wall-bc/wall-bc_volumerecycle_split2.toml
index 24fb262f9..08eb2ed6c 100644
--- a/examples/wall-bc/wall-bc_volumerecycle_split2.toml
+++ b/examples/wall-bc/wall-bc_volumerecycle_split2.toml
@@ -84,12 +84,18 @@ active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 #force_minimum_pdf_value = 0.0
 
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+#force_minimum_pdf_value = 0.0
+
 [krook_collisions]
 use_krook = true
 frequency_option = "reference_parameters"
\ No newline at end of file
diff --git a/examples/wall-bc/wall-bc_volumerecycle_split3.toml b/examples/wall-bc/wall-bc_volumerecycle_split3.toml
index 3441d6a4f..0c8dad98d 100644
--- a/examples/wall-bc/wall-bc_volumerecycle_split3.toml
+++ b/examples/wall-bc/wall-bc_volumerecycle_split3.toml
@@ -84,12 +84,18 @@ active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
 
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
+
 [krook_collisions]
 use_krook = true
 frequency_option = "reference_parameters"
\ No newline at end of file
diff --git a/machines/marconi/julia.env b/machines/marconi/julia.env
index 43b24569e..dfb006696 100644
--- a/machines/marconi/julia.env
+++ b/machines/marconi/julia.env
@@ -2,7 +2,7 @@
 
 module purge
 module load env-skl profile/base profile/advanced
-module load gnu/7.3.0 openmpi/3.1.4--gnu--7.3.0 intel/pe-xe-2018--binary python/3.9.4
+module load gnu/7.3.0 openmpi/3.1.4--gnu--7.3.0 intel/pe-xe-2018--binary python/3.9.4 git/2.17
 # Needed because Julia's Cairo library complains about libz<1.2.9
 module load zlib/1.2.11--intel--pe-xe-2018--binary
 
diff --git a/makie_post_processing/makie_post_processing/src/makie_post_processing.jl b/makie_post_processing/makie_post_processing/src/makie_post_processing.jl
index 31376995f..725a16e86 100644
--- a/makie_post_processing/makie_post_processing/src/makie_post_processing.jl
+++ b/makie_post_processing/makie_post_processing/src/makie_post_processing.jl
@@ -30,10 +30,7 @@ using moment_kinetics.analysis: analyze_fields_data, check_Chodura_condition,
                                 get_unnormalised_f_2d
 using moment_kinetics.array_allocation: allocate_float
 using moment_kinetics.coordinates: define_coordinate
-using moment_kinetics.input_structs: grid_input, advection_input,
-                                     set_defaults_and_check_top_level!,
-                                     set_defaults_and_check_section!, Dict_to_NamedTuple
-using moment_kinetics.krook_collisions: get_collision_frequency
+using moment_kinetics.input_structs
 using moment_kinetics.looping: all_dimensions, ion_dimensions, neutral_dimensions
 using moment_kinetics.manufactured_solns: manufactured_solutions,
                                           manufactured_electric_fields
@@ -303,11 +300,13 @@ function makie_post_process(run_dir::Union{String,Tuple},
         end
     end
 
-    plot_charged_pdf_2D_at_wall(run_info_dfns; plot_prefix=plot_prefix)
+    plot_ion_pdf_2D_at_wall(run_info_dfns; plot_prefix=plot_prefix)
     if has_neutrals
         plot_neutral_pdf_2D_at_wall(run_info_dfns; plot_prefix=plot_prefix)
     end
 
+    constraints_plots(run_info; plot_prefix=plot_prefix)
+
     if has_rdim
         # Plots for 2D instability do not make sense for 1D simulations
         instability_input = input_dict["instability2D"]
@@ -541,11 +540,36 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
         nz_min = 1
     end
     if dfns && has_run_info
-        nvperp_min = minimum(ri.vperp.n for ri in run_info if ri !== nothing)
-        nvpa_min = minimum(ri.vpa.n for ri in run_info if ri !== nothing)
-        nvzeta_min = minimum(ri.vzeta.n for ri in run_info if ri !== nothing)
-        nvr_min = minimum(ri.vr.n for ri in run_info if ri !== nothing)
-        nvz_min = minimum(ri.vz.n for ri in run_info if ri !== nothing)
+        if any(ri.vperp !== nothing for ri ∈ run_info)
+            nvperp_min = minimum(ri.vperp.n for ri in run_info
+                                 if ri !== nothing && ri.vperp !== nothing)
+        else
+            nvperp_min = 1
+        end
+        if any(ri.vpa !== nothing for ri ∈ run_info)
+            nvpa_min = minimum(ri.vpa.n for ri in run_info
+                               if ri !== nothing && ri.vpa !== nothing)
+        else
+            nvpa_min = 1
+        end
+        if any(ri.vzeta !== nothing for ri ∈ run_info)
+            nvzeta_min = minimum(ri.vzeta.n for ri in run_info
+                                 if ri !== nothing && ri.vzeta !== nothing)
+        else
+            nvzeta_min = 1
+        end
+        if any(ri.vr !== nothing for ri ∈ run_info)
+            nvr_min = minimum(ri.vr.n for ri in run_info
+                              if ri !== nothing && ri.vr !== nothing)
+        else
+            nvr_min = 1
+        end
+        if any(ri.vz !== nothing for ri ∈ run_info)
+            nvz_min = minimum(ri.vz.n for ri in run_info
+                              if ri !== nothing && ri.vz !== nothing)
+        else
+            nvz_min = 1
+        end
     else
         nvperp_min = 1
         nvpa_min = 1
@@ -684,6 +708,22 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
         animation_ext=this_input_dict["animation_ext"],
        )
 
+    set_defaults_and_check_section!(
+        this_input_dict, "constraints";
+        plot=false,
+        animate=false,
+        it0=this_input_dict["it0"],
+        ir0=this_input_dict["ir0"],
+        iz0=this_input_dict["iz0"],
+        ivperp0=this_input_dict["ivperp0"],
+        ivpa0=this_input_dict["ivpa0"],
+        ivzeta0=this_input_dict["ivzeta0"],
+        ivr0=this_input_dict["ivr0"],
+        ivz0=this_input_dict["ivz0"],
+        animation_ext=this_input_dict["animation_ext"],
+        show_element_boundaries=this_input_dict["show_element_boundaries"],
+       )
+
     set_defaults_and_check_section!(
         this_input_dict, "Chodura_condition";
         plot_vs_t=false,
@@ -1263,7 +1303,7 @@ end
 for dim ∈ one_dimension_combinations
     function_name_str = "plot_vs_$dim"
     function_name = Symbol(function_name_str)
-    spaces = " " ^ length(function_name_str)
+    spaces = " " ^ (length(function_name_str) + 1)
     dim_str = String(dim)
     if dim == :t
         dim_grid = :( run_info.time )
@@ -1275,17 +1315,17 @@ for dim ∈ one_dimension_combinations
              export $function_name
 
              """
-             function $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, outfile=nothing, yscale=nothing,
-                      transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
-                      $($spaces)ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
-                      $($spaces)ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
-             function $($function_name_str)(run_info, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, ax=nothing, label=nothing,
-                      $($spaces)outfile=nothing, yscale=nothing, transform=identity,
-                      $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
-                      $($spaces)iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
-                      $($spaces)ivr=nothing, ivz=nothing, kwargs...)
+                 $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, outfile=nothing, yscale=nothing,
+                 transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
+                 $($spaces)ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
+                 $($spaces)ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
+                 $($function_name_str)(run_info, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, ax=nothing, label=nothing,
+                 $($spaces)outfile=nothing, yscale=nothing, transform=identity,
+                 $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
+                 $($spaces)iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
+                 $($spaces)ivr=nothing, ivz=nothing, kwargs...)
 
              Plot `var_name` from the run(s) represented by `run_info` (as returned by
              [`get_run_info`](@ref)) vs $($dim_str).
@@ -1350,7 +1390,7 @@ for dim ∈ one_dimension_combinations
                      if input === nothing
                          if run_info[1].dfns
                              if var_name ∈ keys(input_dict_dfns)
-                                 input = input_dict[var_name]
+                                 input = input_dict_dfns[var_name]
                              else
                                  input = input_dict_dfns
                              end
@@ -1412,7 +1452,7 @@ for dim ∈ one_dimension_combinations
                  if input === nothing
                      if run_info.dfns
                          if var_name ∈ keys(input_dict_dfns)
-                             input = input_dict[var_name]
+                             input = input_dict_dfns[var_name]
                          else
                              input = input_dict_dfns
                          end
@@ -1481,7 +1521,7 @@ end
 for (dim1, dim2) ∈ two_dimension_combinations
     function_name_str = "plot_vs_$(dim2)_$(dim1)"
     function_name = Symbol(function_name_str)
-    spaces = " " ^ length(function_name_str)
+    spaces = " " ^ (length(function_name_str) + 1)
     dim1_str = String(dim1)
     dim2_str = String(dim2)
     if dim1 == :t
@@ -1496,19 +1536,19 @@ for (dim1, dim2) ∈ two_dimension_combinations
              export $function_name
 
              """
-             function $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, outfile=nothing, colorscale=identity,
-                      $($spaces)transform=identity, axis_args=Dict{Symbol,Any}(),
-                      $($spaces)it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
-                      $($spaces)ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
-                      $($spaces)kwargs...)
-             function $($function_name_str)(run_info, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, ax=nothing,
-                      $($spaces)colorbar_place=nothing, title=nothing,
-                      $($spaces)outfile=nothing, colorscale=identity, transform=identity,
-                      $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
-                      $($spaces)iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
-                      $($spaces)ivr=nothing, ivz=nothing, kwargs...)
+                 $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, outfile=nothing, colorscale=identity,
+                 $($spaces)transform=identity, axis_args=Dict{Symbol,Any}(),
+                 $($spaces)it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
+                 $($spaces)ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
+                 $($spaces)kwargs...)
+                 $($function_name_str)(run_info, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, ax=nothing,
+                 $($spaces)colorbar_place=nothing, title=nothing,
+                 $($spaces)outfile=nothing, colorscale=identity, transform=identity,
+                 $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
+                 $($spaces)iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
+                 $($spaces)ivr=nothing, ivz=nothing, kwargs...)
 
              Plot `var_name` from the run(s) represented by `run_info` (as returned by
              [`get_run_info`](@ref))vs $($dim1_str) and $($dim2_str).
@@ -1597,7 +1637,7 @@ for (dim1, dim2) ∈ two_dimension_combinations
                  if input === nothing
                      if run_info.dfns
                          if var_name ∈ keys(input_dict_dfns)
-                             input = input_dict[var_name]
+                             input = input_dict_dfns[var_name]
                          else
                              input = input_dict_dfns
                          end
@@ -1688,7 +1728,7 @@ end
 for dim ∈ one_dimension_combinations_no_t
     function_name_str = "animate_vs_$dim"
     function_name = Symbol(function_name_str)
-    spaces = " " ^ length(function_name_str)
+    spaces = " " ^ (length(function_name_str) + 1)
     dim_str = String(dim)
     dim_grid = :( run_info.$dim.grid )
     idim = Symbol(:i, dim)
@@ -1696,19 +1736,19 @@ for dim ∈ one_dimension_combinations_no_t
              export $function_name
 
              """
-             function $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, outfile=nothing, yscale=nothing,
-                      $($spaces)transform=identity, ylims=nothing,
-                      $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
-                      $($spaces)ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
-                      $($spaces)ivz=nothing, kwargs...)
-             function $($function_name_str)(run_info, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, frame_index=nothing, ax=nothing,
-                      $($spaces)fig=nothing, outfile=nothing, yscale=nothing,
-                      $($spaces)transform=identity, ylims=nothing,
-                      $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
-                      $($spaces)ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
-                      $($spaces)ivz=nothing, kwargs...)
+                 $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, outfile=nothing, yscale=nothing,
+                 $($spaces)transform=identity, ylims=nothing,
+                 $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
+                 $($spaces)ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
+                 $($spaces)ivz=nothing, kwargs...)
+                 $($function_name_str)(run_info, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, frame_index=nothing, ax=nothing,
+                 $($spaces)fig=nothing, outfile=nothing, yscale=nothing,
+                 $($spaces)transform=identity, ylims=nothing, label=nothing,
+                 $($spaces)axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
+                 $($spaces)ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
+                 $($spaces)ivz=nothing, kwargs...)
 
              Animate `var_name` from the run(s) represented by `run_info` (as returned by
              [`get_run_info`](@ref))vs $($dim_str).
@@ -1740,6 +1780,9 @@ for dim ∈ one_dimension_combinations_no_t
              When a single `run_info` is passed, an `Axis` can be passed to `ax`. If it
              is, the plot will be added to `ax`.
 
+             When a single `run_info` is passed, `label` can be passed to set a custom
+             label for the line. By default the `run_info.run_name` is used.
+
              `outfile` is required for animations unless `ax` is passed. The animation
              will be saved to a file named `outfile`.  The suffix determines the file
              type. If both `outfile` and `ax` are passed, then the `Figure` containing
@@ -1777,7 +1820,7 @@ for dim ∈ one_dimension_combinations_no_t
                      if input === nothing
                          if run_info[1].dfns
                              if var_name ∈ keys(input_dict_dfns)
-                                 input = input_dict[var_name]
+                                 input = input_dict_dfns[var_name]
                              else
                                  input = input_dict_dfns
                              end
@@ -1801,9 +1844,11 @@ for dim ∈ one_dimension_combinations_no_t
                              all(isapprox.(ri.time, run_info[1].time))
                              for ri ∈ run_info[2:end])
                          # All times are the same
-                         title = lift(i->string("t = ", run_info[1].time[i]), frame_index)
+                         time = select_slice(run_info[1].time, :t; input=input, it=it)
+                         title = lift(i->string("t = ", time[i]), frame_index)
                      else
-                         title = lift(i->join((string("t", irun, " = ", ri.time[i])
+                         time = select_slice(ri.time, :t; input=input, it=it)
+                         title = lift(i->join((string("t", irun, " = ", time[i])
                                                for (irun,ri) ∈ enumerate(run_info)), "; "),
                                       frame_index)
                      end
@@ -1849,14 +1894,14 @@ for dim ∈ one_dimension_combinations_no_t
              function $function_name(run_info, var_name; is=1, data=nothing,
                                      input=nothing, frame_index=nothing, ax=nothing,
                                      fig=nothing, outfile=nothing, yscale=nothing,
-                                     ylims=nothing, axis_args=Dict{Symbol,Any}(),
-                                     it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
-                                     ivpa=nothing, ivzeta=nothing, ivr=nothing,
-                                     ivz=nothing, kwargs...)
+                                     ylims=nothing, label=nothing,
+                                     axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
+                                     iz=nothing, ivperp=nothing, ivpa=nothing,
+                                     ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
                  if input === nothing
                      if run_info.dfns
                          if var_name ∈ keys(input_dict_dfns)
-                             input = input_dict[var_name]
+                             input = input_dict_dfns[var_name]
                          else
                              input = input_dict_dfns
                          end
@@ -1891,20 +1936,24 @@ for dim ∈ one_dimension_combinations_no_t
                      ind = frame_index
                  end
                  if ax === nothing
-                     title = lift(i->string("t = ", run_info.time[i]), ind)
+                     time = select_slice(run_info.time, :t; input=input, it=it)
+                     title = lift(i->string("t = ", time[i]), ind)
                      fig, ax = get_1d_ax(; xlabel="$($dim_str)",
                                          ylabel=get_variable_symbol(var_name),
                                          yscale=yscale, title=title, axis_args...)
                  else
                      fig = nothing
                  end
+                 if label === nothing
+                     label = run_info.run_name
+                 end
 
                  x = $dim_grid
                  if $idim !== nothing
                      x = x[$idim]
                  end
                  animate_1d(x, data; ax=ax, ylims=ylims, frame_index=ind,
-                            label=run_info.run_name, kwargs...)
+                            label=label, kwargs...)
 
                  if input.show_element_boundaries && fig !== nothing
                      element_boundary_inds =
@@ -1941,7 +1990,7 @@ end
 for (dim1, dim2) ∈ two_dimension_combinations_no_t
     function_name_str = "animate_vs_$(dim2)_$(dim1)"
     function_name = Symbol(function_name_str)
-    spaces = " " ^ length(function_name_str)
+    spaces = " " ^ (length(function_name_str) + 1)
     dim1_str = String(dim1)
     dim2_str = String(dim2)
     dim1_grid = :( run_info.$dim1.grid )
@@ -1952,20 +2001,20 @@ for (dim1, dim2) ∈ two_dimension_combinations_no_t
              export $function_name
 
              """
-             function $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, outfile=nothing, colorscale=identity,
-                      $($spaces)transform=identity, axis_args=Dict{Symbol,Any}(),
-                      $($spaces)it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
-                      $($spaces)ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
-                      $($spaces)kwargs...)
-             function $($function_name_str)(run_info, var_name; is=1, data=nothing,
-                      $($spaces)input=nothing, frame_index=nothing, ax=nothing,
-                      $($spaces)fig=nothing, colorbar_place=colorbar_place,
-                      $($spaces)title=nothing, outfile=nothing, colorscale=identity,
-                      $($spaces)transform=identity, axis_args=Dict{Symbol,Any}(),
-                      $($spaces)it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
-                      $($spaces)ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
-                      $($spaces)kwargs...)
+                 $($function_name_str)(run_info::Tuple, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, outfile=nothing, colorscale=identity,
+                 $($spaces)transform=identity, axis_args=Dict{Symbol,Any}(),
+                 $($spaces)it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
+                 $($spaces)ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
+                 $($spaces)kwargs...)
+                 $($function_name_str)(run_info, var_name; is=1, data=nothing,
+                 $($spaces)input=nothing, frame_index=nothing, ax=nothing,
+                 $($spaces)fig=nothing, colorbar_place=colorbar_place,
+                 $($spaces)title=nothing, outfile=nothing, colorscale=identity,
+                 $($spaces)transform=identity, axis_args=Dict{Symbol,Any}(),
+                 $($spaces)it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
+                 $($spaces)ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
+                 $($spaces)kwargs...)
 
              Animate `var_name` from the run(s) represented by `run_info` (as returned by
              [`get_run_info`](@ref))vs $($dim1_str) and $($dim2_str).
@@ -2036,10 +2085,12 @@ for (dim1, dim2) ∈ two_dimension_combinations_no_t
 
                      if length(run_info) > 1
                          title = get_variable_symbol(var_name)
-                         subtitles = (lift(i->string(ri.run_name, "\nt = ", ri.time[i]),
+                         time = select_slice(ri.time, :t; input=input, it=it)
+                         subtitles = (lift(i->string(ri.run_name, "\nt = ", time[i]),
                                            frame_index)
                                       for ri ∈ run_info)
                      else
+                         time = select_slice(run_info[1].time, :t; input=input, it=it)
                          title = lift(i->string(get_variable_symbol(var_name), "\nt = ",
                                                 run_info[1].time[i]),
                                       frame_index)
@@ -2080,7 +2131,7 @@ for (dim1, dim2) ∈ two_dimension_combinations_no_t
                  if input === nothing
                      if run_info.dfns
                          if var_name ∈ keys(input_dict_dfns)
-                             input = input_dict[var_name]
+                             input = input_dict_dfns[var_name]
                          else
                              input = input_dict_dfns
                          end
@@ -2122,6 +2173,7 @@ for (dim1, dim2) ∈ two_dimension_combinations_no_t
                      colormap = input.colormap
                  end
                  if title === nothing && ax == nothing
+                     time = select_slice(run_info.time, :t; input=input, it=it)
                      title = lift(i->string(get_variable_symbol(var_name), "\nt = ",
                                             run_info.time[i]),
                                   ind)
@@ -3524,24 +3576,28 @@ function calculate_steady_state_residual end
 function calculate_steady_state_residual(run_info::Tuple, variable_name; is=1,
                                          data=nothing, plot_prefix=nothing,
                                          fig_axes=nothing)
-    n_runs = length(run_info)
-    if data === nothing
-        data = Tuple(nothing for _ ∈ 1:n_runs)
-    end
-    if fig_axes === nothing
-        fig_axes = _get_steady_state_residual_fig_axes(length(run_info))
-    end
+    try
+        n_runs = length(run_info)
+        if data === nothing
+            data = Tuple(nothing for _ ∈ 1:n_runs)
+        end
+        if fig_axes === nothing
+            fig_axes = _get_steady_state_residual_fig_axes(length(run_info))
+        end
 
-    for (i, (ri, d)) ∈ enumerate(zip(run_info, data))
-        calculate_steady_state_residual(ri, variable_name; is=is, data=d,
-                                        fig_axes=fig_axes, i_run=i)
-    end
+        for (i, (ri, d)) ∈ enumerate(zip(run_info, data))
+            calculate_steady_state_residual(ri, variable_name; is=is, data=d,
+                                            fig_axes=fig_axes, i_run=i)
+        end
 
-    if plot_prefix !== nothing
-        _save_residual_plots(fig_axes, plot_prefix)
-    end
+        if plot_prefix !== nothing
+            _save_residual_plots(fig_axes, plot_prefix)
+        end
 
-    return fig_axes
+        return fig_axes
+    catch e
+        println("Error in calculate_steady_state_residual(). Error was ", e)
+    end
 end
 
 function calculate_steady_state_residual(run_info, variable_name; is=1, data=nothing,
@@ -4302,9 +4358,9 @@ function animate_f_unnorm_vs_vpa_z(run_info; input=nothing, neutral=false, is=1,
 end
 
 """
-    plot_charged_pdf_2D_at_wall(run_info; plot_prefix)
+    plot_ion_pdf_2D_at_wall(run_info; plot_prefix)
 
-Make plots/animations of the charged particle distribution function at wall boundaries.
+Make plots/animations of the ion distribution function at wall boundaries.
 
 The information for the runs to plot is passed in `run_info` (as returned by
 [`get_run_info`](@ref)). If `run_info` is a Tuple, comparison plots are made where line
@@ -4318,7 +4374,7 @@ will be saved with the format `plot_prefix<some_identifying_string>.pdf`. When `
 is not a Tuple, `plot_prefix` is optional - plots/animations will be saved only if it is
 passed.
 """
-function plot_charged_pdf_2D_at_wall(run_info; plot_prefix)
+function plot_ion_pdf_2D_at_wall(run_info; plot_prefix)
     input = Dict_to_NamedTuple(input_dict_dfns["wall_pdf"])
     if !(input.plot || input.animate || input.advection_velocity)
         # nothing to do
@@ -4332,7 +4388,7 @@ function plot_charged_pdf_2D_at_wall(run_info; plot_prefix)
     z_lower = 1
     z_upper = run_info[1].z.n
     if !all(ri.z.n == z_upper for ri ∈ run_info)
-        println("Cannot run plot_charged_pdf_2D_at_wall() for runs with different "
+        println("Cannot run plot_ion_pdf_2D_at_wall() for runs with different "
                 * "z-grid sizes. Got $(Tuple(ri.z.n for ri ∈ run_info))")
         return nothing
     end
@@ -4582,6 +4638,338 @@ function plot_neutral_pdf_2D_at_wall(run_info; plot_prefix)
     return nothing
 end
 
+"""
+    constraints_plots(run_info; plot_prefix=plot_prefix)
+
+Plot and/or animate the coefficients used to correct the normalised distribution
+function(s) (aka shape functions) to obey the moment constraints.
+
+If there were no discretisation errors, we would have \$A=1\$, \$B=0\$, \$C=0\$. The
+plots/animations show \$(A-1)\$ so that all three coefficients can be shown nicely on the
+same axes.
+"""
+function constraints_plots(run_info; plot_prefix=plot_prefix)
+    input = Dict_to_NamedTuple(input_dict["constraints"])
+
+    if !(input.plot || input.animate)
+        return nothing
+    end
+
+    try
+        println("Making plots of moment constraints coefficients")
+
+        if !isa(run_info, Tuple)
+            run_info = (run_info,)
+        end
+
+        it0 = input.it0
+        ir0 = input.ir0
+
+        if input.plot
+            if any(ri.evolve_density || ri.evolve_upar || ri.evolve_ppar
+                   for ri ∈ run_info)
+
+                # Ions
+                frame_index = Observable(1)
+                fig, ax = get_1d_ax(; xlabel="z", ylabel="constraint coefficient")
+                for ri ∈ run_info
+                    if !(ri.evolve_density || ri.evolve_upar || ri.evolve_ppar)
+                        continue
+                    end
+                    nspecies = ri.n_ion_species
+                    for is ∈ 1:nspecies
+                        if length(run_info) > 1
+                            prefix = ri.run_name * ", "
+                        else
+                            prefix = ""
+                        end
+                        if nspecies > 1
+                            suffix = ", species $is"
+                        else
+                            suffix = ""
+                        end
+
+                        varname = "ion_constraints_A_coefficient"
+                        label = prefix * "(A-1)" * suffix
+                        data = get_variable(ri, varname; it=it0, is=is, ir=ir0)
+                        data .-= 1.0
+                        plot_vs_z(ri, varname; label=label, data=data, ax=ax, input=input)
+
+                        varname = "ion_constraints_B_coefficient"
+                        label = prefix * "B" * suffix
+                        plot_vs_z(ri, varname; label=label, ax=ax, it=it0, is=is, ir=ir0,
+                                  input=input)
+
+                        varname = "ion_constraints_C_coefficient"
+                        label = prefix * "C" * suffix
+                        plot_vs_z(ri, varname; label=label, ax=ax, it=it0, is=is, ir=ir0,
+                                  input=input)
+                    end
+                end
+                put_legend_right(fig, ax)
+                save(plot_prefix * "ion_constraints.pdf", fig)
+            end
+
+            # Neutrals
+            if any(ri.n_neutral_species > 1
+                   && (ri.evolve_density || ri.evolve_upar || ri.evolve_ppar)
+                   for ri ∈ run_info)
+
+                fig, ax = get_1d_ax(; xlabel="z", ylabel="constraint coefficient")
+                for ri ∈ run_info
+                    if !(ri.evolve_density || ri.evolve_upar || ri.evolve_ppar)
+                        continue
+                    end
+                    nspecies = ri.n_neutral_species
+                    for is ∈ 1:nspecies
+                        if length(run_info) > 1
+                            prefix = ri.run_name * ", "
+                        else
+                            prefix = ""
+                        end
+                        if nspecies > 1
+                            suffix = ", species $is"
+                        else
+                            suffix = ""
+                        end
+
+                        varname = "neutral_constraints_A_coefficient"
+                        label = prefix * "(A-1)" * suffix
+                        data = get_variable(ri, varname; it=it0, is=is, ir=ir0)
+                        data .-= 1.0
+                        plot_vs_z(ri, varname; label=label, data=data, ax=ax, input=input)
+
+                        varname = "neutral_constraints_B_coefficient"
+                        label = prefix * "B" * suffix
+                        plot_vs_z(ri, varname; label=label, ax=ax, it=it0, is=is, ir=ir0,
+                                  input=input)
+
+                        varname = "neutral_constraints_C_coefficient"
+                        label = prefix * "C" * suffix
+                        plot_vs_z(ri, varname; label=label, ax=ax, it=it0, is=is, ir=ir0,
+                                  input=input)
+                    end
+                end
+                put_legend_right(fig, ax)
+                save(plot_prefix * "neutral_constraints.pdf", fig)
+            end
+
+            # Electrons
+            if any(ri.composition.electron_physics == kinetic_electrons for ri ∈ run_info)
+
+                fig, ax = get_1d_ax(; xlabel="z", ylabel="constraint coefficient")
+                for ri ∈ run_info
+                    if length(run_info) > 1
+                        prefix = ri.run_name * ", "
+                    else
+                        prefix = ""
+                    end
+
+                    varname = "electron_constraints_A_coefficient"
+                    label = prefix * "(A-1)"
+                    data = get_variable(ri, varname; it=it0, ir=ir0)
+                    data .-= 1.0
+                    plot_vs_z(ri, varname; label=label, data=data, ax=ax, input=input)
+
+                    varname = "electron_constraints_B_coefficient"
+                    label = prefix * "B"
+                    plot_vs_z(ri, varname; label=label, ax=ax, it=it0, ir=ir0,
+                              input=input)
+
+                    varname = "electron_constraints_C_coefficient"
+                    label = prefix * "C"
+                    plot_vs_z(ri, varname; label=label, ax=ax, it=it0, ir=ir0,
+                              input=input)
+                end
+                put_legend_right(fig, ax)
+                save(plot_prefix * "electron_constraints.pdf", fig)
+            end
+        end
+
+        if input.animate
+            nt = minimum(ri.nt for ri ∈ run_info)
+
+            if any(ri.evolve_density || ri.evolve_upar || ri.evolve_ppar
+                   for ri ∈ run_info)
+
+                # Ions
+                frame_index = Observable(1)
+                fig, ax = get_1d_ax(; xlabel="z", ylabel="constraint coefficient")
+
+                # Calculate plot limits manually so we can exclude the first time point, which
+                # often has a large value for (A-1) due to the way initialisation is done,
+                # which can make the subsequent values hard to see.
+                ymin = Inf
+                ymax = -Inf
+                for ri ∈ run_info
+                    if !(ri.evolve_density || ri.evolve_upar || ri.evolve_ppar)
+                        continue
+                    end
+                    nspecies = ri.n_ion_species
+                    for is ∈ 1:nspecies
+                        if length(run_info) > 1
+                            prefix = ri.run_name * ", "
+                        else
+                            prefix = ""
+                        end
+                        if nspecies > 1
+                            suffix = ", species $is"
+                        else
+                            suffix = ""
+                        end
+
+                        varname = "ion_constraints_A_coefficient"
+                        label = prefix * "(A-1)" * suffix
+                        data = get_variable(ri, varname; is=is, ir=ir0)
+                        data .-= 1.0
+                        ymin = min(ymin, minimum(data[:,2:end]))
+                        ymax = max(ymax, maximum(data[:,2:end]))
+                        animate_vs_z(ri, varname; label=label, data=data,
+                                     frame_index=frame_index, ax=ax, input=input)
+
+                        varname = "ion_constraints_B_coefficient"
+                        label = prefix * "B" * suffix
+                        data = get_variable(ri, varname; is=is, ir=ir0)
+                        ymin = min(ymin, minimum(data[:,2:end]))
+                        ymax = max(ymax, maximum(data[:,2:end]))
+                        animate_vs_z(ri, varname; label=label, data=data,
+                                     frame_index=frame_index, ax=ax, is=is, ir=ir0,
+                                     input=input)
+
+                        varname = "ion_constraints_C_coefficient"
+                        label = prefix * "C" * suffix
+                        data = get_variable(ri, varname; is=is, ir=ir0)
+                        ymin = min(ymin, minimum(data[:,2:end]))
+                        ymax = max(ymax, maximum(data[:,2:end]))
+                        animate_vs_z(ri, varname; label=label, data=data,
+                                     frame_index=frame_index, ax=ax, is=is, ir=ir0,
+                                     input=input)
+                    end
+                end
+                put_legend_right(fig, ax)
+                ylims!(ax, ymin, ymax)
+                save_animation(fig, frame_index, nt,
+                               plot_prefix * "ion_constraints." * input.animation_ext)
+            end
+
+            # Neutrals
+            if any(ri.n_neutral_species > 1
+                   && (ri.evolve_density || ri.evolve_upar || ri.evolve_ppar)
+                   for ri ∈ run_info)
+
+                frame_index = Observable(1)
+                fig, ax = get_1d_ax(; xlabel="z", ylabel="constraint coefficient")
+
+                # Calculate plot limits manually so we can exclude the first time point, which
+                # often has a large value for (A-1) due to the way initialisation is done,
+                # which can make the subsequent values hard to see.
+                ymin = Inf
+                ymax = -Inf
+                for ri ∈ run_info
+                    if !(ri.evolve_density || ri.evolve_upar || ri.evolve_ppar)
+                        continue
+                    end
+                    nspecies = ri.n_neutral_species
+                    for is ∈ 1:nspecies
+                        if length(run_info) > 1
+                            prefix = ri.run_name * ", "
+                        else
+                            prefix = ""
+                        end
+                        if nspecies > 1
+                            suffix = ", species $is"
+                        else
+                            suffix = ""
+                        end
+
+                        varname = "neutral_constraints_A_coefficient"
+                        label = prefix * "(A-1)" * suffix
+                        data = get_variable(ri, varname; is=is, ir=ir0)
+                        data .-= 1.0
+                        ymin = min(ymin, minimum(data[:,2:end]))
+                        ymax = max(ymax, maximum(data[:,2:end]))
+                        animate_vs_z(ri, varname; label=label, data=data,
+                                     frame_index=frame_index, ax=ax, input=input)
+
+                        varname = "neutral_constraints_B_coefficient"
+                        label = prefix * "B" * suffix
+                        data = get_variable(ri, varname; is=is, ir=ir0)
+                        ymin = min(ymin, minimum(data[:,2:end]))
+                        ymax = max(ymax, maximum(data[:,2:end]))
+                        animate_vs_z(ri, varname; label=label, data=data,
+                                     frame_index=frame_index, ax=ax, is=is, ir=ir0,
+                                     input=input)
+
+                        varname = "neutral_constraints_C_coefficient"
+                        label = prefix * "C" * suffix
+                        data = get_variable(ri, varname; is=is, ir=ir0)
+                        ymin = min(ymin, minimum(data[:,2:end]))
+                        ymax = max(ymax, maximum(data[:,2:end]))
+                        animate_vs_z(ri, varname; label=label, data=data,
+                                     frame_index=frame_index, ax=ax, is=is, ir=ir0,
+                                     input=input)
+                    end
+                end
+                put_legend_right(fig, ax)
+                ylims!(ax, ymin, ymax)
+                save_animation(fig, frame_index, nt,
+                               plot_prefix * "neutral_constraints." * input.animation_ext)
+            end
+
+            # Electrons
+            if any(ri.composition.electron_physics == kinetic_electrons for ri ∈ run_info)
+
+                frame_index = Observable(1)
+                fig, ax = get_1d_ax(; xlabel="z", ylabel="constraint coefficient")
+
+                # Calculate plot limits manually so we can exclude the first time point, which
+                # often has a large value for (A-1) due to the way initialisation is done,
+                # which can make the subsequent values hard to see.
+                ymin = Inf
+                ymax = -Inf
+                for ri ∈ run_info
+                    if length(run_info) > 1
+                        prefix = ri.run_name * ", "
+                    else
+                        prefix = ""
+                    end
+
+                    varname = "electron_constraints_A_coefficient"
+                    label = prefix * "(A-1)"
+                    data = get_variable(ri, varname; ir=ir0)
+                    data .-= 1.0
+                    ymin = min(ymin, minimum(data[:,2:end]))
+                    ymax = max(ymax, maximum(data[:,2:end]))
+                    animate_vs_z(ri, varname; label=label, data=data,
+                                 frame_index=frame_index, ax=ax, input=input)
+
+                    varname = "electron_constraints_B_coefficient"
+                    label = prefix * "B"
+                    data = get_variable(ri, varname; ir=ir0)
+                    ymin = min(ymin, minimum(data[:,2:end]))
+                    ymax = max(ymax, maximum(data[:,2:end]))
+                    animate_vs_z(ri, varname; label=label, data=data,
+                                 frame_index=frame_index, ax=ax, ir=ir0, input=input)
+
+                    varname = "electron_constraints_C_coefficient"
+                    label = prefix * "C"
+                    data = get_variable(ri, varname; ir=ir0)
+                    ymin = min(ymin, minimum(data[:,2:end]))
+                    ymax = max(ymax, maximum(data[:,2:end]))
+                    animate_vs_z(ri, varname; label=label, data=data,
+                                 frame_index=frame_index, ax=ax, ir=ir0, input=input)
+                end
+                put_legend_right(fig, ax)
+                ylims!(ax, ymin, ymax)
+                save_animation(fig, frame_index, nt,
+                               plot_prefix * "electron_constraints." * input.animation_ext)
+            end
+        end
+    catch e
+        println("Error in constraints_plots(). Error was ", e)
+    end
+end
+
 """
     Chodura_condition_plots(run_info::Tuple; plot_prefix)
     Chodura_condition_plots(run_info; plot_prefix=nothing, axes=nothing)
@@ -5772,7 +6160,7 @@ end
                    field_sym_label, norm_label, plot_dims, animate_dims)
 
 Utility function for making plots to avoid duplicated code in
-[`compare_charged_pdf_symbolic_test`](@ref) and
+[`compare_ion_pdf_symbolic_test`](@ref) and
 [`compare_neutral_pdf_symbolic_test`](@ref).
 
 The information for the run to analyse is passed in `run_info` (as returned by
@@ -5922,7 +6310,7 @@ function _MMS_pdf_plots(run_info, input, variable_name, plot_prefix, field_label
 end
 
 """
-    compare_charged_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
+    compare_ion_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
                                       input=nothing)
 
 Compare the computed and manufactured solutions for the ion distribution function.
@@ -5943,7 +6331,7 @@ Note: when calculating error norms, data is loaded only for 1 time point and for
 chunk that is the same size as computed by 1 block of the simulation at run time. This
 should prevent excessive memory requirements for this function.
 """
-function compare_charged_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
+function compare_ion_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
                                            input=nothing)
 
     field_label = L"\tilde{f}_i"
@@ -6473,7 +6861,7 @@ function manufactured_solutions_analysis_dfns(run_info; plot_prefix)
         println_to_stdout_and_file(io, "# ", run_info.run_name)
         println_to_stdout_and_file(io, join(run_info.time, " "), " # time / (Lref/cref): ")
 
-        compare_charged_pdf_symbolic_test(run_info, plot_prefix; io=io, input=input)
+        compare_ion_pdf_symbolic_test(run_info, plot_prefix; io=io, input=input)
 
         if run_info.n_neutral_species > 0
             compare_neutral_pdf_symbolic_test(run_info, plot_prefix; io=io, input=input)
@@ -6739,7 +7127,7 @@ function timestep_diagnostics(run_info; plot_prefix=nothing, it=nothing)
             end
             data = get_variable(run_info, "CFL_ion_z")
             datamin = minimum(minimum(d) for d ∈ data)
-            animate_vs_vpa_z(run_info, "CFL_ion_z"; data=data,
+            animate_vs_vpa_z(run_info, "CFL_ion_z"; data=data, it=it,
                              outfile=plot_prefix * "CFL_ion_z_vs_vpa_z.gif",
                              colorscale=log10,
                              transform=x->positive_or_nan(x; epsilon=1.e-30),
@@ -6750,7 +7138,7 @@ function timestep_diagnostics(run_info; plot_prefix=nothing, it=nothing)
                                             :rightspinevisible=>false))
             data = get_variable(run_info, "CFL_ion_vpa")
             datamin = minimum(minimum(d) for d ∈ data)
-            animate_vs_vpa_z(run_info, "CFL_ion_vpa"; data=data,
+            animate_vs_vpa_z(run_info, "CFL_ion_vpa"; data=data, it=it,
                              outfile=plot_prefix * "CFL_ion_vpa_vs_vpa_z.gif",
                              colorscale=log10,
                              transform=x->positive_or_nan(x; epsilon=1.e-30),
@@ -6762,7 +7150,7 @@ function timestep_diagnostics(run_info; plot_prefix=nothing, it=nothing)
             if any(ri.n_neutral_species > 0 for ri ∈ run_info)
                 data = get_variable(run_info, "CFL_neutral_z")
                 datamin = minimum(minimum(d) for d ∈ data)
-                animate_vs_vz_z(run_info, "CFL_neutral_z"; data=data,
+                animate_vs_vz_z(run_info, "CFL_neutral_z"; data=data, it=it,
                                 outfile=plot_prefix * "CFL_neutral_z_vs_vz_z.gif",
                                 colorscale=log10,
                                 transform=x->positive_or_nan(x; epsilon=1.e-30),
@@ -6773,7 +7161,7 @@ function timestep_diagnostics(run_info; plot_prefix=nothing, it=nothing)
                                                :rightspinevisible=>false))
                 data = get_variable(run_info, "CFL_neutral_vz")
                 datamin = minimum(minimum(d) for d ∈ data)
-                animate_vs_vz_z(run_info, "CFL_neutral_vz"; data=data,
+                animate_vs_vz_z(run_info, "CFL_neutral_vz"; data=data, it=it,
                                 outfile=plot_prefix * "CFL_neutral_vz_vs_vz_z.gif",
                                 colorscale=log10,
                                 transform=x->positive_or_nan(x; epsilon=1.e-30),
diff --git a/moment_kinetics/debug_test/README.md b/moment_kinetics/debug_test/README.md
index 76c190791..10eafdf65 100644
--- a/moment_kinetics/debug_test/README.md
+++ b/moment_kinetics/debug_test/README.md
@@ -96,7 +96,7 @@ Suggested debugging strategy for race conditions is:
   failure. Usually a failure should indicate where there is a missing
   `begin_*_region()` call. There may be places though where synchronization is
   required even though the type of loop macros used does not change (for
-  example when `phi` is calculated contributions from all charged species need
+  example when `phi` is calculated contributions from all ion species need
   to be summed, resulting in an unusual pattern of array accesses); in this
   case `_block_synchronize()` can be called directly.
     * The function `debug_check_shared_memory()` can be inserted between
diff --git a/moment_kinetics/debug_test/restart_interpolation_inputs.jl b/moment_kinetics/debug_test/restart_interpolation_inputs.jl
index dbfda87d7..c914bc231 100644
--- a/moment_kinetics/debug_test/restart_interpolation_inputs.jl
+++ b/moment_kinetics/debug_test/restart_interpolation_inputs.jl
@@ -59,7 +59,8 @@ base_input = Dict(
      "vzeta_nelement" => 1,
      "vr_ngrid" => 1,
      "vr_nelement" => 1,
-     "numerical_dissipation" => Dict{String,Any}("force_minimum_pdf_value" => 0.0))
+     "ion_numerical_dissipation" => Dict{String,Any}("force_minimum_pdf_value" => 0.0),
+     "neutral_numerical_dissipation" => Dict{String,Any}("force_minimum_pdf_value" => 0.0))
 
 test_input =
     merge(base_input,
diff --git a/moment_kinetics/debug_test/runtest_template.jl b/moment_kinetics/debug_test/runtest_template.jl
index 779be8929..6f1cb0b4e 100644
--- a/moment_kinetics/debug_test/runtest_template.jl
+++ b/moment_kinetics/debug_test/runtest_template.jl
@@ -1,7 +1,8 @@
 using moment_kinetics: setup_moment_kinetics, cleanup_moment_kinetics!
 using moment_kinetics.time_advance: time_advance!
 using moment_kinetics.communication
-using moment_kinetics.looping: dimension_combinations, anyv_dimension_combinations
+using moment_kinetics.looping: all_dimensions, dimension_combinations,
+                               anyv_dimension_combinations
 using moment_kinetics.Glob
 using moment_kinetics.Primes
 
@@ -71,8 +72,39 @@ function runtests(; restart=false)
             else
                 dims_to_test = debug_loop_type
             end
+            for d ∈ all_dimensions
+                nelement_name = "$(d)_nelement"
+                if nelement_name ∈ keys(input)
+                    nelement = input[nelement_name]
+                elseif d ∈ (:vperp, :vzeta, :vr)
+                    nelement = 1
+                else
+                    # Dummy value, here it only matters if this is 1 or greater than 1
+                    nelement = 2
+                end
+
+                ngrid_name = "$(d)_ngrid"
+                if ngrid_name ∈ keys(input)
+                    ngrid = input[ngrid_name]
+                elseif d ∈ (:vperp, :vzeta, :vr)
+                    ngrid = 1
+                else
+                    # Dummy value, here it only matters if this is 1 or greater than 1
+                    ngrid = 2
+                end
+
+                if nelement == 1 && ngrid == 1
+                    # Dimension has only one point, so cannot be parallelised - no need to
+                    # test
+                    dims_to_test = Tuple(x for x ∈ dims_to_test if x != d)
+                end
+            end
 
             ndims = length(dims_to_test)
+            if ndims == 0
+                # No dimensions to test here
+                continue
+            end
             for i ∈ 1:(ndims+n_factors-1)÷n_factors
                 debug_loop_parallel_dims =
                     dims_to_test[(i-1)*n_factors+1:min(i*n_factors, ndims)]
diff --git a/moment_kinetics/debug_test/sound_wave_inputs.jl b/moment_kinetics/debug_test/sound_wave_inputs.jl
index 4439c8a99..5814c5662 100644
--- a/moment_kinetics/debug_test/sound_wave_inputs.jl
+++ b/moment_kinetics/debug_test/sound_wave_inputs.jl
@@ -257,22 +257,22 @@ test_input_chebyshev_cx0_1D1V_split_3_moments =
                "evolve_moments_parallel_pressure" => true))
 
 test_input_list = [
-     #test_input_finite_difference,
+     test_input_finite_difference,
      #test_input_finite_difference_split_1_moment,
      #test_input_finite_difference_split_2_moments,
      #test_input_finite_difference_split_3_moments,
-     #test_input_finite_difference_cx0,
+     test_input_finite_difference_cx0,
      #test_input_finite_difference_cx0_split_1_moment,
      #test_input_finite_difference_cx0_split_2_moments,
      #test_input_finite_difference_cx0_split_3_moments,
-     #test_input_finite_difference_1D1V,
-     #test_input_finite_difference_1D1V_split_1_moment,
-     #test_input_finite_difference_1D1V_split_2_moments,
-     #test_input_finite_difference_1D1V_split_3_moments,
-     #test_input_finite_difference_cx0_1D1V,
-     #test_input_finite_difference_cx0_1D1V_split_1_moment,
-     #test_input_finite_difference_cx0_1D1V_split_2_moments,
-     #test_input_finite_difference_cx0_1D1V_split_3_moments,
+     test_input_finite_difference_1D1V,
+     test_input_finite_difference_1D1V_split_1_moment,
+     test_input_finite_difference_1D1V_split_2_moments,
+     test_input_finite_difference_1D1V_split_3_moments,
+     test_input_finite_difference_cx0_1D1V,
+     test_input_finite_difference_cx0_1D1V_split_1_moment,
+     test_input_finite_difference_cx0_1D1V_split_2_moments,
+     test_input_finite_difference_cx0_1D1V_split_3_moments,
      test_input_chebyshev,
      #test_input_chebyshev_split_1_moment,
      #test_input_chebyshev_split_2_moments,
diff --git a/moment_kinetics/ext/manufactured_solns_ext.jl b/moment_kinetics/ext/manufactured_solns_ext.jl
index 2bad8dcf0..cda63a819 100644
--- a/moment_kinetics/ext/manufactured_solns_ext.jl
+++ b/moment_kinetics/ext/manufactured_solns_ext.jl
@@ -450,7 +450,7 @@ using IfElse
                                     geometry_input_data::geometry_input, composition, species, nr, nvperp)
         # calculate the geometry symbolically
         geometry = geometry_sym(geometry_input_data,Lz,Lr,nr)
-        charged_species = species.charged[1]
+        ion_species = species.ion[1]
         if composition.n_neutral_species > 0
             neutral_species = species.neutral[1]
         else
@@ -458,17 +458,17 @@ using IfElse
         end
 
         densi = densi_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species)
+                          ion_species)
         upari = upari_sym(Lr, Lz, r_bc, z_bc, composition, geometry, nr, manufactured_solns_input,
-                          charged_species)
+                          ion_species)
         ppari = ppari_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species)
+                          ion_species)
         pperpi = pperpi_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species, nvperp)
+                          ion_species, nvperp)
         vthi = vthi_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species, nvperp)
+                          ion_species, nvperp)
         dfni = dfni_sym(Lr, Lz, r_bc, z_bc, composition, geometry, nr,
-                        manufactured_solns_input, charged_species)
+                        manufactured_solns_input, ion_species)
 
         densn = densn_sym(Lr, Lz, r_bc, z_bc, geometry,composition,
                           manufactured_solns_input, neutral_species)
@@ -538,7 +538,7 @@ using IfElse
             geometry_input_data::geometry_input, collisions,
             num_diss_params, species)
         geometry = geometry_sym(geometry_input_data,z_coord.L,r_coord.L,r_coord.n)
-        charged_species = species.charged[1]
+        ion_species = species.ion[1]
         if composition.n_neutral_species > 0
             neutral_species = species.neutral[1]
         else
@@ -547,16 +547,16 @@ using IfElse
 
         # ion manufactured solutions
         densi = densi_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition,
-                          manufactured_solns_input, charged_species)
-        upari = upari_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition, geometry, r_coord.n, manufactured_solns_input, charged_species)
+                          manufactured_solns_input, ion_species)
+        upari = upari_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition, geometry, r_coord.n, manufactured_solns_input, ion_species)
         vthi = vthi_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition, manufactured_solns_input,
-                          charged_species, vperp_coord.n)
+                          ion_species, vperp_coord.n)
         dfni = dfni_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition,
-                        geometry, r_coord.n, manufactured_solns_input, charged_species)
+                        geometry, r_coord.n, manufactured_solns_input, ion_species)
         #dfni in vr vz vzeta coordinates
         vrvzvzeta_dfni = cartesian_dfni_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc,
                                             composition, manufactured_solns_input,
-                                            charged_species)
+                                            ion_species)
 
         # neutral manufactured solutions
         densn = densn_sym(r_coord.L,z_coord.L, r_coord.bc, z_coord.bc, geometry,
@@ -604,7 +604,7 @@ using IfElse
         # calculate the electric fields and the potential
         Er, Ez, phi = electric_fields(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc,
                                       composition, r_coord.n, manufactured_solns_input,
-                                      charged_species)
+                                      ion_species)
 
         # the adiabatic invariant (for compactness)
         mu = 0.5*(vperp^2)/Bmag
@@ -638,31 +638,31 @@ using IfElse
             Si += - nuii_krook*(FMaxwellian - dfni)
         end
         include_num_diss_in_MMS = true
-        if num_diss_params.vpa_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
-            Si += - num_diss_params.vpa_dissipation_coefficient*Dvpa(Dvpa(dfni))
+        if num_diss_params.ion.vpa_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
+            Si += - num_diss_params.ion.vpa_dissipation_coefficient*Dvpa(Dvpa(dfni))
         end
-        if num_diss_params.vperp_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
-            Si += - num_diss_params.vperp_dissipation_coefficient*Dvperp(Dvperp(dfni))
+        if num_diss_params.ion.vperp_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
+            Si += - num_diss_params.ion.vperp_dissipation_coefficient*Dvperp(Dvperp(dfni))
         end
-        if num_diss_params.r_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
-            Si += - rfac*num_diss_params.r_dissipation_coefficient*Dr(Dr(dfni))
+        if num_diss_params.ion.r_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
+            Si += - rfac*num_diss_params.ion.r_dissipation_coefficient*Dr(Dr(dfni))
         end
-        if num_diss_params.z_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
-            Si += - num_diss_params.z_dissipation_coefficient*Dz(Dz(dfni))
+        if num_diss_params.ion.z_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
+            Si += - num_diss_params.ion.z_dissipation_coefficient*Dz(Dz(dfni))
         end
 
         Source_i = expand_derivatives(Si)
         
         # the neutral source to maintain the manufactured solution
         Sn = Dt(dfnn) + vz * Dz(dfnn) + rfac*vr * Dr(dfnn) + cx_frequency* (densi*dfnn - densn*vrvzvzeta_dfni) + ionization_frequency*dense*dfnn
-        if num_diss_params.vz_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
-            Sn += - num_diss_params.vz_dissipation_coefficient*Dvz(Dvz(dfnn))
+        if num_diss_params.neutral.vz_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
+            Sn += - num_diss_params.neutral.vz_dissipation_coefficient*Dvz(Dvz(dfnn))
         end
-        if num_diss_params.r_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
-            Sn += - rfac*num_diss_params.r_dissipation_coefficient*Dr(Dr(dfnn))
+        if num_diss_params.neutral.r_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
+            Sn += - rfac*num_diss_params.neutral.r_dissipation_coefficient*Dr(Dr(dfnn))
         end
-        if num_diss_params.z_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
-            Sn += - num_diss_params.z_dissipation_coefficient*Dz(Dz(dfnn))
+        if num_diss_params.neutral.z_dissipation_coefficient > 0.0 && include_num_diss_in_MMS
+            Sn += - num_diss_params.neutral.z_dissipation_coefficient*Dz(Dz(dfnn))
         end
         
         Source_n = expand_derivatives(Sn)
diff --git a/moment_kinetics/src/analysis.jl b/moment_kinetics/src/analysis.jl
index 7daddfd17..fc342e050 100644
--- a/moment_kinetics/src/analysis.jl
+++ b/moment_kinetics/src/analysis.jl
@@ -10,10 +10,10 @@ using ..array_allocation: allocate_float
 using ..calculus: integral
 using ..communication
 using ..coordinates: coordinate
-using ..initial_conditions: vpagrid_to_dzdt
+using ..boundary_conditions: vpagrid_to_dzdt
 using ..interpolation: interpolate_to_grid_1d
 using ..load_data: open_readonly_output_file, get_nranks, load_pdf_data, load_rank_data
-using ..load_data: load_distributed_charged_pdf_slice
+using ..load_data: load_distributed_ion_pdf_slice
 using ..looping
 using ..type_definitions: mk_int
 using ..velocity_moments: integrate_over_vspace
@@ -140,12 +140,12 @@ function check_Chodura_condition(r, z, vperp, vpa, dens, upar, vth, composition,
         end
     end
     if f_lower === nothing
-        f_lower = load_distributed_charged_pdf_slice(run_name, nblocks, t_range,
+        f_lower = load_distributed_ion_pdf_slice(run_name, nblocks, t_range,
                                                      composition.n_ion_species, r, z,
                                                      vperp, vpa; iz=1, ir=ir0)
     end
     if f_upper === nothing
-        f_upper = load_distributed_charged_pdf_slice(run_name, nblocks, t_range,
+        f_upper = load_distributed_ion_pdf_slice(run_name, nblocks, t_range,
                                                      composition.n_ion_species, r, z,
                                                      vperp, vpa; iz=z.n_global, ir=ir0)
     end
@@ -647,17 +647,22 @@ function steady_state_square_residuals(variable, variable_at_previous_time, dt;
 
             if only_max_abs
                 absolute_residual =
-                    _steady_state_absolute_residual(variable, variable_at_previous_time,
+                    _steady_state_absolute_residual(this_slice, this_slice_previous_time,
                                                     reshaped_dt)
                 # Need to wrap the maximum(...) in a call to vec(...) so that we return a
                 # Vector, not an N-dimensional array where the first (N-1) dimensions all
                 # have size 1.
-                local_max_absolute = max.(local_max_absolute,
-                                          vec(maximum(absolute_residual,
-                                                      dims=tuple((1:t_dim-1)...))))
+                this_dims = tuple((1:t_dim-3)...)
+                if this_dims === ()
+                    local_max_absolute = max.(local_max_absolute, [absolute_residual])
+                else
+                    local_max_absolute = max.(local_max_absolute,
+                                              vec(maximum(absolute_residual,
+                                                          dims=this_dims)))
+                end
             else
                 absolute_square_residual, relative_square_residual =
-                    _steady_state_square_residual(variable, variable_at_previous_time,
+                    _steady_state_square_residual(this_slice, this_slice_previous_time,
                                                   reshaped_dt, epsilon, variable_max)
                 # Need to wrap the sum(...) or maximum(...) in a call to vec(...) so that
                 # we return a Vector, not an N-dimensional array where the first (N-1)
diff --git a/moment_kinetics/src/boundary_conditions.jl b/moment_kinetics/src/boundary_conditions.jl
new file mode 100644
index 000000000..61dff1a08
--- /dev/null
+++ b/moment_kinetics/src/boundary_conditions.jl
@@ -0,0 +1,1006 @@
+"""
+Functions for applying boundary conditions
+"""
+module boundary_conditions
+
+export enforce_boundary_conditions!
+export enforce_neutral_boundary_conditions!
+
+using SpecialFunctions: erfc
+
+using ..calculus: reconcile_element_boundaries_MPI!
+using ..coordinates: coordinate
+using ..interpolation: interpolate_to_grid_1d!
+using ..looping
+using ..moment_kinetics_structs: scratch_pdf
+using ..type_definitions: mk_float, mk_int
+using ..velocity_moments: integrate_over_vspace, integrate_over_neutral_vspace,
+                          integrate_over_positive_vz, integrate_over_negative_vz
+
+"""
+enforce boundary conditions in vpa and z on the evolved pdf;
+also enforce boundary conditions in z on all separately evolved velocity space moments of the pdf
+"""
+function enforce_boundary_conditions!(f, f_r_bc, density, upar, ppar, moments, vpa_bc,
+        z_bc, r_bc, vpa, vperp, z, r, vpa_spectral, vperp_spectral, vpa_adv, vperp_adv, z_adv, r_adv, composition, scratch_dummy,
+        r_diffusion, vpa_diffusion, vperp_diffusion)
+    if vpa.n > 1
+        begin_s_r_z_vperp_region()
+        @loop_s_r_z_vperp is ir iz ivperp begin
+            # enforce the vpa BC
+            # use that adv.speed independent of vpa
+            @views enforce_v_boundary_condition_local!(f[:,ivperp,iz,ir,is], vpa_bc,
+                             vpa_adv[is].speed[:,ivperp,iz,ir], vpa_diffusion,
+                             vpa, vpa_spectral)
+        end
+    end
+    if vperp.n > 1
+        begin_s_r_z_vpa_region()
+        enforce_vperp_boundary_condition!(f, vperp.bc, vperp, vperp_spectral,
+                             vperp_adv, vperp_diffusion)
+    end
+    if z.n > 1
+        begin_s_r_vperp_vpa_region()
+        # enforce the z BC on the evolved velocity space moments of the pdf
+        enforce_z_boundary_condition_moments!(density, moments, z_bc)
+        enforce_z_boundary_condition!(f, density, upar, ppar, moments, z_bc, z_adv, z,
+                                      vperp, vpa, composition,
+                                      scratch_dummy.buffer_vpavperprs_1,
+                                      scratch_dummy.buffer_vpavperprs_2,
+                                      scratch_dummy.buffer_vpavperprs_3,
+                                      scratch_dummy.buffer_vpavperprs_4)
+
+    end
+    if r.n > 1
+        begin_s_z_vperp_vpa_region()
+        enforce_r_boundary_condition!(f, f_r_bc, r_bc, r_adv, vpa, vperp, z, r,
+                                      composition, scratch_dummy.buffer_vpavperpzs_1,
+                                      scratch_dummy.buffer_vpavperpzs_2,
+                                      scratch_dummy.buffer_vpavperpzs_3,
+                                      scratch_dummy.buffer_vpavperpzs_4, r_diffusion)
+    end
+end
+function enforce_boundary_conditions!(fvec_out::scratch_pdf, moments, f_r_bc, vpa_bc,
+        z_bc, r_bc, vpa, vperp, z, r, vpa_spectral, vperp_spectral, vpa_adv, vperp_adv, z_adv, r_adv, composition, scratch_dummy,
+        r_diffusion, vpa_diffusion, vperp_diffusion)
+    enforce_boundary_conditions!(fvec_out.pdf, f_r_bc, fvec_out.density, fvec_out.upar,
+        fvec_out.ppar, moments, vpa_bc, z_bc, r_bc, vpa, vperp, z, r,
+        vpa_spectral, vperp_spectral, vpa_adv, vperp_adv, z_adv,
+        r_adv, composition, scratch_dummy, r_diffusion, vpa_diffusion, vperp_diffusion)
+end
+
+"""
+enforce boundary conditions on f in r
+"""
+function enforce_r_boundary_condition!(f::AbstractArray{mk_float,5}, f_r_bc, bc::String,
+        adv, vpa, vperp, z, r, composition, end1::AbstractArray{mk_float,4},
+        end2::AbstractArray{mk_float,4}, buffer1::AbstractArray{mk_float,4},
+        buffer2::AbstractArray{mk_float,4}, r_diffusion::Bool)
+
+    nr = r.n
+
+    if r.nelement_global > r.nelement_local
+        # reconcile internal element boundaries across processes
+        # & enforce periodicity and external boundaries if needed
+        @loop_s_z_vperp_vpa is iz ivperp ivpa begin
+            end1[ivpa,ivperp,iz,is] = f[ivpa,ivperp,iz,1,is]
+            end2[ivpa,ivperp,iz,is] = f[ivpa,ivperp,iz,nr,is]
+        end
+        reconcile_element_boundaries_MPI!(f, end1, end2, buffer1, buffer2, r)
+    end
+
+    # 'periodic' BC enforces periodicity by taking the average of the boundary points
+    # enforce the condition if r is local
+    if bc == "periodic" && r.nelement_global == r.nelement_local
+        @loop_s_z_vperp_vpa is iz ivperp ivpa begin
+            f[ivpa,ivperp,iz,1,is] = 0.5*(f[ivpa,ivperp,iz,nr,is]+f[ivpa,ivperp,iz,1,is])
+            f[ivpa,ivperp,iz,nr,is] = f[ivpa,ivperp,iz,1,is]
+        end
+    end
+    if bc == "Dirichlet"
+        zero = 1.0e-10
+        # use the old distribution to force the new distribution to have
+        # consistant-in-time values at the boundary
+        # with bc = "Dirichlet" and r_diffusion = false
+        # impose bc for incoming parts of velocity space only (Hyperbolic PDE)
+        # with bc = "Dirichlet" and r_diffusion = true
+        # impose bc on both sides of the domain to accomodate a diffusion operator d^2 / d r^2
+        @loop_s_z_vperp_vpa is iz ivperp ivpa begin
+            ir = 1 # r = -L/2 -- check that the point is on lowest rank
+            if r.irank == 0 && (r_diffusion || adv[is].speed[ir,ivpa,ivperp,iz] > zero)
+                f[ivpa,ivperp,iz,ir,is] = f_r_bc[ivpa,ivperp,iz,1,is]
+            end
+            ir = r.n # r = L/2 -- check that the point is on highest rank
+            if r.irank == r.nrank - 1 && (r_diffusion || adv[is].speed[ir,ivpa,ivperp,iz] < -zero)
+                f[ivpa,ivperp,iz,ir,is] = f_r_bc[ivpa,ivperp,iz,end,is]
+            end
+        end
+    end
+end
+
+"""
+enforce boundary conditions on ion particle f in z
+"""
+function enforce_z_boundary_condition!(pdf, density, upar, ppar, moments, bc::String, adv,
+                                       z, vperp, vpa, composition, end1::AbstractArray{mk_float,4},
+                                       end2::AbstractArray{mk_float,4}, buffer1::AbstractArray{mk_float,4},
+                                       buffer2::AbstractArray{mk_float,4})
+    # this block ensures periodic BC can be supported with distributed memory MPI
+    if z.nelement_global > z.nelement_local
+        # reconcile internal element boundaries across processes
+        # & enforce periodicity and external boundaries if needed
+        nz = z.n
+        @loop_s_r_vperp_vpa is ir ivperp ivpa begin
+            end1[ivpa,ivperp,ir,is] = pdf[ivpa,ivperp,1,ir,is]
+            end2[ivpa,ivperp,ir,is] = pdf[ivpa,ivperp,nz,ir,is]
+        end
+        # check on periodic bc happens inside this call below
+        reconcile_element_boundaries_MPI!(pdf, end1, end2, buffer1, buffer2, z)
+    end
+    # define a zero that accounts for finite precision
+    zero = 1.0e-14
+    # 'constant' BC is time-independent f at upwind boundary
+    # and constant f beyond boundary
+    if bc == "constant"
+        begin_s_r_vperp_vpa_region()
+        density_offset = 1.0
+        vwidth = 1.0
+        if z.irank == 0
+            @loop_s_r_vperp_vpa is ir ivperp ivpa begin
+                if adv[is].speed[ivpa,1,ir] > 0.0
+                    pdf[ivpa,ivperp,1,ir,is] = density_offset * exp(-(vpa.grid[ivpa]^2 + vperp.grid[ivperp]^2)/vwidth^2) / sqrt(pi)
+                end
+            end
+        end
+        if z.irank == z.nrank - 1
+            @loop_s_r_vperp_vpa is ir ivperp ivpa begin
+                if adv[is].speed[ivpa,end,ir] > 0.0
+                    pdf[ivpa,ivperp,end,ir,is] = density_offset * exp(-(vpa.grid[ivpa]^2 + vperp.grid[ivperp]^2)/vwidth^2) / sqrt(pi)
+                end
+            end
+        end
+    # 'periodic' BC enforces periodicity by taking the average of the boundary points
+    elseif bc == "periodic" && z.nelement_global == z.nelement_local
+        begin_s_r_vperp_vpa_region()
+        @loop_s_r_vperp_vpa is ir ivperp ivpa begin
+            pdf[ivpa,ivperp,1,ir,is] = 0.5*(pdf[ivpa,ivperp,z.n,ir,is]+pdf[ivpa,ivperp,1,ir,is])
+            pdf[ivpa,ivperp,z.n,ir,is] = pdf[ivpa,ivperp,1,ir,is]
+        end
+    # 'wall' BC enforces wall boundary conditions
+    elseif bc == "wall"
+        # Need integrals over vpa at wall boundaries in z, so cannot parallelize over z
+        # or vpa.
+        begin_s_r_region()
+        @loop_s is begin
+            # zero incoming BC for ions, as they recombine at the wall
+            if moments.evolve_upar
+                @loop_r ir begin
+                    @views enforce_zero_incoming_bc!(
+                        pdf[:,:,:,ir,is], z, vpa, density[:,ir,is], upar[:,ir,is],
+                        ppar[:,ir,is], moments.evolve_upar, moments.evolve_ppar, zero)
+                end
+            else
+                @loop_r ir begin
+                    @views enforce_zero_incoming_bc!(pdf[:,:,:,ir,is],
+                                                     adv[is].speed[:,:,:,ir], z, zero)
+                end
+            end
+        end
+    end
+end
+
+"""
+enforce boundary conditions on neutral particle distribution function
+"""
+function enforce_neutral_boundary_conditions!(f_neutral, f_ion,
+        boundary_distributions, density_neutral, uz_neutral, pz_neutral, moments,
+        density_ion, upar_ion, Er, vzeta_spectral, vr_spectral, vz_spectral, r_adv, z_adv,
+        vzeta_adv, vr_adv, vz_adv, r, z, vzeta, vr, vz, composition, geometry,
+        scratch_dummy, r_diffusion, vz_diffusion)
+
+    # without acceleration of neutrals bc on vz vr vzeta should not be required as no
+    # advection or diffusion in these coordinates
+
+    if vzeta_adv !== nothing && vzeta.n_global > 1 && vzeta.bc != "none"
+        begin_sn_r_z_vr_vz_region()
+        @loop_sn_r_z_vr_vz isn ir iz ivr ivz begin
+            # enforce the vz BC
+            @views enforce_v_boundary_condition_local!(f_neutral[ivz,ivr,:,iz,ir,isn],
+                                                       vzeta.bc,
+                                                       vzeta_adv[isn].speed[ivz,ivr,:,iz,ir],
+                                                       false, vzeta, vzeta_spectral)
+        end
+    end
+    if vr_adv !== nothing && vr.n_global > 1 && vr.bc != "none"
+        begin_sn_r_z_vzeta_vz_region()
+        @loop_sn_r_z_vzeta_vz isn ir iz ivzeta ivz begin
+            # enforce the vz BC
+            @views enforce_v_boundary_condition_local!(f_neutral[ivz,:,ivzeta,iz,ir,isn],
+                                                       vr.bc,
+                                                       vr_adv[isn].speed[ivz,:,ivzeta,iz,ir],
+                                                       false, vr, vr_spectral)
+        end
+    end
+    if vz_adv !== nothing && vz.n_global > 1 && vz.bc != "none"
+        begin_sn_r_z_vzeta_vr_region()
+        @loop_sn_r_z_vzeta_vr isn ir iz ivzeta ivr begin
+            # enforce the vz BC
+            @views enforce_v_boundary_condition_local!(f_neutral[:,ivr,ivzeta,iz,ir,isn],
+                                                       vz.bc,
+                                                       vz_adv[isn].speed[:,ivr,ivzeta,iz,ir],
+                                                       vz_diffusion, vz, vz_spectral)
+        end
+    end
+    # f_initial contains the initial condition for enforcing a fixed-boundary-value condition
+    if z.n > 1
+        begin_sn_r_vzeta_vr_vz_region()
+        enforce_neutral_z_boundary_condition!(f_neutral, density_neutral, uz_neutral,
+            pz_neutral, moments, density_ion, upar_ion, Er, boundary_distributions,
+            z_adv, z, vzeta, vr, vz, composition, geometry,
+            scratch_dummy.buffer_vzvrvzetarsn_1, scratch_dummy.buffer_vzvrvzetarsn_2,
+            scratch_dummy.buffer_vzvrvzetarsn_3, scratch_dummy.buffer_vzvrvzetarsn_4)
+    end
+    if r.n > 1
+        begin_sn_z_vzeta_vr_vz_region()
+        enforce_neutral_r_boundary_condition!(f_neutral, boundary_distributions.pdf_rboundary_neutral,
+                                    r_adv, vz, vr, vzeta, z, r, composition,
+                                    scratch_dummy.buffer_vzvrvzetazsn_1, scratch_dummy.buffer_vzvrvzetazsn_2,
+                                    scratch_dummy.buffer_vzvrvzetazsn_3, scratch_dummy.buffer_vzvrvzetazsn_4,
+                                    r_diffusion)
+    end
+end
+
+function enforce_neutral_r_boundary_condition!(f::AbstractArray{mk_float,6},
+        f_r_bc::AbstractArray{mk_float,6}, adv, vz, vr, vzeta, z, r, composition,
+        end1::AbstractArray{mk_float,5}, end2::AbstractArray{mk_float,5},
+        buffer1::AbstractArray{mk_float,5}, buffer2::AbstractArray{mk_float,5},
+        r_diffusion) #f_initial,
+
+    bc = r.bc
+    nr = r.n
+
+    if r.nelement_global > r.nelement_local
+        # reconcile internal element boundaries across processes
+        # & enforce periodicity and external boundaries if needed
+        @loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
+            end1[ivz,ivr,ivzeta,iz,isn] = f[ivz,ivr,ivzeta,iz,1,isn]
+            end2[ivz,ivr,ivzeta,iz,isn] = f[ivz,ivr,ivzeta,iz,nr,isn]
+        end
+        reconcile_element_boundaries_MPI!(f, end1, end2, buffer1, buffer2, r)
+    end
+    # 'periodic' BC enforces periodicity by taking the average of the boundary points
+    # local case only when no communication required
+    if bc == "periodic" && r.nelement_global == r.nelement_local
+        @loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
+            f[ivz,ivr,ivzeta,iz,1,isn] = 0.5*(f[ivz,ivr,ivzeta,iz,1,isn]+f[ivz,ivr,ivzeta,iz,nr,isn])
+            f[ivz,ivr,ivzeta,iz,nr,isn] = f[ivz,ivr,ivzeta,iz,1,isn]
+        end
+    end
+    # Dirichlet boundary condition for external endpoints
+    if bc == "Dirichlet"
+        zero = 1.0e-10
+        # use the old distribution to force the new distribution to have
+        # consistant-in-time values at the boundary
+        # impose bc for incoming parts of velocity space only (Hyperbolic PDE)
+        @loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
+            ir = 1 # r = -L/2
+            # incoming particles and on lowest rank
+            if r.irank == 0 && (r_diffusion || adv[isn].speed[ir,ivz,ivr,ivzeta,iz] > zero)
+                f[ivz,ivr,ivzeta,iz,ir,isn] = f_r_bc[ivz,ivr,ivzeta,iz,1,isn]
+            end
+            ir = nr # r = L/2
+            # incoming particles and on highest rank
+            if r.irank == r.nrank - 1 && (r_diffusion || adv[isn].speed[ir,ivz,ivr,ivzeta,iz] < -zero)
+                f[ivz,ivr,ivzeta,iz,ir,isn] = f_r_bc[ivz,ivr,ivzeta,iz,end,isn]
+            end
+        end
+    end
+end
+
+"""
+enforce boundary conditions on neutral particle f in z
+"""
+function enforce_neutral_z_boundary_condition!(pdf, density, uz, pz, moments, density_ion,
+                                               upar_ion, Er, boundary_distributions, adv,
+                                               z, vzeta, vr, vz, composition, geometry,
+                                               end1::AbstractArray{mk_float,5}, end2::AbstractArray{mk_float,5},
+                                               buffer1::AbstractArray{mk_float,5}, buffer2::AbstractArray{mk_float,5})
+
+
+    if z.nelement_global > z.nelement_local
+        # reconcile internal element boundaries across processes
+        # & enforce periodicity and external boundaries if needed
+        nz = z.n
+        @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
+            end1[ivz,ivr,ivzeta,ir,isn] = pdf[ivz,ivr,ivzeta,1,ir,isn]
+            end2[ivz,ivr,ivzeta,ir,isn] = pdf[ivz,ivr,ivzeta,nz,ir,isn]
+        end
+        # check on periodic bc occurs within this call below
+        reconcile_element_boundaries_MPI!(pdf, end1, end2, buffer1, buffer2, z)
+    end
+
+    zero = 1.0e-14
+    # 'constant' BC is time-independent f at upwind boundary
+    # and constant f beyond boundary
+    if z.bc == "constant"
+        begin_sn_r_vzeta_vr_vz_region()
+        density_offset = 1.0
+        vwidth = 1.0
+        if z.irank == 0
+            @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
+                if adv[isn].speed[ivz,ivr,ivzeta,1,ir] > 0.0
+                    pdf[ivz,ivr,ivzeta,1,ir,is] = density_offset *
+                        exp(-(vzeta.grid[ivzeta]^2 + vr.grid[ivr] + vz.grid[ivz])/vwidth^2) /
+                        sqrt(pi)
+                end
+            end
+        end
+        if z.irank == z.nrank - 1
+            @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
+                if adv[isn].speed[ivz,ivr,ivzeta,end,ir] > 0.0
+                    pdf[ivz,ivr,ivzeta,end,ir,is] = density_offset *
+                        exp(-(vzeta.grid[ivzeta]^2 + vr.grid[ivr] + vz.grid[ivz])/vwidth^2) /
+                        sqrt(pi)
+                end
+            end
+        end
+    # 'periodic' BC enforces periodicity by taking the average of the boundary points
+    elseif z.bc == "periodic" && z.nelement_global == z.nelement_local
+        begin_sn_r_vzeta_vr_vz_region()
+        @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
+            pdf[ivz,ivr,ivzeta,1,ir,isn] = 0.5*(pdf[ivz,ivr,ivzeta,1,ir,isn] +
+                                                pdf[ivz,ivr,ivzeta,end,ir,isn])
+            pdf[ivz,ivr,ivzeta,end,ir,isn] = pdf[ivz,ivr,ivzeta,1,ir,isn]
+        end
+    # 'wall' BC enforces wall boundary conditions
+    elseif z.bc == "wall"
+        # Need integrals over vpa at wall boundaries in z, so cannot parallelize over z
+        # or vpa.
+        begin_sn_r_region()
+        @loop_sn isn begin
+            # BC for neutrals
+            @loop_r ir begin
+                # define vtfac to avoid repeated computation below
+                vtfac = sqrt(composition.T_wall * composition.mn_over_mi)
+                # Assume for now that the ion species index corresponding to this neutral
+                # species is the same as the neutral species index.
+                # Note, have already calculated moments of ion distribution function(s),
+                # so can use the moments here to get the flux
+                if z.irank == 0
+                    ion_flux_0 = -density_ion[1,ir,isn] * (upar_ion[1,ir,isn]*geometry.bzed[1,ir] - 0.5*geometry.rhostar*Er[1,ir])
+                else
+                    ion_flux_0 = NaN
+                end
+                if z.irank == z.nrank - 1
+                    ion_flux_L = density_ion[end,ir,isn] * (upar_ion[end,ir,isn]*geometry.bzed[end,ir] - 0.5*geometry.rhostar*Er[end,ir])
+                else
+                    ion_flux_L = NaN
+                end
+                # enforce boundary condition on the neutral pdf that all ions and neutrals
+                # that leave the domain re-enter as neutrals
+                @views enforce_neutral_wall_bc!(
+                    pdf[:,:,:,:,ir,isn], z, vzeta, vr, vz, pz[:,ir,isn], uz[:,ir,isn],
+                    density[:,ir,isn], ion_flux_0, ion_flux_L, boundary_distributions,
+                    vtfac, composition.recycling_fraction, moments.evolve_ppar,
+                    moments.evolve_upar, moments.evolve_density, zero)
+            end
+        end
+    end
+end
+
+"""
+enforce a zero incoming BC in z for given species pdf at each radial location
+"""
+function enforce_zero_incoming_bc!(pdf, speed, z, zero)
+    nvpa = size(pdf,1)
+    # no parallel BC should be enforced for dz/dt = 0
+    # note that the parallel velocity coordinate vpa may be dz/dt or
+    # some version of the peculiar velocity (dz/dt - upar),
+    # so use advection speed below instead of vpa
+    if z.irank == 0
+        @loop_vperp_vpa ivperp ivpa begin
+            # for left boundary in zed (z = -Lz/2), want
+            # f(z=-Lz/2, v_parallel > 0) = 0
+            if speed[1,ivpa,ivperp] > zero
+                pdf[ivpa,ivperp,1] = 0.0
+            end
+        end
+    end
+    if z.irank == z.nrank - 1
+        @loop_vperp_vpa ivperp ivpa begin
+            # for right boundary in zed (z = Lz/2), want
+            # f(z=Lz/2, v_parallel < 0) = 0
+            if speed[end,ivpa,ivperp] < -zero
+                pdf[ivpa,ivperp,end] = 0.0
+            end
+        end
+    end
+end
+function enforce_zero_incoming_bc!(pdf, z::coordinate, vpa::coordinate, density, upar,
+                                   ppar, evolve_upar, evolve_ppar, zero)
+    if z.irank != 0 && z.irank != z.nrank - 1
+        # No z-boundary in this block
+        return nothing
+    end
+    nvpa, nvperp, nz = size(pdf)
+    # no parallel BC should be enforced for dz/dt = 0
+    # note that the parallel velocity coordinate vpa may be dz/dt or
+    # some version of the peculiar velocity (dz/dt - upar),
+    # so use advection speed below instead of vpa
+
+    # absolute velocity at left boundary
+    if z.irank == 0
+        @. vpa.scratch = vpagrid_to_dzdt(vpa.grid, sqrt(2.0*(ppar[1]/density[1])),
+                                         upar[1], evolve_ppar, evolve_upar)
+        @loop_vpa ivpa begin
+            # for left boundary in zed (z = -Lz/2), want
+            # f(z=-Lz/2, v_parallel > 0) = 0
+            if vpa.scratch[ivpa] > zero
+                pdf[ivpa,:,1] .= 0.0
+            end
+        end
+    end
+    # absolute velocity at right boundary
+    if z.irank == z.nrank - 1
+        @. vpa.scratch2 = vpagrid_to_dzdt(vpa.grid, sqrt(2.0*(ppar[end]/density[end])),
+                                          upar[end], evolve_ppar, evolve_upar)
+        @loop_vpa ivpa begin
+            # for right boundary in zed (z = Lz/2), want
+            # f(z=Lz/2, v_parallel < 0) = 0
+            if vpa.scratch2[ivpa] < -zero
+                pdf[ivpa,:,end] .= 0.0
+            end
+        end
+    end
+
+    # Special constraint-forcing code that tries to keep the modifications smooth at
+    # v_parallel=0.
+    if z.irank == 0 && z.irank == z.nrank - 1
+        # Both z-boundaries in this block
+        z_range = (1,nz)
+    elseif z.irank == 0
+        z_range = (1,)
+    elseif z.irank == z.nrank - 1
+        z_range = (nz,)
+    else
+        error("No boundary in this block, should have returned already")
+    end
+    for iz ∈ z_range
+        # moment-kinetic approach only implemented for 1V case so far
+        @boundscheck size(pdf,2) == 1
+
+        f = @view pdf[:,1,iz]
+        if evolve_ppar && evolve_upar
+            I0 = integrate_over_vspace(f, vpa.wgts)
+            I1 = integrate_over_vspace(f, vpa.grid, vpa.wgts)
+            I2 = integrate_over_vspace(f, vpa.grid, 2, vpa.wgts)
+
+            # Store v_parallel with upar shift removed in vpa.scratch
+            vth = sqrt(2.0*ppar[iz]/density[iz])
+            @. vpa.scratch = vpa.grid + upar[iz]/vth
+            # Introduce factor to ensure corrections go smoothly to zero near
+            # v_parallel=0
+            @. vpa.scratch2 = f * abs(vpa.scratch) / (1.0 + abs(vpa.scratch))
+            J1 = integrate_over_vspace(vpa.scratch2, vpa.grid, vpa.wgts)
+            J2 = integrate_over_vspace(vpa.scratch2, vpa.grid, 2, vpa.wgts)
+            J3 = integrate_over_vspace(vpa.scratch2, vpa.grid, 3, vpa.wgts)
+            J4 = integrate_over_vspace(vpa.scratch2, vpa.grid, 4, vpa.wgts)
+
+            A = (J3^2 - J2*J4 + 0.5*(J2^2 - J1*J3)) /
+                (I0*(J3^2 - J2*J4) + I1*(J1*J4 - J2*J3) + I2*(J2^2 - J1*J3))
+            B = (0.5*J3 + A*(I1*J4 - I2*J3)) / (J3^2 - J2*J4)
+            C = (0.5 - A*I2 -B*J3) / J4
+
+            @. f = A*f + B*vpa.grid*vpa.scratch2 + C*vpa.grid*vpa.grid*vpa.scratch2
+        elseif evolve_upar
+            I0 = integrate_over_vspace(f, vpa.wgts)
+            I1 = integrate_over_vspace(f, vpa.grid, vpa.wgts)
+
+            # Store v_parallel with upar shift removed in vpa.scratch
+            @. vpa.scratch = vpa.grid + upar[iz]
+            # Introduce factor to ensure corrections go smoothly to zero near
+            # v_parallel=0
+            @. vpa.scratch2 = f * abs(vpa.scratch) / (1.0 + abs(vpa.scratch))
+            J1 = integrate_over_vspace(vpa.scratch2, vpa.grid, vpa.wgts)
+            J2 = integrate_over_vspace(vpa.scratch2, vpa.grid, 2, vpa.wgts)
+
+            A = 1.0 / (I0 - I1*J1/J2)
+            B = -A*I1/J2
+
+            @. f = A*f + B*vpa.grid*vpa.scratch2
+        elseif evolve_density
+            I0 = integrate_over_vspace(f, vpa.wgts)
+            @. f = f / I0
+        end
+    end
+end
+
+"""
+Set up an initial condition that tries to be smoothly compatible with the sheath
+boundary condition for ions, by setting f(±(v_parallel-u0)<0) where u0=0 at the sheath
+boundaries and for z<0 increases linearly to u0=vpa.L at z=0, while for z>0 increases
+from u0=-vpa.L at z=0 to zero at the z=z.L/2 sheath.
+
+To be applied to 'full-f' distribution function on v_parallel grid (not w_parallel
+grid).
+"""
+function enforce_initial_tapered_zero_incoming!(pdf, z::coordinate, vpa::coordinate)
+    nvpa = size(pdf,1)
+    zero = 1.0e-14
+    # no parallel BC should be enforced for dz/dt = 0
+    # note that the parallel velocity coordinate vpa may be dz/dt or
+    # some version of the peculiar velocity (dz/dt - upar),
+    # so use advection speed below instead of vpa
+
+    for iz ∈ 1:z.n
+        u0 = (2.0*z.grid[iz]/z.L - sign(z.grid[iz])) * vpa.L / 2.0
+        if z.grid[iz] < -zero
+            for ivpa ∈ 1:nvpa
+                if vpa.grid[ivpa] > u0 + zero
+                    pdf[ivpa,iz] = 0.0
+                end
+            end
+        elseif z.grid[iz] > zero
+            for ivpa ∈ 1:nvpa
+                if vpa.grid[ivpa] < u0 - zero
+                    pdf[ivpa,iz] = 0.0
+                end
+            end
+        end
+    end
+end
+
+"""
+enforce the wall boundary condition on neutrals;
+i.e., the incoming flux of neutrals equals the sum of the ion/neutral outgoing fluxes
+"""
+function enforce_neutral_wall_bc!(pdf, z, vzeta, vr, vz, pz, uz, density, wall_flux_0,
+                                  wall_flux_L, boundary_distributions, vtfac,
+                                  recycling_fraction, evolve_ppar, evolve_upar,
+                                  evolve_density, zero)
+
+    # Reduce the ion flux by `recycling_fraction` to account for ions absorbed by the
+    # wall.
+    wall_flux_0 *= recycling_fraction
+    wall_flux_L *= recycling_fraction
+
+    if !evolve_density && !evolve_upar
+        knudsen_cosine = boundary_distributions.knudsen
+
+        if z.irank == 0
+            ## treat z = -Lz/2 boundary ##
+
+            # add the neutral species's contribution to the combined ion/neutral particle
+            # flux out of the domain at z=-Lz/2
+            @views wall_flux_0 += integrate_over_negative_vz(abs.(vz.grid) .* pdf[:,:,:,1], vz.grid, vz.wgts, vz.scratch, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+
+            # for left boundary in zed (z = -Lz/2), want
+            # f_n(z=-Lz/2, v_parallel > 0) = Γ_0 * f_KW(v_parallel)
+            @loop_vz ivz begin
+                if vz.grid[ivz] >= -zero
+                    @views @. pdf[ivz,:,:,1] = wall_flux_0 * knudsen_cosine[ivz,:,:]
+                end
+            end
+        end
+
+        if z.irank == z.nrank - 1
+            ## treat the right boundary at z = Lz/2 ##
+
+            # add the neutral species's contribution to the combined ion/neutral particle
+            # flux out of the domain at z=-Lz/2
+            @views wall_flux_L += integrate_over_positive_vz(abs.(vz.grid) .* pdf[:,:,:,end], vz.grid, vz.wgts, vz.scratch, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+
+            # for right boundary in zed (z = Lz/2), want
+            # f_n(z=Lz/2, v_parallel < 0) = Γ_Lz * f_KW(v_parallel)
+            @loop_vz ivz begin
+                if vz.grid[ivz] <= zero
+                    @views @. pdf[ivz,:,:,end] = wall_flux_L * knudsen_cosine[ivz,:,:]
+                end
+            end
+        end
+    elseif !evolve_upar
+        # Evolving density case
+        knudsen_cosine = boundary_distributions.knudsen
+
+        if z.irank == 0
+            ## treat z = -Lz/2 boundary ##
+
+            # Note the numerical integrol of knudsen_cosine was forced to be 1 (to machine
+            # precision) when it was initialised.
+            @views pdf_integral_0 = integrate_over_negative_vz(pdf[:,:,:,1], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            @views pdf_integral_1 = integrate_over_negative_vz(vz.grid .* pdf[:,:,:,1], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            knudsen_integral_0 = integrate_over_positive_vz(knudsen_cosine, vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            knudsen_integral_1 = 1.0 # This is enforced in initialization
+
+            # Calculate normalisation factors N_in for the incoming and N_out for the
+            # Knudsen parts of the distirbution so that ∫dvpa F = 1 and ∫dvpa vpa F = uz
+            # Note wall_flux_0 is the ion flux into the wall (reduced by the recycling
+            # fraction), and the neutral flux should be out of the wall (i.e. uz>0) so
+            # n*uz = |n*uz| = wall_flux_0
+            # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
+            #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = uz
+            uz = wall_flux_0 / density[1]
+            N_in = (1 - uz * knudsen_integral_0 / knudsen_integral_1) /
+                   (pdf_integral_0
+                    - pdf_integral_1 / knudsen_integral_1 * knudsen_integral_0)
+            N_out = (uz - N_in * pdf_integral_1) / knudsen_integral_1
+
+            @loop_vz ivz begin
+                if vz.grid[ivz] >= -zero
+                    @views @. pdf[ivz,:,:,1] = N_out * knudsen_cosine[ivz,:,:]
+                else
+                    @views @. pdf[ivz,:,:,1] *= N_in
+                end
+            end
+        end
+
+        if z.irank == z.nrank - 1
+            ## treat the right boundary at z = Lz/2 ##
+
+            # Note the numerical integrol of knudsen_cosine was forced to be 1 (to machine
+            # precision) when it was initialised.
+            @views pdf_integral_0 = integrate_over_positive_vz(pdf[:,:,:,end], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            @views pdf_integral_1 = integrate_over_positive_vz(vz.grid .* pdf[:,:,:,end], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            knudsen_integral_0 = integrate_over_negative_vz(knudsen_cosine, vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            knudsen_integral_1 = -1.0 # This is enforced in initialization
+
+            # Calculate normalisation factors N_in for the incoming and N_out for the
+            # Knudsen parts of the distirbution so that ∫dvpa F = 1 and ∫dvpa vpa F = uz
+            # Note wall_flux_L is the ion flux into the wall (reduced by the recycling
+            # fraction), and the neutral flux should be out of the wall (i.e. uz<0) so
+            # -n*uz = |n*uz| = wall_flux_L
+            # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
+            #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = uz
+            uz = -wall_flux_L / density[end]
+            N_in = (1 - uz * knudsen_integral_0 / knudsen_integral_1) /
+                   (pdf_integral_0
+                    - pdf_integral_1 / knudsen_integral_1 * knudsen_integral_0)
+            N_out = (uz - N_in * pdf_integral_1) / knudsen_integral_1
+
+            @loop_vz ivz begin
+                if vz.grid[ivz] <= zero
+                    @views @. pdf[ivz,:,:,end] = N_out * knudsen_cosine[ivz,:,:]
+                else
+                    @views @. pdf[ivz,:,:,end] *= N_in
+                end
+            end
+        end
+    else
+        if z.irank == 0
+            ## treat z = -Lz/2 boundary ##
+            # populate vz.scratch2 array with dz/dt values at z = -Lz/2
+            if evolve_ppar
+                vth = sqrt(2.0*pz[1]/density[1])
+            else
+                vth = nothing
+            end
+            @. vz.scratch2 = vpagrid_to_dzdt(vz.grid, vth, uz[1], evolve_ppar, evolve_upar)
+
+            # First apply boundary condition that total neutral outflux is equal to ion
+            # influx to uz
+            uz[1] = wall_flux_0 / density[1]
+            #would setting density work better??
+            #density[1] = - wall_flux_0 / uz[1]
+
+            # Create normalised Knudsen cosine distribution, to use for positive v_parallel
+            # at z = -Lz/2
+            # Note this only makes sense for the 1V case with vr.n=vzeta.n=1
+            @. vz.scratch = (3.0*pi/vtfac^3)*abs(vz.scratch2)*erfc(abs(vz.scratch2)/vtfac)
+
+            # The v_parallel>0 part of the pdf is replaced by the Knudsen cosine
+            # distribution. To ensure the constraints ∫dwpa wpa^m F = 0 are satisfied when
+            # necessary, calculate a normalisation factor for the Knudsen distribution (in
+            # vz.scratch) and correction terms for the incoming pdf similar to
+            # enforce_moment_constraints!().
+            #
+            # Note that it seems to be important that this boundary condition not be
+            # modified by the moment constraints, as that could cause numerical instability.
+            # By ensuring that the constraints are satisfied already here,
+            # enforce_moment_constraints!() will not change the pdf at the boundary. For
+            # ions this is not an issue, because points set to 0 by the bc are not modified
+            # from 0 by enforce_moment_constraints!().
+            knudsen_integral_0 = integrate_over_positive_vz(vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            knudsen_integral_1 = integrate_over_positive_vz(vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+
+            @views pdf_integral_0 = integrate_over_negative_vz(pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            @views pdf_integral_1 = integrate_over_negative_vz(vz.grid .* pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            if !evolve_ppar
+                # Calculate normalisation factors N_in for the incoming and N_out for the
+                # Knudsen parts of the distirbution so that ∫dwpa F = 1 and ∫dwpa wpa F = 0
+                # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
+                #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = 0
+                N_in = 1.0 / (pdf_integral_0 - pdf_integral_1/knudsen_integral_1*knudsen_integral_0)
+                N_out = -N_in * pdf_integral_1 / knudsen_integral_1
+
+                zero_vz_ind = 0
+                for ivz ∈ 1:vz.n
+                    if vz.scratch2[ivz] <= -zero
+                        pdf[ivz,:,:,1] .= N_in*pdf[ivz,:,:,1]
+                    else
+                        zero_vz_ind = ivz
+                        if abs(vz.scratch2[ivz]) < zero
+                            # v_z = 0 point, half contribution from original pdf and half
+                            # from Knudsen cosine distribution, to be consistent with weights
+                            # used in
+                            # integrate_over_positive_vz()/integrate_over_negative_vz().
+                            @. pdf[ivz,:,:,1] = 0.5*(N_in*pdf[ivz,:,:,1] + N_out*vz.scratch[ivz])
+                        else
+                            pdf[ivz,:,:,1] .= N_out*vz.scratch[ivz]
+                        end
+                        break
+                    end
+                end
+                for ivz ∈ zero_vz_ind+1:vz.n
+                    pdf[ivz,:,:,1] .= N_out*vz.scratch[ivz]
+                end
+            else
+                knudsen_integral_2 = integrate_over_positive_vz(vz.grid .* vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+                @views pdf_integral_2 = integrate_over_negative_vz(vz.grid .* vz.grid .* pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+                @views pdf_integral_3 = integrate_over_negative_vz(vz.grid .* vz.grid .* vz.grid .* pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+                # Calculate normalisation factor N_out for the Knudsen part of the
+                # distirbution and normalisation factor N_in and correction term C*wpa*F_in
+                # for the incoming distribution so that ∫dwpa F = 1, ∫dwpa wpa F = 0, and
+                # ∫dwpa wpa^2 F = 1/2
+                # ⇒ N_in*pdf_integral_0 + C*pdf_integral_1 + N_out*knudsen_integral_0 = 1
+                #   N_in*pdf_integral_1 + C*pdf_integral_2 + N_out*knudsen_integral_1 = 0
+                #   N_in*pdf_integral_2 + C*pdf_integral_3 + N_out*knudsen_integral_2 = 1/2
+                N_in = (0.5*knudsen_integral_0*pdf_integral_2 +
+                        knudsen_integral_1*(pdf_integral_3 - 0.5*pdf_integral_1) -
+                        knudsen_integral_2*pdf_integral_2) /
+                       (knudsen_integral_0*(pdf_integral_2^2 - pdf_integral_1*pdf_integral_3) +
+                        knudsen_integral_1*(pdf_integral_0*pdf_integral_3 - pdf_integral_1*pdf_integral_2) +
+                        knudsen_integral_2*(pdf_integral_1^2 - pdf_integral_0*pdf_integral_2))
+                N_out = -(N_in*(pdf_integral_1*pdf_integral_3 - pdf_integral_2^2) + 0.5*pdf_integral_2) /
+                         (knudsen_integral_1*pdf_integral_3 - knudsen_integral_2*pdf_integral_2)
+                C = (0.5 - N_out*knudsen_integral_2 - N_in*pdf_integral_2)/pdf_integral_3
+
+                zero_vz_ind = 0
+                for ivz ∈ 1:vz.n
+                    if vz.scratch2[ivz] <= -zero
+                        @views @. pdf[ivz,:,:,1] = N_in*pdf[ivz,:,:,1] + C*vz.grid[ivz]*pdf[ivz,:,:,1]
+                    else
+                        zero_vz_ind = ivz
+                        if abs(vz.scratch2[ivz]) < zero
+                            # v_parallel = 0 point, half contribution from original pdf and half
+                            # from Knudsen cosine distribution, to be consistent with weights
+                            # used in
+                            # integrate_over_positive_vz()/integrate_over_negative_vz().
+                            @views @. pdf[ivz,:,:,1] = 0.5*(N_in*pdf[ivz,:,:,1] +
+                                                            C*vz.grid[ivz]*pdf[ivz,:,:,1] +
+                                                            N_out*vz.scratch[ivz])
+                        else
+                            @. pdf[ivz,:,:,1] = N_out*vz.scratch[ivz]
+                        end
+                        break
+                    end
+                end
+                for ivz ∈ zero_vz_ind+1:vz.n
+                    @. pdf[ivz,:,:,1] = N_out*vz.scratch[ivz]
+                end
+            end
+        end
+
+        if z.irank == z.nrank - 1
+            ## treat the right boundary at z = Lz/2 ##
+            # populate vz.scratch2 array with dz/dt values at z = Lz/2
+            if evolve_ppar
+                vth = sqrt(2.0*pz[end]/density[end])
+            else
+                vth = nothing
+            end
+            @. vz.scratch2 = vpagrid_to_dzdt(vz.grid, vth, uz[end], evolve_ppar, evolve_upar)
+
+            # First apply boundary condition that total neutral outflux is equal to ion
+            # influx to uz
+            uz[end] = - wall_flux_L / density[end]
+            #would setting density work better??
+            #density[end] = - wall_flux_L / upar[end]
+
+            # obtain the Knudsen cosine distribution at z = Lz/2
+            # the z-dependence is only introduced if the peculiiar velocity is used as vz
+            # Note this only makes sense for the 1V case with vr.n=vzeta.n=1
+            @. vz.scratch = (3.0*pi/vtfac^3)*abs(vz.scratch2)*erfc(abs(vz.scratch2)/vtfac)
+
+            # The v_parallel<0 part of the pdf is replaced by the Knudsen cosine
+            # distribution. To ensure the constraint ∫dwpa wpa F = 0 is satisfied, multiply
+            # the Knudsen distribution (in vz.scratch) by a normalisation factor given by
+            # the integral (over negative v_parallel) of the outgoing Knudsen distribution
+            # and (over positive v_parallel) of the incoming pdf.
+            knudsen_integral_0 = integrate_over_negative_vz(vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            knudsen_integral_1 = integrate_over_negative_vz(vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+
+            @views pdf_integral_0 = integrate_over_positive_vz(pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+            @views pdf_integral_1 = integrate_over_positive_vz(vz.grid .* pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+
+            if !evolve_ppar
+                # Calculate normalisation factors N_in for the incoming and N_out for the
+                # Knudsen parts of the distirbution so that ∫dwpa F = 1 and ∫dwpa wpa F = 0
+                # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
+                #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = 0
+                N_in = 1.0 / (pdf_integral_0 - pdf_integral_1/knudsen_integral_1*knudsen_integral_0)
+                N_out = -N_in * pdf_integral_1 / knudsen_integral_1
+
+                zero_vz_ind = 0
+                for ivz ∈ vz.n:-1:1
+                    if vz.scratch2[ivz] >= zero
+                        @views @. pdf[ivz,:,:,end] = N_in*pdf[ivz,:,:,end]
+                    else
+                        zero_vz_ind = ivz
+                        if abs(vz.scratch2[ivz]) < zero
+                            # v_parallel = 0 point, half contribution from original pdf and half
+                            # from Knudsen cosine distribution, to be consistent with weights
+                            # used in
+                            # integrate_over_positive_vz()/integrate_over_negative_vz().
+                            @views @. pdf[ivz,:,:,end] = 0.5*(N_in*pdf[ivz,:,:,end] + N_out*vz.scratch[ivz])
+                        else
+                            @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
+                        end
+                        break
+                    end
+                end
+                for ivz ∈ 1:zero_vz_ind-1
+                    @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
+                end
+            else
+                knudsen_integral_2 = integrate_over_negative_vz(vz.grid .* vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+                @views pdf_integral_2 = integrate_over_positive_vz(vz.grid .* vz.grid .* pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+                @views pdf_integral_3 = integrate_over_positive_vz(vz.grid .* vz.grid .* vz.grid .* pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
+                # Calculate normalisation factor N_out for the Knudsen part of the
+                # distirbution and normalisation factor N_in and correction term C*wpa*F_in
+                # for the incoming distribution so that ∫dwpa F = 1, ∫dwpa wpa F = 0, and
+                # ∫dwpa wpa^2 F = 1/2
+                # ⇒ N_in*pdf_integral_0 + C*pdf_integral_1 + N_out*knudsen_integral_0 = 1
+                #   N_in*pdf_integral_1 + C*pdf_integral_2 + N_out*knudsen_integral_1 = 0
+                #   N_in*pdf_integral_2 + C*pdf_integral_3 + N_out*knudsen_integral_2 = 1/2
+                N_in = (0.5*knudsen_integral_0*pdf_integral_2 +
+                        knudsen_integral_1*(pdf_integral_3 - 0.5*pdf_integral_1) -
+                        knudsen_integral_2*pdf_integral_2) /
+                       (knudsen_integral_0*(pdf_integral_2^2 - pdf_integral_1*pdf_integral_3) +
+                        knudsen_integral_1*(pdf_integral_0*pdf_integral_3 - pdf_integral_1*pdf_integral_2) +
+                        knudsen_integral_2*(pdf_integral_1^2 - pdf_integral_0*pdf_integral_2))
+                N_out = -(N_in*(pdf_integral_1*pdf_integral_3 - pdf_integral_2^2) + 0.5*pdf_integral_2) /
+                         (knudsen_integral_1*pdf_integral_3 - knudsen_integral_2*pdf_integral_2)
+                C = (0.5 - N_out*knudsen_integral_2 - N_in*pdf_integral_2)/pdf_integral_3
+
+                zero_vz_ind = 0
+                for ivz ∈ vz.n:-1:1
+                    if vz.scratch2[ivz] >= zero
+                        @views @. pdf[ivz,:,:,end] = N_in*pdf[ivz,:,:,end] + C*vz.grid[ivz]*pdf[ivz,:,:,end]
+                    else
+                        zero_vz_ind = ivz
+                        if abs(vz.scratch2[ivz]) < zero
+                            # v_parallel = 0 point, half contribution from original pdf and half
+                            # from Knudsen cosine distribution, to be consistent with weights
+                            # used in
+                            # integrate_over_positive_vz()/integrate_over_negative_vz().
+                            @views @. pdf[ivz,:,:,end] = 0.5*(N_in*pdf[ivz,:,:,end] +
+                                                              C*vz.grid[ivz]*pdf[ivz,:,:,end] +
+                                                              N_out*vz.scratch[ivz])
+                        else
+                            @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
+                        end
+                        break
+                    end
+                end
+                for ivz ∈ 1:zero_vz_ind-1
+                    @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
+                end
+            end
+        end
+    end
+end
+
+"""
+create an array of dz/dt values corresponding to the given vpagrid values
+"""
+function vpagrid_to_dzdt(vpagrid, vth, upar, evolve_ppar, evolve_upar)
+    if evolve_ppar
+        if evolve_upar
+            return vpagrid .* vth .+ upar
+        else
+            return vpagrid .* vth
+        end
+    elseif evolve_upar
+        return vpagrid .+ upar
+    else
+        return vpagrid
+    end
+end
+
+"""
+enforce the z boundary condition on the evolved velocity space moments of f
+"""
+function enforce_z_boundary_condition_moments!(density, moments, bc::String)
+    ## TODO: parallelise
+    #begin_serial_region()
+    #@serial_region begin
+    #    # enforce z boundary condition on density if it is evolved separately from f
+    #	if moments.evolve_density
+    #        # TODO: extend to 'periodic' BC case, as this requires further code modifications to be consistent
+    #        # with finite difference derivatives (should be fine for Chebyshev)
+    #        if bc == "wall"
+    #            @loop_s_r is ir begin
+    #                density[1,ir,is] = 0.5*(density[1,ir,is] + density[end,ir,is])
+    #                density[end,ir,is] = density[1,ir,is]
+    #        	end
+    #        end
+    #    end
+    #end
+end
+
+"""
+"""
+function enforce_v_boundary_condition_local!(f, bc, speed, v_diffusion, v, v_spectral)
+    if bc == "zero"
+        if v_diffusion || speed[1] > 0.0
+            # 'upwind' boundary
+            f[1] = 0.0
+        end
+        if v_diffusion || speed[end] < 0.0
+            # 'upwind' boundary
+            f[end] = 0.0
+        end
+    elseif bc == "both_zero"
+        f[1] = 0.0
+        f[end] = 0.0
+    elseif bc == "zero_gradient"
+        D0 = v_spectral.lobatto.Dmat[1,:]
+        # adjust F(vpa = -L/2) so that d F / d vpa = 0 at vpa = -L/2
+        f[1] = -sum(D0[2:v.ngrid].*f[2:v.ngrid])/D0[1]
+
+        D0 = v_spectral.lobatto.Dmat[end,:]
+        # adjust F(vpa = L/2) so that d F / d vpa = 0 at vpa = L/2
+        f[end] = -sum(D0[1:ngrid-1].*f[end-v.ngrid+1:end-1])/D0[v.ngrid]
+    elseif bc == "periodic"
+        f[1] = 0.5*(f[1]+f[end])
+        f[end] = f[1]
+    else
+        error("Unsupported boundary condition option '$bc' for $(v.name)")
+    end
+end
+
+"""
+enforce zero boundary condition at vperp -> infinity
+"""
+function enforce_vperp_boundary_condition! end
+
+function enforce_vperp_boundary_condition!(f::AbstractArray{mk_float,5}, bc, vperp, vperp_spectral, vperp_advect, diffusion)
+    @loop_s is begin
+        @views enforce_vperp_boundary_condition!(f[:,:,:,:,is], bc, vperp, vperp_spectral, vperp_advect[is], diffusion)
+    end
+    return nothing
+end
+
+function enforce_vperp_boundary_condition!(f::AbstractArray{mk_float,4}, bc, vperp, vperp_spectral, vperp_advect, diffusion)
+    if bc == "zero"
+        nvperp = vperp.n
+        ngrid = vperp.ngrid
+        # set zero boundary condition
+        @loop_r_z_vpa ir iz ivpa begin
+            if diffusion || vperp_advect.speed[nvperp,ivpa,iz,ir] < 0.0
+                f[ivpa,nvperp,iz,ir] = 0.0
+            end
+        end
+        # set regularity condition d F / d vperp = 0 at vperp = 0
+        if vperp.discretization == "gausslegendre_pseudospectral" || vperp.discretization == "chebyshev_pseudospectral"
+            D0 = vperp_spectral.radau.D0
+            buffer = @view vperp.scratch[1:ngrid-1]
+            @loop_r_z_vpa ir iz ivpa begin
+                if diffusion || vperp_advect.speed[1,ivpa,iz,ir] > 0.0
+                    # adjust F(vperp = 0) so that d F / d vperp = 0 at vperp = 0
+                    @views @. buffer = D0[2:ngrid] * f[ivpa,2:ngrid,iz,ir]
+                    f[ivpa,1,iz,ir] = -sum(buffer)/D0[1]
+                end
+            end
+        else
+            println("vperp.bc=\"$bc\" not supported by discretization "
+                    * "$(vperp.discretization)")
+        end
+    elseif bc == "none"
+        # Do nothing
+    else
+        error("Unsupported boundary condition option '$bc' for vperp")
+    end
+end
+
+end # boundary_conditions
diff --git a/moment_kinetics/src/calculus.jl b/moment_kinetics/src/calculus.jl
index 4809182ed..31f07159b 100644
--- a/moment_kinetics/src/calculus.jl
+++ b/moment_kinetics/src/calculus.jl
@@ -347,42 +347,42 @@ in the main code
 
 function assign_endpoint!(df1d::AbstractArray{mk_float,Ndims},
  receive_buffer::AbstractArray{mk_float,Mdims},key::String,coord) where {Ndims,Mdims}
-	if key == "lower"
-		j = 1
-	elseif key == "upper"
-		j = coord.n
-	else
-		println("ERROR: invalid key in assign_endpoint!")
-	end
+    if key == "lower"
+            j = 1
+    elseif key == "upper"
+            j = coord.n
+    else
+            println("ERROR: invalid key in assign_endpoint!")
+    end
     # test against coord name -- make sure to use exact string delimiters e.g. "x" not 'x'
-	# test against Ndims (autodetermined) to choose which array slices to use in assigning endpoints
-	#println("DEBUG MESSAGE: coord.name: ",coord.name," Ndims: ",Ndims," key: ",key)
-	if coord.name == "z" && Ndims==2
-		df1d[j,:] .= receive_buffer[:]
-		#println("ASSIGNING DATA")
-        elseif coord.name == "z" && Ndims==3
-		df1d[j,:,:] .= receive_buffer[:,:]
-		#println("ASSIGNING DATA")
-	elseif coord.name == "z" && Ndims==5
-		df1d[:,:,j,:,:] .= receive_buffer[:,:,:,:]
-		#println("ASSIGNING DATA")
+    # test against Ndims (autodetermined) to choose which array slices to use in assigning endpoints
+    #println("DEBUG MESSAGE: coord.name: ",coord.name," Ndims: ",Ndims," key: ",key)
+    if coord.name == "z" && Ndims==2
+        df1d[j,:] .= receive_buffer[:]
+        #println("ASSIGNING DATA")
+    elseif coord.name == "z" && Ndims==3
+        df1d[j,:,:] .= receive_buffer[:,:]
+        #println("ASSIGNING DATA")
+    elseif coord.name == "z" && Ndims==5
+        df1d[:,:,j,:,:] .= receive_buffer[:,:,:,:]
+        #println("ASSIGNING DATA")
     elseif coord.name == "z" && Ndims==6
-		df1d[:,:,:,j,:,:] .= receive_buffer[:,:,:,:,:]
-		#println("ASSIGNING DATA")
-	elseif coord.name == "r" && Ndims==2
-		df1d[:,j] .= receive_buffer[:]
-		#println("ASSIGNING DATA")
-	elseif coord.name == "r" && Ndims==3
-		df1d[:,j,:] .= receive_buffer[:,:]
-		#println("ASSIGNING DATA")
-	elseif coord.name == "r" && Ndims==5
-		df1d[:,:,:,j,:] .= receive_buffer[:,:,:,:]
-		#println("ASSIGNING DATA")
-	elseif coord.name == "r" && Ndims==6
-		df1d[:,:,:,:,j,:] .= receive_buffer[:,:,:,:,:]
-		#println("ASSIGNING DATA")
-	else
-        println("ERROR: failure to assign endpoints in reconcile_element_boundaries_MPI! (centered): coord.name: ",coord.name," Ndims: ",Ndims," key: ",key)
+        df1d[:,:,:,j,:,:] .= receive_buffer[:,:,:,:,:]
+        #println("ASSIGNING DATA")
+    elseif coord.name == "r" && Ndims==2
+        df1d[:,j] .= receive_buffer[:]
+        #println("ASSIGNING DATA")
+    elseif coord.name == "r" && Ndims==3
+        df1d[:,j,:] .= receive_buffer[:,:]
+        #println("ASSIGNING DATA")
+    elseif coord.name == "r" && Ndims==5
+        df1d[:,:,:,j,:] .= receive_buffer[:,:,:,:]
+        #println("ASSIGNING DATA")
+    elseif coord.name == "r" && Ndims==6
+        df1d[:,:,:,:,j,:] .= receive_buffer[:,:,:,:,:]
+        #println("ASSIGNING DATA")
+    else
+        error("ERROR: failure to assign endpoints in reconcile_element_boundaries_MPI! (centered): coord.name: ",coord.name," Ndims: ",Ndims," key: ",key)
     end
 end
 
diff --git a/moment_kinetics/src/charge_exchange.jl b/moment_kinetics/src/charge_exchange.jl
index 1e4b5a267..66c1bb7fa 100644
--- a/moment_kinetics/src/charge_exchange.jl
+++ b/moment_kinetics/src/charge_exchange.jl
@@ -28,7 +28,7 @@ function charge_exchange_collisions_1V!(f_out, f_neutral_out, fvec_in, moments,
                 f_out[:,1,:,:,is], fvec_in.pdf[:,1,:,:,is],
                 fvec_in.pdf_neutral[:,1,1,:,:,is],
                 fvec_in.density_neutral[:,:,is], fvec_in.upar[:,:,is],
-                fvec_in.uz_neutral[:,:,is], moments.charged.vth[:,:,is],
+                fvec_in.uz_neutral[:,:,is], moments.ion.vth[:,:,is],
                 moments.neutral.vth[:,:,is], moments, vpa, vz, charge_exchange_frequency,
                 vz_spectral, dt)
         end
@@ -42,7 +42,7 @@ function charge_exchange_collisions_1V!(f_out, f_neutral_out, fvec_in, moments,
                 f_neutral_out[:,1,1,:,:,isn], fvec_in.pdf_neutral[:,1,1,:,:,isn],
                 fvec_in.pdf[:,1,:,:,isn], fvec_in.density[:,:,isn],
                 fvec_in.uz_neutral[:,:,isn], fvec_in.upar[:,:,isn],
-                moments.neutral.vth[:,:,isn], moments.charged.vth[:,:,isn], moments,
+                moments.neutral.vth[:,:,isn], moments.ion.vth[:,:,isn], moments,
                 vz, vpa, charge_exchange_frequency, vpa_spectral, dt)
         end
     else
@@ -135,7 +135,7 @@ function charge_exchange_collisions_single_species!(f_out, pdf_in, pdf_other,
     end
 end
 
-function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in, f_charged_vrvzvzeta_in, fvec_in, composition, vz, vr, vzeta, vpa, vperp, z, r,
+function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in, f_ion_vrvzvzeta_in, fvec_in, composition, vz, vr, vzeta, vpa, vperp, z, r,
                                      charge_exchange_frequency, dt)
     # This routine assumes a 3V model with:
     @boundscheck vz.n == size(f_neutral_out,1) || throw(BoundsError(f_neutral_out))
@@ -144,12 +144,12 @@ function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in,
     @boundscheck z.n == size(f_neutral_out,4) || throw(BoundsError(f_neutral_out))
     @boundscheck r.n == size(f_neutral_out,5) || throw(BoundsError(f_neutral_out))
     @boundscheck composition.n_neutral_species == size(f_neutral_out,6) || throw(BoundsError(f_neutral_out))
-    @boundscheck vz.n == size(f_charged_vrvzvzeta_in,1) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck vr.n == size(f_charged_vrvzvzeta_in,2) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck vzeta.n == size(f_charged_vrvzvzeta_in,3) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck z.n == size(f_charged_vrvzvzeta_in,4) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck r.n == size(f_charged_vrvzvzeta_in,5) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck composition.n_neutral_species == size(f_charged_vrvzvzeta_in,6) || throw(BoundsError(f_charged_vrvzvzeta_in))
+    @boundscheck vz.n == size(f_ion_vrvzvzeta_in,1) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck vr.n == size(f_ion_vrvzvzeta_in,2) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck vzeta.n == size(f_ion_vrvzvzeta_in,3) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck z.n == size(f_ion_vrvzvzeta_in,4) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck r.n == size(f_ion_vrvzvzeta_in,5) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck composition.n_neutral_species == size(f_ion_vrvzvzeta_in,6) || throw(BoundsError(f_ion_vrvzvzeta_in))
     @boundscheck vpa.n == size(f_out,1) || throw(BoundsError(f_out))
     @boundscheck vperp.n == size(f_out,2) || throw(BoundsError(f_out))
     @boundscheck z.n == size(f_out,3) || throw(BoundsError(f_out))
@@ -181,7 +181,7 @@ function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in,
         for is ∈ 1:composition.n_ion_species
             f_neutral_out[ivz,ivr,ivzeta,iz,ir,isn] +=
                 dt*charge_exchange_frequency*(
-                    f_charged_vrvzvzeta_in[ivz,ivr,ivzeta,iz,ir,is]*fvec_in.density_neutral[iz,ir,isn]
+                    f_ion_vrvzvzeta_in[ivz,ivr,ivzeta,iz,ir,is]*fvec_in.density_neutral[iz,ir,isn]
                     - fvec_in.pdf_neutral[ivz,ivr,ivzeta,iz,ir,isn]*fvec_in.density[iz,ir,is])
         end
     end
diff --git a/moment_kinetics/src/communication.jl b/moment_kinetics/src/communication.jl
index c43278516..ee1b84f3a 100644
--- a/moment_kinetics/src/communication.jl
+++ b/moment_kinetics/src/communication.jl
@@ -457,7 +457,7 @@ end
         A.accessed[] = true
         return getindex(A.data, I...)
     end
-    function Base.setindex!(A::DebugMPISharedArray{T, N}, v::T, I::Vararg{mk_int,N}) where {T, N}
+    function Base.setindex!(A::DebugMPISharedArray{T, N}, v::Number, I::Vararg{mk_int,N}) where {T, N}
         @debug_track_initialized begin
             A.is_initialized[I...] = 1
         end
@@ -508,12 +508,19 @@ end
     # SparseArray A
     import LinearAlgebra: ldiv!, Factorization
     function ldiv!(Y::DebugMPISharedArray, A::Factorization, B::DebugMPISharedArray)
+        @debug_track_initialized begin
+            Y.is_initialized .= 1
+        end
+        Y.is_written .= true
+        Y.accessed[] = true
         return ldiv!(Y.data, A, B.data)
     end
 
     import MPI: Buffer
     function Buffer(A::DebugMPISharedArray)
-        A.is_initialized .= 1
+        @debug_track_initialized begin
+            A.is_initialized .= 1
+        end
         A.is_read .= true
         A.is_written .= true
         A.accessed[] = true
diff --git a/moment_kinetics/src/continuity.jl b/moment_kinetics/src/continuity.jl
index 80d0183c9..26e9e1314 100644
--- a/moment_kinetics/src/continuity.jl
+++ b/moment_kinetics/src/continuity.jl
@@ -8,7 +8,7 @@ using ..calculus: derivative!
 using ..looping
 
 """
-use the continuity equation dn/dt + d(n*upar)/dz to update the density n for all charged
+use the continuity equation dn/dt + d(n*upar)/dz to update the density n for all ion
 species
 """
 function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spectral,
@@ -18,8 +18,8 @@ function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spect
     @loop_s_r_z is ir iz begin
         # Use ddens_dz is upwinded using upar
         dens_out[iz,ir,is] -=
-            dt*(fvec_in.upar[iz,ir,is]*moments.charged.ddens_dz_upwind[iz,ir,is] +
-                fvec_in.density[iz,ir,is]*moments.charged.dupar_dz[iz,ir,is])
+            dt*(fvec_in.upar[iz,ir,is]*moments.ion.ddens_dz_upwind[iz,ir,is] +
+                fvec_in.density[iz,ir,is]*moments.ion.dupar_dz[iz,ir,is])
     end
 
     # update the density to account for ionization collisions;
@@ -31,7 +31,7 @@ function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spect
     end
 
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_density_amplitude
+        source_amplitude = moments.ion.external_source_density_amplitude
         @loop_s_r_z is ir iz begin
             dens_out[iz,ir,is] +=
                 dt * source_amplitude[iz,ir]
@@ -39,10 +39,10 @@ function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spect
     end
 
     # Ad-hoc diffusion to stabilise numerics...
-    diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
+    diffusion_coefficient = num_diss_params.ion.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_s_r_z is ir iz begin
-            dens_out[iz,ir,is] += dt*diffusion_coefficient*moments.charged.d2dens_dz2[iz,ir,is]
+            dens_out[iz,ir,is] += dt*diffusion_coefficient*moments.ion.d2dens_dz2[iz,ir,is]
         end
     end
 end
@@ -80,7 +80,7 @@ function neutral_continuity_equation!(dens_out, fvec_in, moments, composition, d
     end
 
     # Ad-hoc diffusion to stabilise numerics...
-    diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
+    diffusion_coefficient = num_diss_params.neutral.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_sn_r_z isn ir iz begin
             dens_out[iz,ir,isn] += dt*diffusion_coefficient*moments.neutral.d2dens_dz2[iz,ir,isn]
diff --git a/moment_kinetics/src/coordinates.jl b/moment_kinetics/src/coordinates.jl
index 13ab8abdb..95ce99da6 100644
--- a/moment_kinetics/src/coordinates.jl
+++ b/moment_kinetics/src/coordinates.jl
@@ -7,9 +7,10 @@ export equally_spaced_grid
 export set_element_boundaries
 
 using ..type_definitions: mk_float, mk_int
-using ..array_allocation: allocate_float, allocate_int
+using ..array_allocation: allocate_float, allocate_shared_float, allocate_int
 using ..calculus: derivative!
 using ..chebyshev: scaled_chebyshev_grid, scaled_chebyshev_radau_grid, setup_chebyshev_pseudospectral
+using ..communication
 using ..finite_differences: finite_difference_info
 using ..gauss_legendre: scaled_gauss_legendre_lobatto_grid, scaled_gauss_legendre_radau_grid, setup_gausslegendre_pseudospectral
 using ..quadrature: composite_simpson_weights
@@ -21,7 +22,7 @@ using MPI
 """
 structure containing basic information related to coordinates
 """
-struct coordinate
+struct coordinate{T <: AbstractVector{mk_float}}
     # name is the name of the variable associated with this coordiante
     name::String
     # n_global is the total number of grid points associated with this coordinate
@@ -76,6 +77,12 @@ struct coordinate
     scratch2::Array{mk_float,1}
     # scratch3 is an array used for intermediate calculations requiring n entries
     scratch3::Array{mk_float,1}
+    # scratch_shared is a shared-memory array used for intermediate calculations requiring
+    # n entries
+    scratch_shared::T
+    # scratch_shared2 is a shared-memory array used for intermediate calculations requiring
+    # n entries
+    scratch_shared2::T
     # scratch_2d and scratch2_2d are arrays used for intermediate calculations requiring
     # ngrid x nelement entries
     scratch_2d::Array{mk_float,2}
@@ -138,6 +145,22 @@ function define_coordinate(input, parallel_io::Bool=false; run_directory=nothing
     duniform_dgrid = allocate_float(input.ngrid, input.nelement_local)
     # scratch is an array used for intermediate calculations requiring n entries
     scratch = allocate_float(n_local)
+    if ignore_MPI
+        scratch_shared = allocate_float(n_local)
+        scratch_shared2 = allocate_float(n_local)
+    else
+        scratch_shared = allocate_shared_float(n_local)
+        scratch_shared2 = allocate_shared_float(n_local)
+    end
+    # Initialise scratch_shared and scratch_shared2 so that the debug checks do not
+    # complain when they get printed by `println(io, all_inputs)` in mk_input().
+    if block_rank[] == 0
+        scratch_shared .= NaN
+        scratch_shared2 .= NaN
+    end
+    if !ignore_MPI
+        _block_synchronize()
+    end
     # scratch_2d is an array used for intermediate calculations requiring ngrid x nelement entries
     scratch_2d = allocate_float(input.ngrid, input.nelement_local)
     # struct containing the advection speed options/inputs for this coordinate
@@ -167,7 +190,7 @@ function define_coordinate(input, parallel_io::Bool=false; run_directory=nothing
     coord = coordinate(input.name, n_global, n_local, input.ngrid,
         input.nelement_global, input.nelement_local, input.nrank, input.irank, input.L, grid,
         cell_width, igrid, ielement, imin, imax, igrid_full, input.discretization, input.fd_option, input.cheb_option,
-        input.bc, wgts, uniform_grid, duniform_dgrid, scratch, copy(scratch), copy(scratch),
+        input.bc, wgts, uniform_grid, duniform_dgrid, scratch, copy(scratch), copy(scratch), scratch_shared, scratch_shared2,
         scratch_2d, copy(scratch_2d), advection, send_buffer, receive_buffer, input.comm,
         local_io_range, global_io_range, element_scale, element_shift, input.element_spacing_option,
         element_boundaries)
diff --git a/moment_kinetics/src/derivatives.jl b/moment_kinetics/src/derivatives.jl
index beeb45e66..409274b0f 100644
--- a/moment_kinetics/src/derivatives.jl
+++ b/moment_kinetics/src/derivatives.jl
@@ -19,7 +19,7 @@ using ..looping
 Centered derivatives
 df/dr group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -31,6 +31,8 @@ function derivative_r!(dfdr::AbstractArray{mk_float,2}, f::AbstractArray{mk_floa
         r_receive_buffer1::AbstractArray{mk_float,1},
         r_receive_buffer2::AbstractArray{mk_float,1}, r_spectral, r)
 
+        begin_z_region()
+
 	# differentiate f w.r.t r
 	@loop_z iz begin
 		@views derivative!(dfdr[iz,:], f[iz,:], r, r_spectral)
@@ -87,13 +89,15 @@ function derivative_r!(dfdr::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
 end
 
 #df/dr
-#5D version for f[vpa,vperp,z,r,s] -> charged particle dfn (species indexing taken outside this loop)
+#5D version for f[vpa,vperp,z,r,s] -> ion particle dfn
 function derivative_r!(dfdr::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         dfdr_lower_endpoints::AbstractArray{mk_float,4},
         dfdr_upper_endpoints::AbstractArray{mk_float,4},
         r_receive_buffer1::AbstractArray{mk_float,4},
         r_receive_buffer2::AbstractArray{mk_float,4}, r_spectral, r)
 
+        begin_s_z_vperp_vpa_region()
+
 	# differentiate f w.r.t r
 	@loop_s_z_vperp_vpa is iz ivperp ivpa begin
 		@views derivative!(dfdr[ivpa,ivperp,iz,:,is], f[ivpa,ivperp,iz,:,is], r, r_spectral)
@@ -118,6 +122,8 @@ function derivative_r!(dfdr::AbstractArray{mk_float,6}, f::AbstractArray{mk_floa
         r_receive_buffer1::AbstractArray{mk_float,5},
         r_receive_buffer2::AbstractArray{mk_float,5}, r_spectral, r)
 
+        begin_sn_z_vzeta_vr_vz_region()
+
 	# differentiate f w.r.t r
 	@loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
 		@views derivative!(dfdr[ivz,ivr,ivzeta,iz,:,isn], f[ivz,ivr,ivzeta,iz,:,isn], r, r_spectral)
@@ -139,7 +145,7 @@ end
 Centered derivatives
 df/dz group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -151,6 +157,8 @@ function derivative_z!(dfdz::AbstractArray{mk_float,2}, f::AbstractArray{mk_floa
         z_send_buffer::AbstractArray{mk_float,1},
         z_receive_buffer::AbstractArray{mk_float,1}, z_spectral, z)
 
+        begin_r_region()
+
 	# differentiate f w.r.t z
 	@loop_r ir begin
 		@views derivative!(dfdz[:,ir], f[:,ir], z, z_spectral)
@@ -206,13 +214,15 @@ function derivative_z!(dfdz::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
     end
 end
 
-#5D version for f[vpa,vperp,z,r,s] -> dfn charged particles
+#5D version for f[vpa,vperp,z,r,s] -> dfn ions
 function derivative_z!(dfdz::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         dfdz_lower_endpoints::AbstractArray{mk_float,4},
         dfdz_upper_endpoints::AbstractArray{mk_float,4},
         z_send_buffer::AbstractArray{mk_float,4},
         z_receive_buffer::AbstractArray{mk_float,4}, z_spectral, z)
 
+        begin_s_r_vperp_vpa_region()
+
 	# differentiate f w.r.t z
 	@loop_s_r_vperp_vpa is ir ivperp ivpa begin
 		@views derivative!(dfdz[ivpa,ivperp,:,ir,is], f[ivpa,ivperp,:,ir,is], z, z_spectral)
@@ -237,6 +247,8 @@ function derivative_z!(dfdz::AbstractArray{mk_float,6}, f::AbstractArray{mk_floa
         z_send_buffer::AbstractArray{mk_float,5},
         z_receive_buffer::AbstractArray{mk_float,5}, z_spectral, z)
 
+        begin_sn_r_vzeta_vr_vz_region()
+
 	# differentiate f w.r.t z
 	@loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
 		@views derivative!(dfdz[ivz,ivr,ivzeta,:,ir,isn], f[ivz,ivr,ivzeta,:,ir,isn], z, z_spectral)
@@ -258,7 +270,7 @@ end
 Upwind derivatives
 df/dr group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -272,6 +284,8 @@ function derivative_r!(dfdr::AbstractArray{mk_float,2}, f::AbstractArray{mk_floa
         r_receive_buffer1::AbstractArray{mk_float,1},
         r_receive_buffer2::AbstractArray{mk_float,1}, r_spectral, r)
 
+    begin_z_region()
+
     # differentiate f w.r.t r
     @loop_z iz begin
         @views derivative!(dfdr[iz,:], f[iz,:], r, adv_fac[:,iz], r_spectral)
@@ -335,7 +349,7 @@ function derivative_r!(dfdr::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
 end
 
 #df/dr
-#5D version for f[vpa,vperp,z,r,s] -> charged particle dfn (species indexing taken outside this loop)
+#5D version for f[vpa,vperp,z,r,s] -> ion particle dfn
 function derivative_r!(dfdr::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         advect, adv_fac_lower_buffer::AbstractArray{mk_float,4},
         adv_fac_upper_buffer::AbstractArray{mk_float,4},
@@ -344,6 +358,8 @@ function derivative_r!(dfdr::AbstractArray{mk_float,5}, f::AbstractArray{mk_floa
         r_receive_buffer1::AbstractArray{mk_float,4},
         r_receive_buffer2::AbstractArray{mk_float,4}, r_spectral, r)
 
+        begin_s_z_vperp_vpa_region()
+
 	# differentiate f w.r.t r
 	@loop_s_z_vperp_vpa is iz ivperp ivpa begin
 		@views derivative!(dfdr[ivpa,ivperp,iz,:,is], f[ivpa,ivperp,iz,:,is], r, advect[is].adv_fac[:,ivpa,ivperp,iz], r_spectral)
@@ -373,6 +389,8 @@ function derivative_r!(dfdr::AbstractArray{mk_float,6}, f::AbstractArray{mk_floa
         r_receive_buffer1::AbstractArray{mk_float,5},
         r_receive_buffer2::AbstractArray{mk_float,5}, r_spectral, r)
 
+        begin_sn_z_vzeta_vr_vz_region()
+
 	# differentiate f w.r.t r
 	@loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
 		@views derivative!(dfdr[ivz,ivr,ivzeta,iz,:,isn], f[ivz,ivr,ivzeta,iz,:,isn],
@@ -398,7 +416,7 @@ end
 Upwind derivatives
 df/dz group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -411,6 +429,8 @@ function derivative_z!(dfdz::AbstractArray{mk_float,2}, f::AbstractArray{mk_floa
         z_send_buffer::AbstractArray{mk_float,1},
         z_receive_buffer::AbstractArray{mk_float,1}, z_spectral, z)
 
+    begin_r_region()
+
     # differentiate f w.r.t z
     @loop_r ir begin
         @views derivative!(dfdz[:,ir], f[:,ir], z, adv_fac[:,ir], z_spectral)
@@ -472,7 +492,7 @@ function derivative_z!(dfdz::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
     end
 end
 
-#5D version for f[vpa,vperp,z,r,s] -> dfn charged particles
+#5D version for f[vpa,vperp,z,r,s] -> dfn ion particles
 function derivative_z!(dfdz::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         advect, adv_fac_lower_buffer::AbstractArray{mk_float,4},
         adv_fac_upper_buffer::AbstractArray{mk_float,4},
@@ -481,6 +501,8 @@ function derivative_z!(dfdz::AbstractArray{mk_float,5}, f::AbstractArray{mk_floa
         z_send_buffer::AbstractArray{mk_float,4},
         z_receive_buffer::AbstractArray{mk_float,4}, z_spectral, z)
 
+        begin_s_r_vperp_vpa_region()
+
 	# differentiate f w.r.t z
 	@loop_s_r_vperp_vpa is ir ivperp ivpa begin
 		@views derivative!(dfdz[ivpa,ivperp,:,ir,is], f[ivpa,ivperp,:,ir,is], z, advect[is].adv_fac[:,ivpa,ivperp,ir], z_spectral)
@@ -510,6 +532,8 @@ function derivative_z!(dfdz::AbstractArray{mk_float,6}, f::AbstractArray{mk_floa
         z_send_buffer::AbstractArray{mk_float,5},
         z_receive_buffer::AbstractArray{mk_float,5}, z_spectral, z)
 
+        begin_sn_r_vzeta_vr_vz_region()
+
 	# differentiate f w.r.t z
 	@loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
 		@views derivative!(dfdz[ivz,ivr,ivzeta,:,ir,isn], f[ivz,ivr,ivzeta,:,ir,isn],
diff --git a/moment_kinetics/src/energy_equation.jl b/moment_kinetics/src/energy_equation.jl
index efafe09de..8890be3b6 100644
--- a/moment_kinetics/src/energy_equation.jl
+++ b/moment_kinetics/src/energy_equation.jl
@@ -17,22 +17,23 @@ function energy_equation!(ppar, fvec, moments, collisions, dt, spectral, composi
     begin_s_r_z_region()
 
     @loop_s_r_z is ir iz begin
-        ppar[iz,ir,is] += dt*(-fvec.upar[iz,ir,is]*moments.charged.dppar_dz_upwind[iz,ir,is]
-                              - moments.charged.dqpar_dz[iz,ir,is]
-                              - 3.0*fvec.ppar[iz,ir,is]*moments.charged.dupar_dz[iz,ir,is])
+        ppar[iz,ir,is] += dt*(-fvec.upar[iz,ir,is]*moments.ion.dppar_dz_upwind[iz,ir,is]
+                              - moments.ion.dqpar_dz[iz,ir,is]
+                              - 3.0*fvec.ppar[iz,ir,is]*moments.ion.dupar_dz[iz,ir,is])
     end
 
+
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_pressure_amplitude
+        source_amplitude = moments.ion.external_source_pressure_amplitude
         @loop_s_r_z is ir iz begin
             ppar[iz,ir,is] += dt * source_amplitude[iz,ir]
         end
     end
 
-    diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
+    diffusion_coefficient = num_diss_params.ion.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_s_r_z is ir iz begin
-            ppar[iz,ir,is] += dt*diffusion_coefficient*moments.charged.d2ppar_dz2[iz,ir,is]
+            ppar[iz,ir,is] += dt*diffusion_coefficient*moments.ion.d2ppar_dz2[iz,ir,is]
         end
     end
 
@@ -81,7 +82,7 @@ function neutral_energy_equation!(pz, fvec, moments, collisions, dt, spectral,
         end
     end
 
-    diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
+    diffusion_coefficient = num_diss_params.neutral.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_sn_r_z isn ir iz begin
             pz[iz,ir,isn] += dt*diffusion_coefficient*moments.neutral.d2pz_dz2[iz,ir,isn]
diff --git a/moment_kinetics/src/external_sources.jl b/moment_kinetics/src/external_sources.jl
index 8218c610e..08b23bd5f 100644
--- a/moment_kinetics/src/external_sources.jl
+++ b/moment_kinetics/src/external_sources.jl
@@ -237,10 +237,10 @@ end
     initialize_external_source_amplitude!(moments, external_source_settings, vperp,
                                           vzeta, vr, n_neutral_species)
 
-Initialize the arrays `moments.charged.external_source_amplitude`,
-`moments.charged.external_source_density_amplitude`,
-`moments.charged.external_source_momentum_amplitude`,
-`moments.charged.external_source_pressure_amplitude`,
+Initialize the arrays `moments.ion.external_source_amplitude`,
+`moments.ion.external_source_density_amplitude`,
+`moments.ion.external_source_momentum_amplitude`,
+`moments.ion.external_source_pressure_amplitude`,
 `moments.neutral.external_source_amplitude`,
 `moments.neutral.external_source_density_amplitude`,
 `moments.neutral.external_source_momentum_amplitude`, and
@@ -255,20 +255,20 @@ function initialize_external_source_amplitude!(moments, external_source_settings
     if ion_source_settings.active
         if ion_source_settings.source_type == "energy"
             @loop_r_z ir iz begin
-                moments.charged.external_source_amplitude[iz,ir] =
+                moments.ion.external_source_amplitude[iz,ir] =
                     ion_source_settings.source_strength *
                     ion_source_settings.r_amplitude[ir] *
                     ion_source_settings.z_amplitude[iz]
             end
             if moments.evolve_density
                 @loop_r_z ir iz begin
-                    moments.charged.external_source_density_amplitude[iz,ir] = 0.0
+                    moments.ion.external_source_density_amplitude[iz,ir] = 0.0
                 end
             end
             if moments.evolve_upar
                 @loop_r_z ir iz begin
-                    moments.charged.external_source_momentum_amplitude[iz,ir] =
-                        - moments.charged.dens[iz,ir] * moments.charged.upar[iz,ir] *
+                    moments.ion.external_source_momentum_amplitude[iz,ir] =
+                        - moments.ion.dens[iz,ir] * moments.ion.upar[iz,ir] *
                           ion_source_settings.source_strength *
                           ion_source_settings.r_amplitude[ir] *
                           ion_source_settings.z_amplitude[iz]
@@ -276,9 +276,9 @@ function initialize_external_source_amplitude!(moments, external_source_settings
             end
             if moments.evolve_ppar
                 @loop_r_z ir iz begin
-                    moments.charged.external_source_pressure_amplitude[iz,ir] =
+                    moments.ion.external_source_pressure_amplitude[iz,ir] =
                         (0.5 * ion_source_settings.source_T +
-                         moments.charged.upar[iz,ir]^2 - moments.charged.ppar[iz,ir]) *
+                         moments.ion.upar[iz,ir]^2 - moments.ion.ppar[iz,ir]) *
                         ion_source_settings.source_strength *
                         ion_source_settings.r_amplitude[ir] *
                         ion_source_settings.z_amplitude[iz]
@@ -286,14 +286,14 @@ function initialize_external_source_amplitude!(moments, external_source_settings
             end
         else
             @loop_r_z ir iz begin
-                moments.charged.external_source_amplitude[iz,ir] =
+                moments.ion.external_source_amplitude[iz,ir] =
                     ion_source_settings.source_strength *
                     ion_source_settings.r_amplitude[ir] *
                     ion_source_settings.z_amplitude[iz]
             end
             if moments.evolve_density
                 @loop_r_z ir iz begin
-                    moments.charged.external_source_density_amplitude[iz,ir] =
+                    moments.ion.external_source_density_amplitude[iz,ir] =
                         ion_source_settings.source_strength *
                         ion_source_settings.r_amplitude[ir] *
                         ion_source_settings.z_amplitude[iz]
@@ -301,14 +301,14 @@ function initialize_external_source_amplitude!(moments, external_source_settings
             end
             if moments.evolve_upar
                 @loop_r_z ir iz begin
-                    moments.charged.external_source_momentum_amplitude[iz,ir] = 0.0
+                    moments.ion.external_source_momentum_amplitude[iz,ir] = 0.0
                 end
             end
             if moments.evolve_ppar
                 @loop_r_z ir iz begin
-                    moments.charged.external_source_pressure_amplitude[iz,ir] =
+                    moments.ion.external_source_pressure_amplitude[iz,ir] =
                         (0.5 * ion_source_settings.source_T +
-                         moments.charged.upar[iz,ir]^2) *
+                         moments.ion.upar[iz,ir]^2) *
                         ion_source_settings.source_strength *
                         ion_source_settings.r_amplitude[ir] *
                         ion_source_settings.z_amplitude[iz]
@@ -393,7 +393,7 @@ end
 function initialize_external_source_controller_integral!(
              moments, external_source_settings, n_neutral_species)
 
-Initialize the arrays `moments.charged.external_source_controller_integral` and
+Initialize the arrays `moments.ion.external_source_controller_integral` and
 `moments.neutral.external_source_controller_integral`, using the settings in
 `external_source_settings`
 """
@@ -406,7 +406,7 @@ function initialize_external_source_controller_integral!(
             if ion_source_settings.PI_density_controller_I != 0.0 &&
                 ion_source_settings.source_type ∈ ("density_profile_control",
                                                    "density_midpoint_control")
-                moments.charged.external_source_controller_integral .= 0.0
+                moments.ion.external_source_controller_integral .= 0.0
             end
         end
 
@@ -433,7 +433,7 @@ Add external source term to the ion kinetic equation.
 function external_ion_source!(pdf, fvec, moments, ion_source_settings, vperp, vpa, dt, scratch_dummy)
     
     source_type =  ion_source_settings.source_type
-    source_amplitude = moments.charged.external_source_amplitude
+    source_amplitude = moments.ion.external_source_amplitude
     source_T = ion_source_settings.source_T
     source_n = ion_source_settings.source_n
     if vperp.n == 1
@@ -446,7 +446,7 @@ function external_ion_source!(pdf, fvec, moments, ion_source_settings, vperp, vp
     if source_type in ("Maxwellian","energy")
         begin_s_r_z_vperp_region()
         if moments.evolve_ppar && moments.evolve_upar && moments.evolve_density
-            vth = moments.charged.vth
+            vth = moments.ion.vth
             density = fvec.density
             upar = fvec.upar
             @loop_s_r_z is ir iz begin
@@ -744,7 +744,7 @@ function external_ion_source_controller!(fvec_in, moments, ion_source_settings,
     begin_r_z_region()
 
     is = 1
-    ion_moments = moments.charged
+    ion_moments = moments.ion
 
     if ion_source_settings.source_type == "Maxwellian"
         if moments.evolve_ppar
diff --git a/moment_kinetics/src/file_io.jl b/moment_kinetics/src/file_io.jl
index 300b09079..bae07d9bc 100644
--- a/moment_kinetics/src/file_io.jl
+++ b/moment_kinetics/src/file_io.jl
@@ -19,7 +19,6 @@ using ..type_definitions: mk_float, mk_int
 using LibGit2
 using MPI
 using Pkg
-using UUIDs
 using TOML
 
 @debug_shared_array using ..communication: DebugMPISharedArray
@@ -39,10 +38,10 @@ structure containing the various input/output streams
 """
 struct ascii_ios{T <: Union{IOStream,Nothing}}
     # corresponds to the ascii file to which the distribution function is written
-    #ff::T
+    ff::T
     # corresponds to the ascii file to which velocity space moments of the
     # distribution function such as density and pressure are written
-    moments_charged::T
+    moments_ion::T
     moments_neutral::T
     # corresponds to the ascii file to which electromagnetic fields
     # such as the electrostatic potential are written
@@ -55,7 +54,8 @@ moments & fields only
 """
 struct io_moments_info{Tfile, Ttime, Tphi, Tmomi, Tmomn, Tchodura_lower,
                        Tchodura_upper, Texti1, Texti2, Texti3, Texti4,
-                       Texti5, Textn1, Textn2, Textn3, Textn4, Textn5, Tint, Tfailcause}
+                       Texti5, Textn1, Textn2, Textn3, Textn4, Textn5, Tconstri, Tconstrn,
+                       Tint, Tfailcause}
     # file identifier for the binary file to which data is written
     fid::Tfile
     # handle for the time variable
@@ -66,19 +66,19 @@ struct io_moments_info{Tfile, Ttime, Tphi, Tmomi, Tmomn, Tchodura_lower,
     Er::Tphi
     # handle for the z electric field variable
     Ez::Tphi
-    # handle for the charged species density
+    # handle for the ion species density
     density::Tmomi
-    # handle for the charged species parallel flow
+    # handle for the ion species parallel flow
     parallel_flow::Tmomi
-    # handle for the charged species parallel pressure
+    # handle for the ion species parallel pressure
     parallel_pressure::Tmomi
-    # handle for the charged species perpendicular pressure
+    # handle for the ion species perpendicular pressure
     perpendicular_pressure::Tmomi
-    # handle for the charged species parallel heat flux
+    # handle for the ion species parallel heat flux
     parallel_heat_flux::Tmomi
-    # handle for the charged species thermal speed
+    # handle for the ion species thermal speed
     thermal_speed::Tmomi
-    # handle for the charged species entropy production
+    # handle for the ion species entropy production
     entropy_production::Tmomi
     # handle for chodura diagnostic (lower)
     chodura_integral_lower::Tchodura_lower
@@ -103,6 +103,14 @@ struct io_moments_info{Tfile, Ttime, Tphi, Tmomi, Tmomn, Tchodura_lower,
     external_source_neutral_pressure_amplitude::Textn4
     external_source_neutral_controller_integral::Textn5
 
+    # handles for constraint coefficients
+    ion_constraints_A_coefficient::Tconstri
+    ion_constraints_B_coefficient::Tconstri
+    ion_constraints_C_coefficient::Tconstri
+    neutral_constraints_A_coefficient::Tconstrn
+    neutral_constraints_B_coefficient::Tconstrn
+    neutral_constraints_C_coefficient::Tconstrn
+
     # cumulative wall clock time taken by the run
     time_for_run::Ttime
     # cumulative number of timesteps taken
@@ -130,7 +138,7 @@ distribution function data only
 struct io_dfns_info{Tfile, Tfi, Tfn, Tmoments}
     # file identifier for the binary file to which data is written
     fid::Tfile
-    # handle for the charged species distribution function variable
+    # handle for the ion species distribution function variable
     f::Tfi
     # handle for the neutral species distribution function variable
     f_neutral::Tfn
@@ -197,16 +205,16 @@ function setup_file_io(io_input, boundary_distributions, vz, vr, vzeta, vpa, vpe
         out_prefix = joinpath(io_input.output_dir, io_input.run_name)
 
         if io_input.ascii_output
-            #ff_io = open_ascii_output_file(out_prefix, "f_vs_t")
-            mom_chrg_io = open_ascii_output_file(out_prefix, "moments_charged_vs_t")
+            ff_io = open_ascii_output_file(out_prefix, "f_vs_t")
+            mom_ion_io = open_ascii_output_file(out_prefix, "moments_ion_vs_t")
             mom_ntrl_io = open_ascii_output_file(out_prefix, "moments_neutral_vs_t")
             fields_io = open_ascii_output_file(out_prefix, "fields_vs_t")
-            ascii = ascii_ios(mom_chrg_io, mom_ntrl_io, fields_io)
+            ascii = ascii_ios(ff_io, mom_ion_io, mom_ntrl_io, fields_io)
         else
-            ascii = ascii_ios(nothing, nothing, nothing)
+            ascii = ascii_ios(nothing, nothing, nothing, nothing)
         end
 
-        run_id = string(uuid4())
+        run_id = io_input.run_id
 
         io_moments = setup_moments_io(out_prefix, io_input.binary_format, vz, vr, vzeta,
                                       vpa, vperp, r, z, composition, collisions,
@@ -306,14 +314,6 @@ Write provenance tracking information, to allow runs to be reproduced.
 function write_provenance_tracking_info!(fid, parallel_io, run_id, restart_time_index,
                                          input_dict, previous_runs_info)
 
-    if !parallel_io
-        # Communicate run_id to all blocks
-        # Need to convert run_id to a Vector{Char} for MPI
-        run_id_chars = [run_id...]
-        MPI.Bcast!(run_id_chars, 0, comm_inter_block[])
-        run_id = string(run_id_chars...)
-    end
-
     @serial_region begin
         provenance_tracking = create_io_group(fid, "provenance_tracking")
 
@@ -426,14 +426,14 @@ function write_boundary_distributions!(fid, boundary_distributions, parallel_io,
     @serial_region begin
         boundary_distributions_io = create_io_group(fid, "boundary_distributions")
 
-        write_single_value!(boundary_distributions_io, "pdf_rboundary_charged_left",
-            boundary_distributions.pdf_rboundary_charged[:,:,:,1,:], vpa, vperp, z,
+        write_single_value!(boundary_distributions_io, "pdf_rboundary_ion_left",
+            boundary_distributions.pdf_rboundary_ion[:,:,:,1,:], vpa, vperp, z,
             parallel_io=parallel_io, n_ion_species=composition.n_ion_species,
-            description="Initial charged-particle pdf at left radial boundary")
-        write_single_value!(boundary_distributions_io, "pdf_rboundary_charged_right",
-            boundary_distributions.pdf_rboundary_charged[:,:,:,2,:], vpa, vperp, z,
+            description="Initial ion-particle pdf at left radial boundary")
+        write_single_value!(boundary_distributions_io, "pdf_rboundary_ion_right",
+            boundary_distributions.pdf_rboundary_ion[:,:,:,2,:], vpa, vperp, z,
             parallel_io=parallel_io, n_ion_species=composition.n_ion_species,
-            description="Initial charged-particle pdf at right radial boundary")
+            description="Initial ion-particle pdf at right radial boundary")
         write_single_value!(boundary_distributions_io, "pdf_rboundary_neutral_left",
             boundary_distributions.pdf_rboundary_neutral[:,:,:,:,1,:], vz, vr, vzeta, z,
             parallel_io=parallel_io, n_neutral_species=composition.n_neutral_species,
@@ -454,12 +454,16 @@ function define_io_coordinates!(fid, vz, vr, vzeta, vpa, vperp, z, r, parallel_i
     @serial_region begin
         # create the "coords" group that will contain coordinate information
         coords = create_io_group(fid, "coords")
-        # create the "z" sub-group of "coords" that will contain z coordinate info,
-        # including total number of grid points and grid point locations
-        define_io_coordinate!(coords, z, "z", "spatial coordinate z", parallel_io)
-        # create the "r" sub-group of "coords" that will contain r coordinate info,
-        # including total number of grid points and grid point locations
-        define_io_coordinate!(coords, r, "r", "spatial coordinate r", parallel_io)
+        if z !== nothing
+            # create the "z" sub-group of "coords" that will contain z coordinate info,
+            # including total number of grid points and grid point locations
+            define_io_coordinate!(coords, z, "z", "spatial coordinate z", parallel_io)
+        end
+        if r !== nothing
+            # create the "r" sub-group of "coords" that will contain r coordinate info,
+            # including total number of grid points and grid point locations
+            define_io_coordinate!(coords, r, "r", "spatial coordinate r", parallel_io)
+        end
 
         if parallel_io
             # Parallel I/O produces a single file, so effectively a 'single block'
@@ -487,24 +491,34 @@ function define_io_coordinates!(fid, vz, vr, vzeta, vpa, vperp, z, r, parallel_i
                                 parallel_io=parallel_io, description="number of zr blocks")
         end
 
-        # create the "vz" sub-group of "coords" that will contain vz coordinate info,
-        # including total number of grid points and grid point locations
-        define_io_coordinate!(coords, vz, "vz", "velocity coordinate v_z", parallel_io)
-        # create the "vr" sub-group of "coords" that will contain vr coordinate info,
-        # including total number of grid points and grid point locations
-        define_io_coordinate!(coords, vr, "vr", "velocity coordinate v_r", parallel_io)
-        # create the "vzeta" sub-group of "coords" that will contain vzeta coordinate info,
-        # including total number of grid points and grid point locations
-        define_io_coordinate!(coords, vzeta, "vzeta", "velocity coordinate v_zeta",
-                              parallel_io)
-        # create the "vpa" sub-group of "coords" that will contain vpa coordinate info,
-        # including total number of grid points and grid point locations
-        define_io_coordinate!(coords, vpa, "vpa", "velocity coordinate v_parallel",
-                              parallel_io)
-        # create the "vperp" sub-group of "coords" that will contain vperp coordinate info,
-        # including total number of grid points and grid point locations
-        define_io_coordinate!(coords, vperp, "vperp", "velocity coordinate v_perp",
-                              parallel_io)
+        if vz !== nothing
+            # create the "vz" sub-group of "coords" that will contain vz coordinate info,
+            # including total number of grid points and grid point locations
+            define_io_coordinate!(coords, vz, "vz", "velocity coordinate v_z", parallel_io)
+        end
+        if vr !== nothing
+            # create the "vr" sub-group of "coords" that will contain vr coordinate info,
+            # including total number of grid points and grid point locations
+            define_io_coordinate!(coords, vr, "vr", "velocity coordinate v_r", parallel_io)
+        end
+        if vzeta !== nothing
+            # create the "vzeta" sub-group of "coords" that will contain vzeta coordinate info,
+            # including total number of grid points and grid point locations
+            define_io_coordinate!(coords, vzeta, "vzeta", "velocity coordinate v_zeta",
+                                  parallel_io)
+        end
+        if vpa !== nothing
+            # create the "vpa" sub-group of "coords" that will contain vpa coordinate info,
+            # including total number of grid points and grid point locations
+            define_io_coordinate!(coords, vpa, "vpa", "velocity coordinate v_parallel",
+                                  parallel_io)
+        end
+        if vperp !== nothing
+            # create the "vperp" sub-group of "coords" that will contain vperp coordinate info,
+            # including total number of grid points and grid point locations
+            define_io_coordinate!(coords, vperp, "vperp", "velocity coordinate v_perp",
+                                  parallel_io)
+        end
     end
 
     return nothing
@@ -637,233 +651,31 @@ function define_dynamic_moment_variables!(fid, n_ion_species, n_neutral_species,
         io_time = create_dynamic_variable!(dynamic, "time", mk_float; parallel_io=parallel_io,
                                            description="simulation time")
 
-        # io_phi is the handle referring to the electrostatic potential phi
-        io_phi = create_dynamic_variable!(dynamic, "phi", mk_float, z, r;
-                                          parallel_io=parallel_io,
-                                          description="electrostatic potential",
-                                          units="T_ref/e")
-        # io_Er is the handle for the radial component of the electric field
-        io_Er = create_dynamic_variable!(dynamic, "Er", mk_float, z, r;
-                                         parallel_io=parallel_io,
-                                         description="radial electric field",
-                                         units="T_ref/e L_ref")
-        # io_Ez is the handle for the zed component of the electric field
-        io_Ez = create_dynamic_variable!(dynamic, "Ez", mk_float, z, r;
-                                         parallel_io=parallel_io,
-                                         description="vertical electric field",
-                                         units="T_ref/e L_ref")
-
-        # io_density is the handle for the ion particle density
-        io_density = create_dynamic_variable!(dynamic, "density", mk_float, z, r;
-                                              n_ion_species=n_ion_species,
-                                              parallel_io=parallel_io,
-                                              description="charged species density",
-                                              units="n_ref")
-
-        # io_upar is the handle for the ion parallel flow density
-        io_upar = create_dynamic_variable!(dynamic, "parallel_flow", mk_float, z, r;
-                                           n_ion_species=n_ion_species,
-                                           parallel_io=parallel_io,
-                                           description="charged species parallel flow",
-                                           units="c_ref = sqrt(2*T_ref/mi)")
-
-        # io_ppar is the handle for the ion parallel pressure
-        io_ppar = create_dynamic_variable!(dynamic, "parallel_pressure", mk_float, z, r;
-                                           n_ion_species=n_ion_species,
-                                           parallel_io=parallel_io,
-                                           description="charged species parallel pressure",
-                                           units="n_ref*T_ref")
-        
-        # io_pperp is the handle for the ion parallel pressure
-        io_pperp = create_dynamic_variable!(dynamic, "perpendicular_pressure", mk_float, z, r;
-                                           n_ion_species=n_ion_species,
-                                           parallel_io=parallel_io,
-                                           description="charged species perpendicular pressure",
-                                           units="n_ref*T_ref")
-
-        # io_qpar is the handle for the ion parallel heat flux
-        io_qpar = create_dynamic_variable!(dynamic, "parallel_heat_flux", mk_float, z, r;
-                                           n_ion_species=n_ion_species,
-                                           parallel_io=parallel_io,
-                                           description="charged species parallel heat flux",
-                                           units="n_ref*T_ref*c_ref")
-
-        # io_vth is the handle for the ion thermal speed
-        io_vth = create_dynamic_variable!(dynamic, "thermal_speed", mk_float, z, r;
-                                          n_ion_species=n_ion_species,
-                                          parallel_io=parallel_io,
-                                          description="charged species thermal speed",
-                                          units="c_ref")
-
-        # io_dSdt is the handle for the entropy production (due to collisions)
-        io_dSdt = create_dynamic_variable!(dynamic, "entropy_production", mk_float, z, r;
-                                          n_ion_species=n_ion_species,
-                                          parallel_io=parallel_io,
-                                          description="charged species entropy production",
-                                          units="")
-
-        if parallel_io || z.irank == 0
-            # io_chodura_lower is the handle for the ion thermal speed
-            io_chodura_lower = create_dynamic_variable!(dynamic, "chodura_integral_lower", mk_float, r;
-                                              n_ion_species=n_ion_species,
-                                              parallel_io=parallel_io,
-                                              description="Generalised Chodura integral lower sheath entrance",
-                                              units="c_ref")
-        else
-            io_chodura_lower = nothing
-        end
-        if parallel_io || z.irank == z.nrank - 1
-            # io_chodura_upper is the handle for the ion thermal speed
-            io_chodura_upper = create_dynamic_variable!(dynamic, "chodura_integral_upper", mk_float, r;
-                                              n_ion_species=n_ion_species,
-                                              parallel_io=parallel_io,
-                                              description="Generalised Chodura integral upper sheath entrance",
-                                              units="c_ref")
-        else
-            io_chodura_upper = nothing
-        end
-        # io_density_neutral is the handle for the neutral particle density
-        io_density_neutral = create_dynamic_variable!(dynamic, "density_neutral", mk_float, z, r;
-                                                      n_neutral_species=n_neutral_species,
-                                                      parallel_io=parallel_io,
-                                                      description="neutral species density",
-                                                      units="n_ref")
-
-        # io_uz_neutral is the handle for the neutral z momentum density
-        io_uz_neutral = create_dynamic_variable!(dynamic, "uz_neutral", mk_float, z, r;
-                                                 n_neutral_species=n_neutral_species,
-                                                 parallel_io=parallel_io,
-                                                 description="neutral species mean z velocity",
-                                                 units="c_ref = sqrt(2*T_ref/mi)")
-
-        # io_pz_neutral is the handle for the neutral species zz pressure
-        io_pz_neutral = create_dynamic_variable!(dynamic, "pz_neutral", mk_float, z, r;
-                                                 n_neutral_species=n_neutral_species,
-                                                 parallel_io=parallel_io,
-                                                 description="neutral species mean zz pressure",
-                                                 units="n_ref*T_ref")
-
-        # io_qz_neutral is the handle for the neutral z heat flux
-        io_qz_neutral = create_dynamic_variable!(dynamic, "qz_neutral", mk_float, z, r;
-                                                 n_neutral_species=n_neutral_species,
-                                                 parallel_io=parallel_io,
-                                                 description="neutral species z heat flux",
-                                                 units="n_ref*T_ref*c_ref")
-
-        # io_thermal_speed_neutral is the handle for the neutral thermal speed
-        io_thermal_speed_neutral = create_dynamic_variable!(
-            dynamic, "thermal_speed_neutral", mk_float, z, r;
-            n_neutral_species=n_neutral_species,
-            parallel_io=parallel_io, description="neutral species thermal speed",
-            units="c_ref")
-
-        ion_source_settings = external_source_settings.ion
-        if ion_source_settings.active
-            external_source_amplitude = create_dynamic_variable!(
-                dynamic, "external_source_amplitude", mk_float, z, r;
-                parallel_io=parallel_io, description="Amplitude of the external source for ions",
-                units="n_ref/c_ref^3*c_ref/L_ref")
-            if evolve_density
-                external_source_density_amplitude = create_dynamic_variable!(
-                    dynamic, "external_source_density_amplitude", mk_float, z, r;
-                    parallel_io=parallel_io, description="Amplitude of the external density source for ions",
-                    units="n_ref*c_ref/L_ref")
-            else
-                external_source_density_amplitude = nothing
-            end
-            if evolve_upar
-                external_source_momentum_amplitude = create_dynamic_variable!(
-                    dynamic, "external_source_momentum_amplitude", mk_float, z, r;
-                    parallel_io=parallel_io, description="Amplitude of the external momentum source for ions",
-                    units="m_ref*n_ref*c_ref*c_ref/L_ref")
-            else
-                external_source_momentum_amplitude = nothing
-            end
-            if evolve_ppar
-                external_source_pressure_amplitude = create_dynamic_variable!(
-                    dynamic, "external_source_pressure_amplitude", mk_float, z, r;
-                    parallel_io=parallel_io, description="Amplitude of the external pressure source for ions",
-                    units="m_ref*n_ref*c_ref^2*c_ref/L_ref")
-            else
-                external_source_pressure_amplitude = nothing
-            end
-            if ion_source_settings.PI_density_controller_I != 0.0 &&
-                    ion_source_settings.source_type ∈ ("density_profile_control", "density_midpoint_control")
-                if ion_source_settings.source_type == "density_profile_control"
-                    external_source_controller_integral = create_dynamic_variable!(
-                        dynamic, "external_source_controller_integral", mk_float, z, r;
-                        parallel_io=parallel_io,
-                        description="Integral term for the PID controller of the external source for ions")
-                else
-                    external_source_controller_integral = create_dynamic_variable!(
-                        dynamic, "external_source_controller_integral", mk_float;
-                        parallel_io=parallel_io,
-                        description="Integral term for the PID controller of the external source for ions")
-                end
-            else
-                external_source_controller_integral = nothing
-            end
-        else
-            external_source_amplitude = nothing
-            external_source_density_amplitude = nothing
-            external_source_momentum_amplitude = nothing
-            external_source_pressure_amplitude = nothing
-            external_source_controller_integral = nothing
-        end
-
-        neutral_source_settings = external_source_settings.neutral
-        if n_neutral_species > 0 && neutral_source_settings.active
-            external_source_neutral_amplitude = create_dynamic_variable!(
-                dynamic, "external_source_neutral_amplitude", mk_float, z, r;
-                parallel_io=parallel_io, description="Amplitude of the external source for neutrals",
-                units="n_ref/c_ref^3*c_ref/L_ref")
-            if evolve_density
-                external_source_neutral_density_amplitude = create_dynamic_variable!(
-                    dynamic, "external_source_neutral_density_amplitude", mk_float, z, r;
-                    parallel_io=parallel_io, description="Amplitude of the external density source for neutrals",
-                    units="n_ref*c_ref/L_ref")
-            else
-                external_source_neutral_density_amplitude = nothing
-            end
-            if evolve_upar
-                external_source_neutral_momentum_amplitude = create_dynamic_variable!(
-                    dynamic, "external_source_neutral_momentum_amplitude", mk_float, z, r;
-                    parallel_io=parallel_io, description="Amplitude of the external momentum source for neutrals",
-                    units="m_ref*n_ref*c_ref*c_ref/L_ref")
-            else
-                external_source_neutral_momentum_amplitude = nothing
-            end
-            if evolve_ppar
-                external_source_neutral_pressure_amplitude = create_dynamic_variable!(
-                    dynamic, "external_source_neutral_pressure_amplitude", mk_float, z, r;
-                    parallel_io=parallel_io, description="Amplitude of the external pressure source for neutrals",
-                    units="m_ref*n_ref*c_ref^2*c_ref/L_ref")
-            else
-                external_source_neutral_pressure_amplitude = nothing
-            end
-            if neutral_source_settings.PI_density_controller_I != 0.0 &&
-                    neutral_source_settings.source_type ∈ ("density_profile_control", "density_midpoint_control")
-                if neutral_source_settings.source_type == "density_profile_control"
-                    external_source_neutral_controller_integral = create_dynamic_variable!(
-                        dynamic, "external_source_neutral_controller_integral", mk_float, z, r;
-                        parallel_io=parallel_io,
-                        description="Integral term for the PID controller of the external source for neutrals")
-                else
-                    external_source_neutral_controller_integral = create_dynamic_variable!(
-                        dynamic, "external_source_neutral_controller_integral", mk_float;
-                        parallel_io=parallel_io,
-                        description="Integral term for the PID controller of the external source for neutrals")
-                end
-            else
-                external_source_neutral_controller_integral = nothing
-            end
-        else
-            external_source_neutral_amplitude = nothing
-            external_source_neutral_density_amplitude = nothing
-            external_source_neutral_momentum_amplitude = nothing
-            external_source_neutral_pressure_amplitude = nothing
-            external_source_neutral_controller_integral = nothing
-        end
+        io_phi, io_Er, io_Ez =
+            define_dynamic_em_field_variables!(fid, r, z, parallel_io)
+
+        io_density, io_upar, io_ppar, io_pperp, io_qpar, io_vth, io_dSdt,
+        external_source_amplitude, external_source_density_amplitude,
+        external_source_momentum_amplitude, external_source_pressure_amplitude,
+        external_source_controller_integral, io_chodura_lower, io_chodura_upper,
+        ion_constraints_A_coefficient, ion_constraints_B_coefficient,
+        ion_constraints_C_coefficient =
+            define_dynamic_ion_moment_variables!(fid, n_ion_species, r, z, parallel_io,
+                                                 external_source_settings, evolve_density,
+                                                 evolve_upar, evolve_ppar)
+
+        io_density_neutral, io_uz_neutral, io_pz_neutral, io_qz_neutral,
+        io_thermal_speed_neutral, external_source_neutral_amplitude,
+        external_source_neutral_density_amplitude,
+        external_source_neutral_momentum_amplitude,
+        external_source_neutral_pressure_amplitude,
+        external_source_neutral_controller_integral, neutral_constraints_A_coefficient,
+        neutral_constraints_B_coefficient, neutral_constraints_C_coefficient =
+            define_dynamic_neutral_moment_variables!(fid, n_neutral_species, r, z,
+                                                     parallel_io,
+                                                     external_source_settings,
+                                                     evolve_density, evolve_upar,
+                                                     evolve_ppar)
 
         io_time_for_run = create_dynamic_variable!(
             dynamic, "time_for_run", mk_float; parallel_io=parallel_io,
@@ -907,7 +719,8 @@ function define_dynamic_moment_variables!(fid, n_ion_species, n_neutral_species,
                         * "used by adaptve timestepping algorithm")
 
         return io_moments_info(fid, io_time, io_phi, io_Er, io_Ez, io_density, io_upar,
-                               io_ppar, io_pperp, io_qpar, io_vth, io_dSdt, io_chodura_lower, io_chodura_upper, io_density_neutral, io_uz_neutral,
+                               io_ppar, io_pperp, io_qpar, io_vth, io_dSdt, io_chodura_lower, io_chodura_upper,
+                               io_density_neutral, io_uz_neutral,
                                io_pz_neutral, io_qz_neutral, io_thermal_speed_neutral,
                                external_source_amplitude,
                                external_source_density_amplitude,
@@ -919,6 +732,12 @@ function define_dynamic_moment_variables!(fid, n_ion_species, n_neutral_species,
                                external_source_neutral_momentum_amplitude,
                                external_source_neutral_pressure_amplitude,
                                external_source_neutral_controller_integral,
+                               ion_constraints_A_coefficient,
+                               ion_constraints_B_coefficient,
+                               ion_constraints_C_coefficient,
+                               neutral_constraints_A_coefficient,
+                               neutral_constraints_B_coefficient,
+                               neutral_constraints_C_coefficient,
                                io_time_for_run, io_step_counter, io_dt,
                                io_failure_counter, io_failure_caused_by,
                                io_limit_caused_by, io_dt_before_last_fail, parallel_io)
@@ -928,18 +747,337 @@ function define_dynamic_moment_variables!(fid, n_ion_species, n_neutral_species,
     return nothing
 end
 
+"""
+define dynamic (time-evolving) electromagnetic field variables for writing to the hdf5
+file
+"""
+function define_dynamic_em_field_variables!(fid, r::coordinate, z::coordinate,
+                                            parallel_io)
+
+    dynamic = get_group(fid, "dynamic_data")
+
+    # io_phi is the handle referring to the electrostatic potential phi
+    io_phi = create_dynamic_variable!(dynamic, "phi", mk_float, z, r;
+                                      parallel_io=parallel_io,
+                                      description="electrostatic potential",
+                                      units="T_ref/e")
+    # io_Er is the handle for the radial component of the electric field
+    io_Er = create_dynamic_variable!(dynamic, "Er", mk_float, z, r;
+                                     parallel_io=parallel_io,
+                                     description="radial electric field",
+                                     units="T_ref/e L_ref")
+    # io_Ez is the handle for the zed component of the electric field
+    io_Ez = create_dynamic_variable!(dynamic, "Ez", mk_float, z, r;
+                                     parallel_io=parallel_io,
+                                     description="vertical electric field",
+                                     units="T_ref/e L_ref")
+
+    return io_phi, io_Er, io_Ez
+end
+
+"""
+define dynamic (time-evolving) ion moment variables for writing to the hdf5 file
+"""
+function define_dynamic_ion_moment_variables!(fid, n_ion_species, r::coordinate,
+        z::coordinate, parallel_io, external_source_settings, evolve_density, evolve_upar,
+        evolve_ppar)
+
+    dynamic = get_group(fid, "dynamic_data")
+
+    # io_density is the handle for the ion particle density
+    io_density = create_dynamic_variable!(dynamic, "density", mk_float, z, r;
+                                          n_ion_species=n_ion_species,
+                                          parallel_io=parallel_io,
+                                          description="ion species density",
+                                          units="n_ref")
+
+    # io_upar is the handle for the ion parallel flow density
+    io_upar = create_dynamic_variable!(dynamic, "parallel_flow", mk_float, z, r;
+                                       n_ion_species=n_ion_species,
+                                       parallel_io=parallel_io,
+                                       description="ion species parallel flow",
+                                       units="c_ref = sqrt(2*T_ref/mi)")
+
+    # io_ppar is the handle for the ion parallel pressure
+    io_ppar = create_dynamic_variable!(dynamic, "parallel_pressure", mk_float, z, r;
+                                       n_ion_species=n_ion_species,
+                                       parallel_io=parallel_io,
+                                       description="ion species parallel pressure",
+                                       units="n_ref*T_ref")
+
+    # io_pperp is the handle for the ion parallel pressure
+    io_pperp = create_dynamic_variable!(dynamic, "perpendicular_pressure", mk_float, z, r;
+                                        n_ion_species=n_ion_species,
+                                        parallel_io=parallel_io,
+                                        description="ion species perpendicular pressure",
+                                        units="n_ref*T_ref")
+
+    # io_qpar is the handle for the ion parallel heat flux
+    io_qpar = create_dynamic_variable!(dynamic, "parallel_heat_flux", mk_float, z, r;
+                                       n_ion_species=n_ion_species,
+                                       parallel_io=parallel_io,
+                                       description="ion species parallel heat flux",
+                                       units="n_ref*T_ref*c_ref")
+
+    # io_vth is the handle for the ion thermal speed
+    io_vth = create_dynamic_variable!(dynamic, "thermal_speed", mk_float, z, r;
+                                      n_ion_species=n_ion_species,
+                                      parallel_io=parallel_io,
+                                      description="ion species thermal speed",
+                                      units="c_ref")
+
+    # io_dSdt is the handle for the entropy production (due to collisions)
+    io_dSdt = create_dynamic_variable!(dynamic, "entropy_production", mk_float, z, r;
+                                      n_ion_species=n_ion_species,
+                                      parallel_io=parallel_io,
+                                      description="ion species entropy production",
+                                      units="")
+
+    ion_source_settings = external_source_settings.ion
+    if ion_source_settings.active
+        external_source_amplitude = create_dynamic_variable!(
+            dynamic, "external_source_amplitude", mk_float, z, r;
+            parallel_io=parallel_io, description="Amplitude of the external source for ions",
+            units="n_ref/c_ref^3*c_ref/L_ref")
+        if evolve_density
+            external_source_density_amplitude = create_dynamic_variable!(
+                dynamic, "external_source_density_amplitude", mk_float, z, r;
+                parallel_io=parallel_io, description="Amplitude of the external density source for ions",
+                units="n_ref*c_ref/L_ref")
+        else
+            external_source_density_amplitude = nothing
+        end
+        if evolve_upar
+            external_source_momentum_amplitude = create_dynamic_variable!(
+                dynamic, "external_source_momentum_amplitude", mk_float, z, r;
+                parallel_io=parallel_io, description="Amplitude of the external momentum source for ions",
+                units="m_ref*n_ref*c_ref*c_ref/L_ref")
+        else
+            external_source_momentum_amplitude = nothing
+        end
+        if evolve_ppar
+            external_source_pressure_amplitude = create_dynamic_variable!(
+                dynamic, "external_source_pressure_amplitude", mk_float, z, r;
+                parallel_io=parallel_io, description="Amplitude of the external pressure source for ions",
+                units="m_ref*n_ref*c_ref^2*c_ref/L_ref")
+        else
+            external_source_pressure_amplitude = nothing
+        end
+        if ion_source_settings.PI_density_controller_I != 0.0 &&
+                ion_source_settings.source_type ∈ ("density_profile_control", "density_midpoint_control")
+            if ion_source_settings.source_type == "density_profile_control"
+                external_source_controller_integral = create_dynamic_variable!(
+                    dynamic, "external_source_controller_integral", mk_float, z, r;
+                    parallel_io=parallel_io,
+                    description="Integral term for the PID controller of the external source for ions")
+            else
+                external_source_controller_integral = create_dynamic_variable!(
+                    dynamic, "external_source_controller_integral", mk_float;
+                    parallel_io=parallel_io,
+                    description="Integral term for the PID controller of the external source for ions")
+            end
+        else
+            external_source_controller_integral = nothing
+        end
+    else
+        external_source_amplitude = nothing
+        external_source_density_amplitude = nothing
+        external_source_momentum_amplitude = nothing
+        external_source_pressure_amplitude = nothing
+        external_source_controller_integral = nothing
+    end
+
+    if parallel_io || z.irank == 0
+        # io_chodura_lower is the handle for the ion thermal speed
+        io_chodura_lower = create_dynamic_variable!(dynamic, "chodura_integral_lower", mk_float, r;
+                                          n_ion_species=n_ion_species,
+                                          parallel_io=parallel_io,
+                                          description="Generalised Chodura integral lower sheath entrance",
+                                          units="c_ref")
+    else
+        io_chodura_lower = nothing
+    end
+    if parallel_io || z.irank == z.nrank - 1
+        # io_chodura_upper is the handle for the ion thermal speed
+        io_chodura_upper = create_dynamic_variable!(dynamic, "chodura_integral_upper", mk_float, r;
+                                          n_ion_species=n_ion_species,
+                                          parallel_io=parallel_io,
+                                          description="Generalised Chodura integral upper sheath entrance",
+                                          units="c_ref")
+    else
+        io_chodura_upper = nothing
+    end
+
+    if evolve_density || evolve_upar || evolve_ppar
+        ion_constraints_A_coefficient =
+            create_dynamic_variable!(dynamic, "ion_constraints_A_coefficient", mk_float, z, r;
+                                   n_ion_species=n_ion_species,
+                                   parallel_io=parallel_io,
+                                   description="'A' coefficient enforcing density constraint for ions")
+        ion_constraints_B_coefficient =
+            create_dynamic_variable!(dynamic, "ion_constraints_B_coefficient", mk_float, z, r;
+                                   n_ion_species=n_ion_species,
+                                   parallel_io=parallel_io,
+                                   description="'B' coefficient enforcing flow constraint for ions")
+        ion_constraints_C_coefficient =
+            create_dynamic_variable!(dynamic, "ion_constraints_C_coefficient", mk_float, z, r;
+                                   n_ion_species=n_ion_species,
+                                   parallel_io=parallel_io,
+                                   description="'C' coefficient enforcing pressure constraint for ions")
+    else
+           ion_constraints_A_coefficient = nothing
+           ion_constraints_B_coefficient = nothing
+           ion_constraints_C_coefficient = nothing
+    end
+
+    return io_density, io_upar, io_ppar, io_pperp, io_qpar, io_vth, io_dSdt,
+           external_source_amplitude, external_source_density_amplitude,
+           external_source_momentum_amplitude, external_source_pressure_amplitude,
+           external_source_controller_integral, io_chodura_lower, io_chodura_upper,
+           ion_constraints_A_coefficient, ion_constraints_B_coefficient,
+           ion_constraints_C_coefficient
+end
+
+"""
+define dynamic (time-evolving) neutral moment variables for writing to the hdf5 file
+"""
+function define_dynamic_neutral_moment_variables!(fid, n_neutral_species, r::coordinate,
+        z::coordinate, parallel_io, external_source_settings, evolve_density, evolve_upar,
+        evolve_ppar)
+
+    dynamic = get_group(fid, "dynamic_data")
+
+    # io_density_neutral is the handle for the neutral particle density
+    io_density_neutral = create_dynamic_variable!(dynamic, "density_neutral", mk_float, z, r;
+                                                  n_neutral_species=n_neutral_species,
+                                                  parallel_io=parallel_io,
+                                                  description="neutral species density",
+                                                  units="n_ref")
+
+    # io_uz_neutral is the handle for the neutral z momentum density
+    io_uz_neutral = create_dynamic_variable!(dynamic, "uz_neutral", mk_float, z, r;
+                                             n_neutral_species=n_neutral_species,
+                                             parallel_io=parallel_io,
+                                             description="neutral species mean z velocity",
+                                             units="c_ref = sqrt(2*T_ref/mi)")
+
+    # io_pz_neutral is the handle for the neutral species zz pressure
+    io_pz_neutral = create_dynamic_variable!(dynamic, "pz_neutral", mk_float, z, r;
+                                             n_neutral_species=n_neutral_species,
+                                             parallel_io=parallel_io,
+                                             description="neutral species mean zz pressure",
+                                             units="n_ref*T_ref")
+
+    # io_qz_neutral is the handle for the neutral z heat flux
+    io_qz_neutral = create_dynamic_variable!(dynamic, "qz_neutral", mk_float, z, r;
+                                             n_neutral_species=n_neutral_species,
+                                             parallel_io=parallel_io,
+                                             description="neutral species z heat flux",
+                                             units="n_ref*T_ref*c_ref")
+
+    # io_thermal_speed_neutral is the handle for the neutral thermal speed
+    io_thermal_speed_neutral = create_dynamic_variable!(
+        dynamic, "thermal_speed_neutral", mk_float, z, r;
+        n_neutral_species=n_neutral_species,
+        parallel_io=parallel_io, description="neutral species thermal speed",
+        units="c_ref")
+
+    neutral_source_settings = external_source_settings.neutral
+    if n_neutral_species > 0 && neutral_source_settings.active
+        external_source_neutral_amplitude = create_dynamic_variable!(
+            dynamic, "external_source_neutral_amplitude", mk_float, z, r;
+            parallel_io=parallel_io, description="Amplitude of the external source for neutrals",
+            units="n_ref/c_ref^3*c_ref/L_ref")
+        if evolve_density
+            external_source_neutral_density_amplitude = create_dynamic_variable!(
+                dynamic, "external_source_neutral_density_amplitude", mk_float, z, r;
+                parallel_io=parallel_io, description="Amplitude of the external density source for neutrals",
+                units="n_ref*c_ref/L_ref")
+        else
+            external_source_neutral_density_amplitude = nothing
+        end
+        if evolve_upar
+            external_source_neutral_momentum_amplitude = create_dynamic_variable!(
+                dynamic, "external_source_neutral_momentum_amplitude", mk_float, z, r;
+                parallel_io=parallel_io, description="Amplitude of the external momentum source for neutrals",
+                units="m_ref*n_ref*c_ref*c_ref/L_ref")
+        else
+            external_source_neutral_momentum_amplitude = nothing
+        end
+        if evolve_ppar
+            external_source_neutral_pressure_amplitude = create_dynamic_variable!(
+                dynamic, "external_source_neutral_pressure_amplitude", mk_float, z, r;
+                parallel_io=parallel_io, description="Amplitude of the external pressure source for neutrals",
+                units="m_ref*n_ref*c_ref^2*c_ref/L_ref")
+        else
+            external_source_neutral_pressure_amplitude = nothing
+        end
+        if neutral_source_settings.PI_density_controller_I != 0.0 &&
+                neutral_source_settings.source_type ∈ ("density_profile_control", "density_midpoint_control")
+            if neutral_source_settings.source_type == "density_profile_control"
+                external_source_neutral_controller_integral = create_dynamic_variable!(
+                    dynamic, "external_source_neutral_controller_integral", mk_float, z, r;
+                    parallel_io=parallel_io,
+                    description="Integral term for the PID controller of the external source for neutrals")
+            else
+                external_source_neutral_controller_integral = create_dynamic_variable!(
+                    dynamic, "external_source_neutral_controller_integral", mk_float;
+                    parallel_io=parallel_io,
+                    description="Integral term for the PID controller of the external source for neutrals")
+            end
+        else
+            external_source_neutral_controller_integral = nothing
+        end
+    else
+        external_source_neutral_amplitude = nothing
+        external_source_neutral_density_amplitude = nothing
+        external_source_neutral_momentum_amplitude = nothing
+        external_source_neutral_pressure_amplitude = nothing
+        external_source_neutral_controller_integral = nothing
+    end
+
+    if evolve_density || evolve_upar || evolve_ppar
+        neutral_constraints_A_coefficient =
+            create_dynamic_variable!(dynamic, "neutral_constraints_A_coefficient", mk_float, z, r;
+                                   n_neutral_species=n_neutral_species,
+                                   parallel_io=parallel_io,
+                                   description="'A' coefficient enforcing density constraint for neutrals")
+        neutral_constraints_B_coefficient =
+            create_dynamic_variable!(dynamic, "neutral_constraints_B_coefficient", mk_float, z, r;
+                                   n_neutral_species=n_neutral_species,
+                                   parallel_io=parallel_io,
+                                   description="'B' coefficient enforcing flow constraint for neutrals")
+        neutral_constraints_C_coefficient =
+            create_dynamic_variable!(dynamic, "neutral_constraints_C_coefficient", mk_float, z, r;
+                                   n_neutral_species=n_neutral_species,
+                                   parallel_io=parallel_io,
+                                   description="'C' coefficient enforcing pressure constraint for neutrals")
+    else
+           neutral_constraints_A_coefficient = nothing
+           neutral_constraints_B_coefficient = nothing
+           neutral_constraints_C_coefficient = nothing
+    end
+
+    return io_density_neutral, io_uz_neutral, io_pz_neutral, io_qz_neutral,
+           io_thermal_speed_neutral, external_source_neutral_amplitude,
+           external_source_neutral_density_amplitude,
+           external_source_neutral_momentum_amplitude,
+           external_source_neutral_pressure_amplitude,
+           external_source_neutral_controller_integral, neutral_constraints_A_coefficient,
+           neutral_constraints_B_coefficient, neutral_constraints_C_coefficient
+end
+
 """
 define dynamic (time-evolving) distribution function variables for writing to the output
 file
 """
-function define_dynamic_dfn_variables!(fid, r, z, vperp, vpa, vzeta, vr, vz,
-                                       n_ion_species, n_neutral_species, parallel_io,
-                                       external_source_settings, evolve_density,
-                                       evolve_upar, evolve_ppar)
+function define_dynamic_dfn_variables!(fid, r, z, vperp, vpa, vzeta, vr, vz, composition,
+                                       parallel_io, external_source_settings,
+                                       evolve_density, evolve_upar, evolve_ppar)
 
     @serial_region begin
-        io_moments = define_dynamic_moment_variables!(fid, n_ion_species,
-                                                      n_neutral_species, r, z,
+        io_moments = define_dynamic_moment_variables!(fid, composition.n_ion_species,
+                                                      composition.n_neutral_species, r, z,
                                                       parallel_io,
                                                       external_source_settings,
                                                       evolve_density, evolve_upar,
@@ -949,13 +1087,13 @@ function define_dynamic_dfn_variables!(fid, r, z, vperp, vpa, vzeta, vr, vz,
 
         # io_f is the handle for the ion pdf
         io_f = create_dynamic_variable!(dynamic, "f", mk_float, vpa, vperp, z, r;
-                                        n_ion_species=n_ion_species,
+                                        n_ion_species=composition.n_ion_species,
                                         parallel_io=parallel_io,
-                                        description="charged species distribution function")
+                                        description="ion species distribution function")
 
         # io_f_neutral is the handle for the neutral pdf
         io_f_neutral = create_dynamic_variable!(dynamic, "f_neutral", mk_float, vz, vr, vzeta, z, r;
-                                                n_neutral_species=n_neutral_species,
+                                                n_neutral_species=composition.n_neutral_species,
                                                 parallel_io=parallel_io,
                                                 description="neutral species distribution function")
 
@@ -1091,6 +1229,12 @@ function reopen_moments_io(file_info)
                                getvar("external_source_neutral_momentum_amplitude"),
                                getvar("external_source_neutral_pressure_amplitude"),
                                getvar("external_source_neutral_controller_integral"),
+                               getvar("ion_constraints_A_coefficient"),
+                               getvar("ion_constraints_B_coefficient"),
+                               getvar("ion_constraints_C_coefficient"),
+                               getvar("neutral_constraints_A_coefficient"),
+                               getvar("neutral_constraints_B_coefficient"),
+                               getvar("neutral_constraints_C_coefficient"),
                                getvar("time_for_run"), getvar("step_counter"),
                                getvar("dt"), getvar("failure_counter"),
                                getvar("failure_caused_by"), getvar("limit_caused_by"),
@@ -1143,9 +1287,8 @@ function setup_dfns_io(prefix, binary_format, boundary_distributions, r, z, vper
         ### create variables for time-dependent quantities and store them ###
         ### in a struct for later access ###
         io_dfns = define_dynamic_dfn_variables!(
-            fid, r, z, vperp, vpa, vzeta, vr, vz, composition.n_ion_species,
-            composition.n_neutral_species, parallel_io, external_source_settings,
-            evolve_density, evolve_upar, evolve_ppar)
+            fid, r, z, vperp, vpa, vzeta, vr, vz, composition, parallel_io,
+            external_source_settings, evolve_density, evolve_upar, evolve_ppar)
 
         close(fid)
 
@@ -1193,6 +1336,12 @@ function reopen_dfns_io(file_info)
                                      getvar("external_source_neutral_momentum_amplitude"),
                                      getvar("external_source_neutral_pressure_amplitude"),
                                      getvar("external_source_neutral_controller_integral"),
+                                     getvar("ion_constraints_A_coefficient"),
+                                     getvar("ion_constraints_B_coefficient"),
+                                     getvar("ion_constraints_C_coefficient"),
+                                     getvar("neutral_constraints_A_coefficient"),
+                                     getvar("neutral_constraints_B_coefficient"),
+                                     getvar("neutral_constraints_C_coefficient"),
                                      getvar("time_for_run"), getvar("step_counter"),
                                      getvar("dt"), getvar("failure_counter"),
                                      getvar("failure_caused_by"),
@@ -1229,11 +1378,11 @@ function append_to_dynamic_var end
 end
 
 """
-write time-dependent moments data to the binary output file
+write time-dependent moments data for ions and neutrals to the binary output file
 """
-function write_moments_data_to_binary(moments, fields, t, n_ion_species,
-                                      n_neutral_species, io_or_file_info_moments, t_idx,
-                                      time_for_run, t_params, r, z)
+function write_all_moments_data_to_binary(moments, fields, t, n_ion_species,
+                                          n_neutral_species, io_or_file_info_moments,
+                                          t_idx, time_for_run, t_params, r, z)
     @serial_region begin
         # Only read/write from first process in each 'block'
 
@@ -1250,145 +1399,228 @@ function write_moments_data_to_binary(moments, fields, t, n_ion_species,
         # add the time for this time slice to the hdf5 file
         append_to_dynamic_var(io_moments.time, t, t_idx, parallel_io)
 
+        write_em_fields_data_to_binary(fields, io_moments, t_idx, r, z)
+
+        write_ion_moments_data_to_binary(moments, n_ion_species, io_moments,
+                                         t_idx, r, z)
+
+        write_neutral_moments_data_to_binary(moments, n_neutral_species,
+                                             io_moments, t_idx, r, z)
+
+        append_to_dynamic_var(io_moments.time_for_run, time_for_run, t_idx, parallel_io)
+        append_to_dynamic_var(io_moments.step_counter, t_params.step_counter[], t_idx, parallel_io)
+        append_to_dynamic_var(io_moments.dt, t_params.dt_before_output[], t_idx, parallel_io)
+        append_to_dynamic_var(io_moments.failure_counter, t_params.failure_counter[], t_idx, parallel_io)
+        append_to_dynamic_var(io_moments.failure_caused_by, t_params.failure_caused_by,
+                              t_idx, parallel_io, length(t_params.failure_caused_by);
+                              only_root=true)
+        append_to_dynamic_var(io_moments.limit_caused_by, t_params.limit_caused_by, t_idx,
+                              parallel_io, length(t_params.limit_caused_by);
+                              only_root=true)
+        append_to_dynamic_var(io_moments.dt_before_last_fail,
+                              t_params.dt_before_last_fail[], t_idx, parallel_io)
+
+        closefile && close(io_moments.fid)
+    end
+
+    return nothing
+end
+
+"""
+write time-dependent EM fields data to the binary output file
+
+Note: should only be called from within a function that (re-)opens the output file.
+"""
+function write_em_fields_data_to_binary(fields, io_moments::io_moments_info, t_idx,
+                                        r, z)
+    @serial_region begin
+        # Only read/write from first process in each 'block'
+
+        parallel_io = io_moments.parallel_io
+
         # add the electrostatic potential and electric field components at this time slice to the hdf5 file
         append_to_dynamic_var(io_moments.phi, fields.phi, t_idx, parallel_io, z, r)
         append_to_dynamic_var(io_moments.Er, fields.Er, t_idx, parallel_io, z, r)
         append_to_dynamic_var(io_moments.Ez, fields.Ez, t_idx, parallel_io, z, r)
+    end
+
+    return nothing
+end
+
+"""
+write time-dependent moments data for ions to the binary output file
+
+Note: should only be called from within a function that (re-)opens the output file.
+"""
+function write_ion_moments_data_to_binary(moments, n_ion_species,
+                                          io_moments::io_moments_info, t_idx, r, z)
+    @serial_region begin
+        # Only read/write from first process in each 'block'
+
+        parallel_io = io_moments.parallel_io
 
         # add the density data at this time slice to the output file
-        append_to_dynamic_var(io_moments.density, moments.charged.dens, t_idx,
+        append_to_dynamic_var(io_moments.density, moments.ion.dens, t_idx,
                               parallel_io, z, r, n_ion_species)
-        append_to_dynamic_var(io_moments.parallel_flow, moments.charged.upar, t_idx,
+        append_to_dynamic_var(io_moments.parallel_flow, moments.ion.upar, t_idx,
                               parallel_io, z, r, n_ion_species)
-        append_to_dynamic_var(io_moments.parallel_pressure, moments.charged.ppar, t_idx,
+        append_to_dynamic_var(io_moments.parallel_pressure, moments.ion.ppar, t_idx,
                               parallel_io, z, r, n_ion_species)
-        append_to_dynamic_var(io_moments.perpendicular_pressure, moments.charged.pperp, t_idx,
+        append_to_dynamic_var(io_moments.perpendicular_pressure, moments.ion.pperp, t_idx,
                               parallel_io, z, r, n_ion_species)
-        append_to_dynamic_var(io_moments.parallel_heat_flux, moments.charged.qpar, t_idx,
+        append_to_dynamic_var(io_moments.parallel_heat_flux, moments.ion.qpar, t_idx,
                               parallel_io, z, r, n_ion_species)
-        append_to_dynamic_var(io_moments.thermal_speed, moments.charged.vth, t_idx,
+        append_to_dynamic_var(io_moments.thermal_speed, moments.ion.vth, t_idx,
                               parallel_io, z, r, n_ion_species)
-        append_to_dynamic_var(io_moments.entropy_production, moments.charged.dSdt, t_idx,
+        append_to_dynamic_var(io_moments.entropy_production, moments.ion.dSdt, t_idx,
                               parallel_io, z, r, n_ion_species)
         if z.irank == 0 # lower wall 
             append_to_dynamic_var(io_moments.chodura_integral_lower,
-                                  moments.charged.chodura_integral_lower, t_idx,
+                                  moments.ion.chodura_integral_lower, t_idx,
                                   parallel_io, r, n_ion_species)
         elseif io_moments.chodura_integral_lower !== nothing
             append_to_dynamic_var(io_moments.chodura_integral_lower,
-                                  moments.charged.chodura_integral_lower, t_idx,
+                                  moments.ion.chodura_integral_lower, t_idx,
                                   parallel_io, 0, n_ion_species)
         end
         if z.irank == z.nrank - 1 # upper wall
             append_to_dynamic_var(io_moments.chodura_integral_upper,
-                                  moments.charged.chodura_integral_upper, t_idx,
+                                  moments.ion.chodura_integral_upper, t_idx,
                                   parallel_io, r, n_ion_species)
         elseif io_moments.chodura_integral_upper !== nothing
             append_to_dynamic_var(io_moments.chodura_integral_upper,
-                                  moments.charged.chodura_integral_upper, t_idx,
+                                  moments.ion.chodura_integral_upper, t_idx,
                                   parallel_io, 0, n_ion_species)
         end
         if io_moments.external_source_amplitude !== nothing
             append_to_dynamic_var(io_moments.external_source_amplitude,
-                                  moments.charged.external_source_amplitude, t_idx,
+                                  moments.ion.external_source_amplitude, t_idx,
                                   parallel_io, z, r)
             if moments.evolve_density
                 append_to_dynamic_var(io_moments.external_source_density_amplitude,
-                                      moments.charged.external_source_density_amplitude,
+                                      moments.ion.external_source_density_amplitude,
                                       t_idx, parallel_io, z, r)
             end
             if moments.evolve_upar
                 append_to_dynamic_var(io_moments.external_source_momentum_amplitude,
-                                      moments.charged.external_source_momentum_amplitude,
+                                      moments.ion.external_source_momentum_amplitude,
                                       t_idx, parallel_io, z, r)
             end
             if moments.evolve_ppar
                 append_to_dynamic_var(io_moments.external_source_pressure_amplitude,
-                                      moments.charged.external_source_pressure_amplitude,
+                                      moments.ion.external_source_pressure_amplitude,
                                       t_idx, parallel_io, z, r)
             end
         end
         if io_moments.external_source_controller_integral !== nothing
-            if size(moments.charged.external_source_controller_integral) == (1,1)
+            if size(moments.ion.external_source_controller_integral) == (1,1)
                 append_to_dynamic_var(io_moments.external_source_controller_integral,
-                                      moments.charged.external_source_controller_integral[1,1],
+                                      moments.ion.external_source_controller_integral[1,1],
                                       t_idx, parallel_io)
             else
                 append_to_dynamic_var(io_moments.external_source_controller_integral,
-                                      moments.charged.external_source_controller_integral,
+                                      moments.ion.external_source_controller_integral,
                                       t_idx, parallel_io, z, r)
             end
         end
-        if n_neutral_species > 0
-            append_to_dynamic_var(io_moments.density_neutral, moments.neutral.dens, t_idx,
-                                  parallel_io, z, r, n_neutral_species)
-            append_to_dynamic_var(io_moments.uz_neutral, moments.neutral.uz, t_idx,
+        if moments.evolve_density || moments.evolve_upar || moments.evolve_ppar
+            append_to_dynamic_var(io_moments.ion_constraints_A_coefficient,
+                                  moments.ion.constraints_A_coefficient, t_idx,
+                                  parallel_io, z, r, n_ion_species)
+            append_to_dynamic_var(io_moments.ion_constraints_B_coefficient,
+                                  moments.ion.constraints_B_coefficient, t_idx,
+                                  parallel_io, z, r, n_ion_species)
+            append_to_dynamic_var(io_moments.ion_constraints_C_coefficient,
+                                  moments.ion.constraints_C_coefficient, t_idx,
+                                  parallel_io, z, r, n_ion_species)
+        end
+    end
+
+    return nothing
+end
+
+"""
+write time-dependent moments data for neutrals to the binary output file
+
+Note: should only be called from within a function that (re-)opens the output file.
+"""
+function write_neutral_moments_data_to_binary(moments, n_neutral_species,
+                                              io_moments::io_moments_info, t_idx, r, z)
+    if n_neutral_species ≤ 0
+        return nothing
+    end
+
+    @serial_region begin
+        # Only read/write from first process in each 'block'
+
+        parallel_io = io_moments.parallel_io
+
+        append_to_dynamic_var(io_moments.density_neutral, moments.neutral.dens, t_idx,
+                              parallel_io, z, r, n_neutral_species)
+        append_to_dynamic_var(io_moments.uz_neutral, moments.neutral.uz, t_idx,
+                              parallel_io, z, r, n_neutral_species)
+        append_to_dynamic_var(io_moments.pz_neutral, moments.neutral.pz, t_idx,
+                              parallel_io, z, r, n_neutral_species)
+        append_to_dynamic_var(io_moments.qz_neutral, moments.neutral.qz, t_idx,
+                              parallel_io, z, r, n_neutral_species)
+        append_to_dynamic_var(io_moments.thermal_speed_neutral, moments.neutral.vth,
+                              t_idx, parallel_io, z, r, n_neutral_species)
+
+        if io_moments.external_source_neutral_amplitude !== nothing
+            append_to_dynamic_var(io_moments.external_source_neutral_amplitude,
+                                  moments.neutral.external_source_amplitude, t_idx,
+                                  parallel_io, z, r)
+            if moments.evolve_density
+                append_to_dynamic_var(io_moments.external_source_neutral_density_amplitude,
+                                      moments.neutral.external_source_density_amplitude,
+                                      t_idx, parallel_io, z, r)
+            end
+            if moments.evolve_upar
+                append_to_dynamic_var(io_moments.external_source_neutral_momentum_amplitude,
+                                      moments.neutral.external_source_momentum_amplitude,
+                                      t_idx, parallel_io, z, r)
+            end
+            if moments.evolve_ppar
+                append_to_dynamic_var(io_moments.external_source_neutral_pressure_amplitude,
+                                      moments.neutral.external_source_pressure_amplitude,
+                                      t_idx, parallel_io, z, r)
+            end
+        end
+        if io_moments.external_source_neutral_controller_integral !== nothing
+            if size(moments.neutral.external_source_neutral_controller_integral) == (1,1)
+                append_to_dynamic_var(io_moments.external_source_neutral_controller_integral,
+                                      moments.neutral.external_source_controller_integral[1,1],
+                                      t_idx, parallel_io)
+            else
+                append_to_dynamic_var(io_moments.external_source_neutral_controller_integral,
+                                      moments.neutral.external_source_controller_integral,
+                                      t_idx, parallel_io, z, r)
+            end
+        end
+        if moments.evolve_density || moments.evolve_upar || moments.evolve_ppar
+            append_to_dynamic_var(io_moments.neutral_constraints_A_coefficient,
+                                  moments.neutral.constraints_A_coefficient, t_idx,
                                   parallel_io, z, r, n_neutral_species)
-            append_to_dynamic_var(io_moments.pz_neutral, moments.neutral.pz, t_idx,
+            append_to_dynamic_var(io_moments.neutral_constraints_B_coefficient,
+                                  moments.neutral.constraints_B_coefficient, t_idx,
                                   parallel_io, z, r, n_neutral_species)
-            append_to_dynamic_var(io_moments.qz_neutral, moments.neutral.qz, t_idx,
+            append_to_dynamic_var(io_moments.neutral_constraints_C_coefficient,
+                                  moments.neutral.constraints_C_coefficient, t_idx,
                                   parallel_io, z, r, n_neutral_species)
-            append_to_dynamic_var(io_moments.thermal_speed_neutral, moments.neutral.vth,
-                                  t_idx, parallel_io, z, r, n_neutral_species)
-
-            if io_moments.external_source_neutral_amplitude !== nothing
-                append_to_dynamic_var(io_moments.external_source_neutral_amplitude,
-                                      moments.neutral.external_source_amplitude, t_idx,
-                                      parallel_io, z, r)
-                if moments.evolve_density
-                    append_to_dynamic_var(io_moments.external_source_neutral_density_amplitude,
-                                          moments.neutral.external_source_density_amplitude,
-                                          t_idx, parallel_io, z, r)
-                end
-                if moments.evolve_upar
-                    append_to_dynamic_var(io_moments.external_source_neutral_momentum_amplitude,
-                                          moments.neutral.external_source_momentum_amplitude,
-                                          t_idx, parallel_io, z, r)
-                end
-                if moments.evolve_ppar
-                    append_to_dynamic_var(io_moments.external_source_neutral_pressure_amplitude,
-                                          moments.neutral.external_source_pressure_amplitude,
-                                          t_idx, parallel_io, z, r)
-                end
-            end
-            if io_moments.external_source_neutral_controller_integral !== nothing
-                if size(moments.neutral.external_source_neutral_controller_integral) == (1,1)
-                    append_to_dynamic_var(io_moments.external_source_neutral_controller_integral,
-                                          moments.neutral.external_source_controller_integral[1,1],
-                                          t_idx, parallel_io)
-                else
-                    append_to_dynamic_var(io_moments.external_source_neutral_controller_integral,
-                                          moments.neutral.external_source_controller_integral,
-                                          t_idx, parallel_io, z, r)
-                end
-            end
         end
-
-        append_to_dynamic_var(io_moments.time_for_run, time_for_run, t_idx, parallel_io)
-        append_to_dynamic_var(io_moments.step_counter, t_params.step_counter[], t_idx, parallel_io)
-        append_to_dynamic_var(io_moments.dt, t_params.dt_before_output[], t_idx, parallel_io)
-        append_to_dynamic_var(io_moments.failure_counter, t_params.failure_counter[], t_idx, parallel_io)
-        append_to_dynamic_var(io_moments.failure_caused_by, t_params.failure_caused_by,
-                              t_idx, parallel_io, length(t_params.failure_caused_by);
-                              only_root=true)
-        append_to_dynamic_var(io_moments.limit_caused_by, t_params.limit_caused_by, t_idx,
-                              parallel_io, length(t_params.limit_caused_by);
-                              only_root=true)
-        append_to_dynamic_var(io_moments.dt_before_last_fail,
-                              t_params.dt_before_last_fail[], t_idx, parallel_io)
-
-        closefile && close(io_moments.fid)
     end
+
     return nothing
 end
 
 """
-write time-dependent distribution function data to the binary output file
+write time-dependent distribution function data for ions and neutrals to the
+binary output file
 """
-function write_dfns_data_to_binary(ff, ff_neutral, moments, fields, t, n_ion_species,
-                                   n_neutral_species, io_or_file_info_dfns, t_idx,
-                                   time_for_run, t_params, r, z, vperp, vpa, vzeta, vr,
-                                   vz)
+function write_all_dfns_data_to_binary(pdf, moments, fields, t, n_ion_species,
+                                       n_neutral_species, io_or_file_info_dfns, t_idx,
+                                       time_for_run, t_params, r, z, vperp, vpa, vzeta, vr,
+                                       vz)
     @serial_region begin
         # Only read/write from first process in each 'block'
 
@@ -1402,21 +1634,56 @@ function write_dfns_data_to_binary(ff, ff_neutral, moments, fields, t, n_ion_spe
 
         # Write the moments for this time slice to the output file.
         # This also updates the time.
-        write_moments_data_to_binary(moments, fields, t, n_ion_species, n_neutral_species,
-                                     io_dfns.io_moments, t_idx, time_for_run, t_params, r,
-                                     z)
+        write_all_moments_data_to_binary(moments, fields, t, n_ion_species,
+                                         n_neutral_species, io_dfns.io_moments, t_idx,
+                                         time_for_run, t_params, r, z)
+
+        # add the distribution function data at this time slice to the output file
+        write_ion_dfns_data_to_binary(pdf.ion.norm, n_ion_species, io_dfns, t_idx, r, z,
+                                      vperp, vpa)
+        write_neutral_dfns_data_to_binary(pdf.neutral.norm, n_neutral_species, io_dfns,
+                                          t_idx, r, z, vzeta, vr, vz)
+
+        closefile && close(io_dfns.fid)
+    end
+    return nothing
+end
+
+"""
+write time-dependent distribution function data for ions to the binary output file
+
+Note: should only be called from within a function that (re-)opens the output file.
+"""
+function write_ion_dfns_data_to_binary(ff, n_ion_species, io_dfns::io_dfns_info,
+                                       t_idx, r, z, vperp, vpa)
+    @serial_region begin
+        # Only read/write from first process in each 'block'
 
         parallel_io = io_dfns.parallel_io
 
-        # add the distribution function data at this time slice to the output file
         append_to_dynamic_var(io_dfns.f, ff, t_idx, parallel_io, vpa, vperp, z, r,
                               n_ion_species)
+    end
+    return nothing
+end
+
+"""
+write time-dependent distribution function data for neutrals to the binary output file
+
+Note: should only be called from within a function that (re-)opens the output file.
+"""
+function write_neutral_dfns_data_to_binary(ff_neutral, n_neutral_species,
+                                           io_dfns::io_dfns_info, t_idx, r, z, vzeta, vr,
+                                           vz)
+    @serial_region begin
+        # Only read/write from first process in each 'block'
+
+        parallel_io = io_dfns.parallel_io
+
         if n_neutral_species > 0
             append_to_dynamic_var(io_dfns.f_neutral, ff_neutral, t_idx, parallel_io, vz,
                                   vr, vzeta, z, r, n_neutral_species)
         end
-
-        closefile && close(io_dfns.fid)
     end
     return nothing
 end
@@ -1455,9 +1722,9 @@ include("file_io_hdf5.jl")
 
 """
 """
-function write_data_to_ascii(moments, fields, vpa, vperp, z, r, t, n_ion_species,
+function write_data_to_ascii(pdf, moments, fields, vpa, vperp, z, r, t, n_ion_species,
                              n_neutral_species, ascii_io::Union{ascii_ios,Nothing})
-    if ascii_io === nothing || ascii_io.moments_charged === nothing
+    if ascii_io === nothing || ascii_io.moments_ion === nothing
         # ascii I/O is disabled
         return nothing
     end
@@ -1465,8 +1732,8 @@ function write_data_to_ascii(moments, fields, vpa, vperp, z, r, t, n_ion_species
     @serial_region begin
         # Only read/write from first process in each 'block'
 
-        #write_f_ascii(ff, z, vpa, t, ascii_io.ff)
-        write_moments_charged_ascii(moments.charged, z, r, t, n_ion_species, ascii_io.moments_charged)
+        write_f_ascii(pdf, z, vpa, t, ascii_io.ff)
+        write_moments_ion_ascii(moments.ion, z, r, t, n_ion_species, ascii_io.moments_ion)
         if n_neutral_species > 0
             write_moments_neutral_ascii(moments.neutral, z, r, t, n_neutral_species, ascii_io.moments_neutral)
         end
@@ -1483,27 +1750,28 @@ function write_f_ascii(f, z, vpa, t, ascii_io)
         # Only read/write from first process in each 'block'
 
         @inbounds begin
-            n_species = size(f,3)
-            for is ∈ 1:n_species
+            #n_species = size(f,3)
+            #for is ∈ 1:n_species
                 for j ∈ 1:vpa.n
                     for i ∈ 1:z.n
-                        println(ascii_io,"t: ", t, "   spec: ", is, ",   z: ", z.grid[i],
-                            ",  vpa: ", vpa.grid[j], ",   f: ", f[i,j,is])
+                        println(ascii_io,"t: ", t, "   z: ", z.grid[i],
+                            "  vpa: ", vpa.grid[j], "   fion: ", f.ion.norm[i,j,1], 
+                            "   fneutral: ", f.neutral.norm[i,j,1])
                     end
                     println(ascii_io)
                 end
                 println(ascii_io)
-            end
-            println(ascii_io)
+            #end
+            #println(ascii_io)
         end
     end
     return nothing
 end
 
 """
-write moments of the charged species distribution function f at this time slice
+write moments of the ion species distribution function f at this time slice
 """
-function write_moments_charged_ascii(mom, z, r, t, n_species, ascii_io)
+function write_moments_ion_ascii(mom, z, r, t, n_species, ascii_io)
     @serial_region begin
         # Only read/write from first process in each 'block'
 
@@ -1556,7 +1824,8 @@ function write_fields_ascii(flds, z, r, t, ascii_io)
         @inbounds begin
             for ir ∈ 1:r.n
                 for iz ∈ 1:z.n
-                    println(ascii_io,"t: ", t, "   r: ", r.grid[ir],"   z: ", z.grid[iz], "  phi: ", flds.phi[iz,ir])
+                    println(ascii_io,"t: ", t, "   r: ", r.grid[ir],"   z: ", z.grid[iz], "  phi: ", flds.phi[iz,ir],
+                            " Ez: ", flds.Ez[iz,ir])
                 end
             end
         end
@@ -1704,9 +1973,9 @@ function debug_dump(vz::coordinate, vr::coordinate, vzeta::coordinate, vpa::coor
         debug_output_file.label[debug_output_counter[]] = label
         # add the distribution function data at this time slice to the netcdf file
         if ff === nothing
-            debug_output_file.dfns.charged_f[:,:,:,:,:,debug_output_counter[]] = 0.0
+            debug_output_file.dfns.ion_f[:,:,:,:,:,debug_output_counter[]] = 0.0
         else
-            debug_output_file.dfns.charged_f[:,:,:,:,:,debug_output_counter[]] = ff
+            debug_output_file.dfns.ion_f[:,:,:,:,:,debug_output_counter[]] = ff
         end
         # add the moments data at this time slice to the netcdf file
         if dens === nothing
diff --git a/moment_kinetics/src/file_io_hdf5.jl b/moment_kinetics/src/file_io_hdf5.jl
index 6c9de806e..c40dea9d5 100644
--- a/moment_kinetics/src/file_io_hdf5.jl
+++ b/moment_kinetics/src/file_io_hdf5.jl
@@ -80,9 +80,9 @@ end
 # HDF5.H5DataStore is the supertype for HDF5.File and HDF5.Group
 function write_single_value!(file_or_group::HDF5.H5DataStore, name,
                              data::Union{Number, AbstractString, AbstractArray{T,N}},
-                             coords...; parallel_io, n_ion_species=nothing,
-                             n_neutral_species=nothing, description=nothing,
-                             units=nothing) where {T,N}
+                             coords::Union{coordinate,mk_int}...; parallel_io,
+                             n_ion_species=nothing, n_neutral_species=nothing,
+                             description=nothing, units=nothing) where {T,N}
     if isa(data, Union{Number, AbstractString})
         file_or_group[name] = data
         if description !== nothing
diff --git a/moment_kinetics/src/fokker_planck.jl b/moment_kinetics/src/fokker_planck.jl
index 5b2922328..0352f9a1f 100644
--- a/moment_kinetics/src/fokker_planck.jl
+++ b/moment_kinetics/src/fokker_planck.jl
@@ -52,7 +52,7 @@ using ..velocity_moments: integrate_over_vspace
 using ..velocity_moments: get_density, get_upar, get_ppar, get_pperp, get_qpar, get_pressure, get_rmom
 using ..looping
 using ..input_structs: fkpl_collisions_input, set_defaults_and_check_section!
-using ..reference_parameters: get_reference_collision_frequency
+using ..reference_parameters: get_reference_collision_frequency_ii
 using ..fokker_planck_calculus: init_Rosenbluth_potential_integration_weights!
 using ..fokker_planck_calculus: init_Rosenbluth_potential_boundary_integration_weights!
 using ..fokker_planck_calculus: allocate_boundary_integration_weights
@@ -82,7 +82,7 @@ frequency_option = "manual"
 """
 function setup_fkpl_collisions_input(toml_input::Dict, reference_params)
     # get reference collision frequency (note factor of 1/2 due to definition choices)
-    nuii_fkpl_default = 0.5*get_reference_collision_frequency(reference_params)
+    nuii_fkpl_default = 0.5*get_reference_collision_frequency_ii(reference_params)
     # read the input toml and specify a sensible default
     input_section = set_defaults_and_check_section!(toml_input, "fokker_planck_collisions",
        # begin default inputs (as kwargs)
diff --git a/moment_kinetics/src/force_balance.jl b/moment_kinetics/src/force_balance.jl
index 562f59972..902c3901e 100644
--- a/moment_kinetics/src/force_balance.jl
+++ b/moment_kinetics/src/force_balance.jl
@@ -23,14 +23,14 @@ function force_balance!(pflx, density_out, fvec, moments, fields, collisions, dt
     upar = fvec.upar
     @loop_s_r_z is ir iz begin
         pflx[iz,ir,is] = density[iz,ir,is]*upar[iz,ir,is] -
-                         dt*(moments.charged.dppar_dz[iz,ir,is] +
-                             upar[iz,ir,is]*upar[iz,ir,is]*moments.charged.ddens_dz_upwind[iz,ir,is] +
-                             2.0*density[iz,ir,is]*upar[iz,ir,is]*moments.charged.dupar_dz_upwind[iz,ir,is] -
+                         dt*(moments.ion.dppar_dz[iz,ir,is] +
+                             upar[iz,ir,is]*upar[iz,ir,is]*moments.ion.ddens_dz_upwind[iz,ir,is] +
+                             2.0*density[iz,ir,is]*upar[iz,ir,is]*moments.ion.dupar_dz_upwind[iz,ir,is] -
                              0.5*geometry.bzed[iz,ir]*fields.Ez[iz,ir]*density[iz,ir,is])
     end
 
     if ion_source_settings.active && false
-        source_amplitude = moments.charged.external_source_momentum_amplitude
+        source_amplitude = moments.ion.external_source_momentum_amplitude
         @loop_s_r_z is ir iz begin
             pflx[iz,ir,is] +=
                 dt * source_amplitude[iz,ir]
@@ -38,10 +38,10 @@ function force_balance!(pflx, density_out, fvec, moments, fields, collisions, dt
     end
 
     # Ad-hoc diffusion to stabilise numerics...
-    diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
+    diffusion_coefficient = num_diss_params.ion.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_s_r_z is ir iz begin
-            pflx[iz,ir,is] += dt*diffusion_coefficient*moments.charged.d2upar_dz2[iz,ir,is]*density[iz,ir,is]
+            pflx[iz,ir,is] += dt*diffusion_coefficient*moments.ion.d2upar_dz2[iz,ir,is]*density[iz,ir,is]
         end
     end
 
@@ -92,7 +92,7 @@ function neutral_force_balance!(pflx, density_out, fvec, moments, fields, collis
     end
 
     # Ad-hoc diffusion to stabilise numerics...
-    diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
+    diffusion_coefficient = num_diss_params.neutral.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_sn_r_z isn ir iz begin
             pflx[iz,ir,isn] += dt*diffusion_coefficient*moments.neutral.d2uz_dz2[iz,ir,isn]*density[iz,ir,isn]
diff --git a/moment_kinetics/src/initial_conditions.jl b/moment_kinetics/src/initial_conditions.jl
index 8c5ab2520..7f724c6bc 100644
--- a/moment_kinetics/src/initial_conditions.jl
+++ b/moment_kinetics/src/initial_conditions.jl
@@ -4,8 +4,6 @@ module initial_conditions
 
 export allocate_pdf_and_moments
 export init_pdf_and_moments!
-export enforce_boundary_conditions!
-export enforce_neutral_boundary_conditions!
 
 # functional testing 
 export create_boundary_distributions
@@ -17,18 +15,16 @@ using SpecialFunctions: erfc
 using ..type_definitions: mk_float, mk_int
 using ..array_allocation: allocate_float, allocate_shared_float
 using ..bgk: init_bgk_pdf!
+using ..boundary_conditions: vpagrid_to_dzdt
 using ..communication
-using ..calculus: reconcile_element_boundaries_MPI!
-using ..coordinates: coordinate
 using ..external_sources
 using ..interpolation: interpolate_to_grid_1d!
 using ..looping
-using ..moment_kinetics_structs: scratch_pdf
+using ..moment_kinetics_structs: scratch_pdf, pdf_substruct,
+                                 pdf_struct, moments_struct, boundary_distributions_struct
 using ..velocity_moments: integrate_over_vspace, integrate_over_neutral_vspace
-using ..velocity_moments: integrate_over_positive_vpa, integrate_over_negative_vpa
 using ..velocity_moments: integrate_over_positive_vz, integrate_over_negative_vz
-using ..velocity_moments: create_moments_charged, create_moments_neutral, update_qpar!
-using ..velocity_moments: moments_charged_substruct, moments_neutral_substruct
+using ..velocity_moments: create_moments_ion, create_moments_neutral, update_qpar!
 using ..velocity_moments: update_neutral_density!, update_neutral_pz!, update_neutral_pr!, update_neutral_pzeta!
 using ..velocity_moments: update_neutral_uz!, update_neutral_ur!, update_neutral_uzeta!, update_neutral_qz!
 using ..velocity_moments: update_ppar!, update_upar!, update_density!, update_pperp!, update_vth!, reset_moments_status!
@@ -37,53 +33,12 @@ using ..manufactured_solns: manufactured_solutions
 
 using MPI
 
-"""
-"""
-struct pdf_substruct{n_distribution}
-    norm::MPISharedArray{mk_float,n_distribution}
-    buffer::MPISharedArray{mk_float,n_distribution} # for collision operator terms when pdfs must be interpolated onto different velocity space grids, and for gyroaveraging
-end
-
-# struct of structs neatly contains i+n info?
-struct pdf_struct
-    #charged particles: s + r + z + vperp + vpa
-    charged::pdf_substruct{5}
-    #neutral particles: s + r + z + vzeta + vr + vz
-    neutral::pdf_substruct{6}
-end
-
-struct moments_struct
-    charged::moments_charged_substruct
-    neutral::moments_neutral_substruct
-    # flag that indicates if the density should be evolved via continuity equation
-    evolve_density::Bool
-    # flag that indicates if particle number should be conserved for each species
-    # effects like ionisation or net particle flux from the domain would lead to
-    # non-conservation
-    particle_number_conserved::Bool
-    # flag that indicates if exact particle conservation should be enforced
-    enforce_conservation::Bool
-    # flag that indicates if the parallel flow should be evolved via force balance
-    evolve_upar::Bool
-    # flag that indicates if the parallel pressure should be evolved via the energy equation
-    evolve_ppar::Bool
-end
-
-struct boundary_distributions_struct
-    # knudsen cosine distribution for imposing the neutral wall boundary condition
-    knudsen::MPISharedArray{mk_float,3}
-    # charged particle r boundary values (vpa,vperp,z,r,s)
-    pdf_rboundary_charged::MPISharedArray{mk_float,5}
-    # neutral particle r boundary values (vz,vr,vzeta,z,r,s)
-    pdf_rboundary_neutral::MPISharedArray{mk_float,6}
-end
-
 """
 Creates the structs for the pdf and the velocity-space moments
 """
 function allocate_pdf_and_moments(composition, r, z, vperp, vpa, vzeta, vr, vz,
                                   evolve_moments, collisions, external_source_settings,
-                                  numerical_dissipation)
+                                  num_diss_params)
     pdf = create_pdf(composition, r, z, vperp, vpa, vzeta, vr, vz)
 
     # create the 'moments' struct that contains various v-space moments and other
@@ -91,14 +46,14 @@ function allocate_pdf_and_moments(composition, r, z, vperp, vpa, vzeta, vr, vz,
     # the time-dependent entries are not initialised.
     # moments arrays have same r and z grids for both ion and neutral species
     # and so are included in the same struct
-    charged = create_moments_charged(z.n, r.n, composition.n_ion_species,
+    ion = create_moments_ion(z.n, r.n, composition.n_ion_species,
         evolve_moments.density, evolve_moments.parallel_flow,
         evolve_moments.parallel_pressure, external_source_settings.ion,
-        numerical_dissipation)
+        num_diss_params)
     neutral = create_moments_neutral(z.n, r.n, composition.n_neutral_species,
         evolve_moments.density, evolve_moments.parallel_flow,
         evolve_moments.parallel_pressure, external_source_settings.neutral,
-        numerical_dissipation)
+        num_diss_params)
 
     if abs(collisions.ionization) > 0.0 || z.bc == "wall"
         # if ionization collisions are included or wall BCs are enforced, then particle
@@ -109,7 +64,7 @@ function allocate_pdf_and_moments(composition, r, z, vperp, vpa, vzeta, vr, vz,
         particle_number_conserved = true
     end
 
-    moments = moments_struct(charged, neutral, evolve_moments.density,
+    moments = moments_struct(ion, neutral, evolve_moments.density,
                              particle_number_conserved,
                              evolve_moments.conservation,
                              evolve_moments.parallel_flow,
@@ -126,14 +81,13 @@ Allocate arrays for pdfs
 """
 function create_pdf(composition, r, z, vperp, vpa, vzeta, vr, vz)
     # allocate pdf arrays
-    pdf_charged_norm = allocate_shared_float(vpa.n, vperp.n, z.n, r.n, composition.n_ion_species)
-    # buffer array is for ion-neutral collisions, not for storing charged pdf
-    pdf_charged_buffer = allocate_shared_float(vpa.n, vperp.n, z.n, r.n, composition.n_neutral_species) # n.b. n_species is n_neutral_species here
+    pdf_ion_norm = allocate_shared_float(vpa.n, vperp.n, z.n, r.n, composition.n_ion_species)
+    # buffer array is for ion-neutral collisions, not for storing ion pdf
+    pdf_ion_buffer = allocate_shared_float(vpa.n, vperp.n, z.n, r.n, composition.n_neutral_species) # n.b. n_species is n_neutral_species here
     pdf_neutral_norm = allocate_shared_float(vz.n, vr.n, vzeta.n, z.n, r.n, composition.n_neutral_species)
     # buffer array is for neutral-ion collisions, not for storing neutral pdf
     pdf_neutral_buffer = allocate_shared_float(vz.n, vr.n, vzeta.n, z.n, r.n, composition.n_ion_species)
-    
-    return pdf_struct(pdf_substruct(pdf_charged_norm, pdf_charged_buffer),
+    return pdf_struct(pdf_substruct(pdf_ion_norm, pdf_ion_buffer),
                       pdf_substruct(pdf_neutral_norm, pdf_neutral_buffer))
 
 end
@@ -156,33 +110,52 @@ function init_pdf_and_moments!(pdf, moments, boundary_distributions, geometry,
         n_ion_species = composition.n_ion_species
         n_neutral_species = composition.n_neutral_species
         @serial_region begin
-            # initialise the density profile
-            init_density!(moments.charged.dens, z, r, species.charged, n_ion_species)
-            # initialise the parallel flow profile
-            init_upar!(moments.charged.upar, z, r, species.charged, n_ion_species)
-            # initialise the parallel thermal speed profile
-            init_vth!(moments.charged.vth, z, r, species.charged, n_ion_species)
+            # initialise the ion density profile
+            init_density!(moments.ion.dens, z, r, species.ion, n_ion_species)
+            # initialise the ion parallel flow profile
+            init_upar!(moments.ion.upar, z, r, species.ion, n_ion_species)
+            # initialise the ion parallel thermal speed profile
+            init_vth!(moments.ion.vth, z, r, species.ion, n_ion_species)
+            @. moments.ion.ppar = 0.5 * moments.ion.dens * moments.ion.vth^2
             # initialise pressures assuming isotropic distribution
-            @. moments.charged.ppar = 0.5 * moments.charged.dens * moments.charged.vth^2
-            @. moments.charged.pperp = moments.charged.ppar
+            @. moments.ion.ppar = 0.5 * moments.ion.dens * moments.ion.vth^2
+            @. moments.ion.pperp = moments.ion.ppar
+            if moments.evolve_density || moments.evolve_upar || moments.evolve_ppar
+                @. moments.ion.constraints_A_coefficient = 1.0
+                @. moments.ion.constraints_B_coefficient = 0.0
+                @. moments.ion.constraints_C_coefficient = 0.0
+            end
             if n_neutral_species > 0
-                #neutral particles
+                # initialise the neutral density profile
                 init_density!(moments.neutral.dens, z, r, species.neutral, n_neutral_species)
+                # initialise the z-component of the neutral flow
                 init_uz!(moments.neutral.uz, z, r, species.neutral, n_neutral_species)
+                # initialise the r-component of the neutral flow
                 init_ur!(moments.neutral.ur, z, r, species.neutral, n_neutral_species)
+                # initialise the zeta-component of the neutral flow
                 init_uzeta!(moments.neutral.uzeta, z, r, species.neutral, n_neutral_species)
+                # initialise the neutral thermal speed
                 init_vth!(moments.neutral.vth, z, r, species.neutral, n_neutral_species)
+                # calculate the z-component of the neutral pressure
                 @. moments.neutral.pz = 0.5 * moments.neutral.dens * moments.neutral.vth^2
+                # calculate the total neutral pressure
                 @. moments.neutral.ptot = 1.5 * moments.neutral.dens * moments.neutral.vth^2
+                if moments.evolve_density || moments.evolve_upar || moments.evolve_ppar
+                    @. moments.neutral.constraints_A_coefficient = 1.0
+                    @. moments.neutral.constraints_B_coefficient = 0.0
+                    @. moments.neutral.constraints_C_coefficient = 0.0
+                end
             end
         end
-        moments.charged.dens_updated .= true
-        moments.charged.upar_updated .= true
-        moments.charged.ppar_updated .= true
+        # reflect the fact that the ion moments have now been updated
+        moments.ion.dens_updated .= true
+        moments.ion.upar_updated .= true
+        moments.ion.ppar_updated .= true
+        # account for the fact that the neutral moments have now been updated
         moments.neutral.dens_updated .= true
         moments.neutral.uz_updated .= true
         moments.neutral.pz_updated .= true
-        # create and initialise the normalised particle distribution function (pdf)
+        # create and initialise the normalised, ion particle distribution function (pdf)
         # such that ∫dwpa pdf.norm = 1, ∫dwpa wpa * pdf.norm = 0, and ∫dwpa wpa^2 * pdf.norm = 1/2
         # note that wpa = vpa - upar, unless moments.evolve_ppar = true, in which case wpa = (vpa - upar)/vth
         # the definition of pdf.norm changes accordingly from pdf_unnorm / density to pdf_unnorm * vth / density
@@ -191,9 +164,9 @@ function init_pdf_and_moments!(pdf, moments, boundary_distributions, geometry,
                         vpa, vzeta, vr, vz, vpa_spectral, vz_spectral, species)
         begin_s_r_z_region()
         # calculate the initial parallel heat flux from the initial un-normalised pdf
-        update_qpar!(moments.charged.qpar, moments.charged.qpar_updated,
-                     moments.charged.dens, moments.charged.upar, moments.charged.vth,
-                     pdf.charged.norm, vpa, vperp, z, r, composition,
+        update_qpar!(moments.ion.qpar, moments.ion.qpar_updated,
+                     moments.ion.dens, moments.ion.upar, moments.ion.vth,
+                     pdf.ion.norm, vpa, vperp, z, r, composition,
                      moments.evolve_density, moments.evolve_upar, moments.evolve_ppar)
 
         initialize_external_source_amplitude!(moments, external_source_settings, vperp,
@@ -222,7 +195,7 @@ function init_pdf_and_moments!(pdf, moments, boundary_distributions, geometry,
     # collision operator will not be calculated before the initial values are written to
     # file.
     @serial_region begin
-        moments.charged.dSdt .= 0.0
+        moments.ion.dSdt .= 0.0
     end
 
     init_boundary_distributions!(boundary_distributions, pdf, vz, vr, vzeta, vpa, vperp,
@@ -242,30 +215,30 @@ function initialize_pdf!(pdf, moments, boundary_distributions, composition, r, z
         for is ∈ 1:composition.n_ion_species, ir ∈ 1:r.n
             # Add ion contributions to wall flux here. Neutral contributions will be
             # added in init_neutral_pdf_over_density!()
-            if species.charged[is].z_IC.initialization_option == "bgk" || species.charged[is].vpa_IC.initialization_option == "bgk"
-                @views init_bgk_pdf!(pdf.charged.norm[:,1,:,ir,is], 0.0, species.charged[is].initial_temperature, z.grid, z.L, vpa.grid)
+            if species.ion[is].z_IC.initialization_option == "bgk" || species.ion[is].vpa_IC.initialization_option == "bgk"
+                @views init_bgk_pdf!(pdf.ion.norm[:,1,:,ir,is], 0.0, species.ion[is].initial_temperature, z.grid, z.L, vpa.grid)
             else
                 # updates pdf_norm to contain pdf / density, so that ∫dvpa pdf.norm = 1,
                 # ∫dwpa wpa * pdf.norm = 0, and ∫dwpa m_s (wpa/vths)^2 pdf.norm = 1/2
                 # to machine precision
-                @views init_charged_pdf_over_density!(
-                    pdf.charged.norm[:,:,:,ir,is], species.charged[is], composition, vpa, vperp,
-                    z, vpa_spectral, moments.charged.dens[:,ir,is],
-                    moments.charged.upar[:,ir,is], moments.charged.ppar[:,ir,is],
-                    moments.charged.vth[:,ir,is],
-                    moments.charged.v_norm_fac[:,ir,is], moments.evolve_density,
+                @views init_ion_pdf_over_density!(
+                    pdf.ion.norm[:,:,:,ir,is], species.ion[is], composition, vpa, vperp,
+                    z, vpa_spectral, moments.ion.dens[:,ir,is],
+                    moments.ion.upar[:,ir,is], moments.ion.ppar[:,ir,is],
+                    moments.ion.vth[:,ir,is],
+                    moments.ion.v_norm_fac[:,ir,is], moments.evolve_density,
                     moments.evolve_upar, moments.evolve_ppar)
             end
-            @views wall_flux_0[ir,is] = -(moments.charged.dens[1,ir,is] *
-                                          moments.charged.upar[1,ir,is])
-            @views wall_flux_L[ir,is] = moments.charged.dens[end,ir,is] *
-                                        moments.charged.upar[end,ir,is]
+            @views wall_flux_0[ir,is] = -(moments.ion.dens[1,ir,is] *
+                                          moments.ion.upar[1,ir,is])
+            @views wall_flux_L[ir,is] = moments.ion.dens[end,ir,is] *
+                                        moments.ion.upar[end,ir,is]
 
             @loop_z iz begin
                 if moments.evolve_ppar
-                    @. pdf.charged.norm[:,:,iz,ir,is] *= moments.charged.vth[iz,ir,is]
+                    @. pdf.ion.norm[:,:,iz,ir,is] *= moments.ion.vth[iz,ir,is]
                 elseif moments.evolve_density == false
-                    @. pdf.charged.norm[:,:,iz,ir,is] *= moments.charged.dens[iz,ir,is]
+                    @. pdf.ion.norm[:,:,iz,ir,is] *= moments.ion.dens[iz,ir,is]
                 end
             end
         end
@@ -529,7 +502,7 @@ end
 
 """
 """
-function init_charged_pdf_over_density!(pdf, spec, composition, vpa, vperp, z,
+function init_ion_pdf_over_density!(pdf, spec, composition, vpa, vperp, z,
         vpa_spectral, density, upar, ppar, vth, v_norm_fac, evolve_density, evolve_upar,
         evolve_ppar)
 
@@ -563,7 +536,7 @@ function init_charged_pdf_over_density!(pdf, spec, composition, vpa, vperp, z,
             end
 
             # Only do this correction for runs without wall bc, because consistency of
-            # pdf and moments is taken care of by convert_full_f_charged_to_normalised!()
+            # pdf and moments is taken care of by convert_full_f_ion_to_normalised!()
             # for wall bc cases.
             for iz ∈ 1:z.n
                 # densfac = the integral of the pdf over v-space, which should be unity,
@@ -623,7 +596,7 @@ function init_charged_pdf_over_density!(pdf, spec, composition, vpa, vperp, z,
                     @. pdf[:,ivperp,iz] *= 1.0 - exp(-vpa.grid^2*inverse_width)
                 end
             end
-            # Can use non-shared memory here because `init_charged_pdf_over_density!()` is
+            # Can use non-shared memory here because `init_ion_pdf_over_density!()` is
             # called inside a `@serial_region`
             lower_z_pdf_buffer = allocate_float(vpa.n, vperp.n)
             upper_z_pdf_buffer = allocate_float(vpa.n, vperp.n)
@@ -665,7 +638,7 @@ function init_charged_pdf_over_density!(pdf, spec, composition, vpa, vperp, z,
 
             # Get the unnormalised pdf and the moments of the constructed full-f
             # distribution function (which will be modified from the input moments).
-            convert_full_f_charged_to_normalised!(pdf, density, upar, ppar, vth, vperp,
+            convert_full_f_ion_to_normalised!(pdf, density, upar, ppar, vth, vperp,
                                                   vpa, vpa_spectral, evolve_density,
                                                   evolve_upar, evolve_ppar)
 
@@ -829,7 +802,7 @@ function init_neutral_pdf_over_density!(pdf, boundary_distributions, spec, compo
                     @. pdf[:,ivr,ivzeta,iz] *= 1.0 - exp(-vz.grid^2*inverse_width)
                 end
             end
-            # Can use non-shared memory here because `init_charged_pdf_over_density!()` is
+            # Can use non-shared memory here because `init_ion_pdf_over_density!()` is
             # called inside a `@serial_region`
             lower_z_pdf_buffer = allocate_float(vz.n, vr.n, vzeta.n)
             upper_z_pdf_buffer = allocate_float(vz.n, vr.n, vzeta.n)
@@ -954,31 +927,30 @@ function init_pdf_moments_manufactured_solns!(pdf, moments, vz, vr, vzeta, vpa,
     #nb manufactured functions not functions of species
     begin_s_r_z_region()
     @loop_s_r_z is ir iz begin
-        moments.charged.dens[iz,ir,is] = densi_func(z.grid[iz],r.grid[ir],0.0)
+        moments.ion.dens[iz,ir,is] = densi_func(z.grid[iz],r.grid[ir],0.0)
         @loop_vperp_vpa ivperp ivpa begin
-            pdf.charged.norm[ivpa,ivperp,iz,ir,is] = dfni_func(vpa.grid[ivpa],vperp.grid[ivperp],z.grid[iz],r.grid[ir],0.0)
+            pdf.ion.norm[ivpa,ivperp,iz,ir,is] = dfni_func(vpa.grid[ivpa],vperp.grid[ivperp],z.grid[iz],r.grid[ir],0.0)
         end
     end
     # update upar, ppar, qpar, vth consistent with manufactured solns
-    reset_moments_status!(moments)
-    update_density!(moments.charged.dens, moments.charged.dens_updated,
-                    pdf.charged.norm, vpa, vperp, z, r, composition)
+    update_density!(moments.ion.dens, moments.ion.dens_updated,
+                    pdf.ion.norm, vpa, vperp, z, r, composition)
     # get particle flux
-    update_upar!(moments.charged.upar, moments.charged.upar_updated,
-                 moments.charged.dens, moments.charged.ppar, pdf.charged.norm,
+    update_upar!(moments.ion.upar, moments.ion.upar_updated,
+                 moments.ion.dens, moments.ion.ppar, pdf.ion.norm,
                  vpa, vperp, z, r, composition, moments.evolve_density,
                  moments.evolve_ppar)
-    update_ppar!(moments.charged.ppar, moments.charged.ppar_updated,
-                 moments.charged.dens, moments.charged.upar, pdf.charged.norm,
+    update_ppar!(moments.ion.ppar, moments.ion.ppar_updated,
+                 moments.ion.dens, moments.ion.upar, pdf.ion.norm,
                  vpa, vperp, z, r, composition, moments.evolve_density,
                  moments.evolve_upar)
-    update_pperp!(moments.charged.pperp, pdf.charged.norm, vpa, vperp, z, r, composition)
-    update_qpar!(moments.charged.qpar, moments.charged.qpar_updated,
-                 moments.charged.dens, moments.charged.upar,
-                 moments.charged.vth, pdf.charged.norm, vpa, vperp, z, r,
+    update_pperp!(moments.ion.pperp, pdf.ion.norm, vpa, vperp, z, r, composition)
+    update_qpar!(moments.ion.qpar, moments.ion.qpar_updated,
+                 moments.ion.dens, moments.ion.upar,
+                 moments.ion.vth, pdf.ion.norm, vpa, vperp, z, r,
                  composition, moments.evolve_density, moments.evolve_upar,
                  moments.evolve_ppar)
-    update_vth!(moments.charged.vth, moments.charged.ppar, moments.charged.pperp, moments.charged.dens, vperp, z, r, composition)
+    update_vth!(moments.ion.vth, moments.ion.ppar, moments.ion.pperp, moments.ion.dens, vperp, z, r, composition)
 
     if n_neutral_species > 0
         begin_sn_r_z_region()
@@ -1036,7 +1008,7 @@ function init_pdf_moments_manufactured_solns!(pdf, moments, vz, vr, vzeta, vpa,
         begin_sn_r_z_region()
         @loop_sn_r_z isn ir iz begin
             # get vth for neutrals
-            moments.charged.vth[iz,ir,isn] = sqrt(2.0*moments.neutral.ptot[iz,ir,isn]/moments.neutral.dens[iz,ir,isn])
+            moments.neutral.vth[iz,ir,isn] = sqrt(2.0*moments.neutral.ptot[iz,ir,isn]/moments.neutral.dens[iz,ir,isn])
         end
     end
     return nothing
@@ -1106,7 +1078,7 @@ function init_knudsen_cosine!(knudsen_cosine, vz, vr, vzeta, vpa, vperp, composi
     return knudsen_cosine
 end
 
-function init_rboundary_pdfs!(rboundary_charged, rboundary_neutral, pdf::pdf_struct, vz,
+function init_rboundary_pdfs!(rboundary_ion, rboundary_neutral, pdf::pdf_struct, vz,
                               vr, vzeta, vpa, vperp, z, r, composition)
     n_ion_species = composition.n_ion_species
     n_neutral_species = composition.n_neutral_species
@@ -1114,8 +1086,8 @@ function init_rboundary_pdfs!(rboundary_charged, rboundary_neutral, pdf::pdf_str
 
     begin_s_z_region() #do not parallelise r here
     @loop_s_z_vperp_vpa is iz ivperp ivpa begin
-        rboundary_charged[ivpa,ivperp,iz,1,is] = pdf.charged.norm[ivpa,ivperp,iz,1,is]
-        rboundary_charged[ivpa,ivperp,iz,end,is] = pdf.charged.norm[ivpa,ivperp,iz,end,is]
+        rboundary_ion[ivpa,ivperp,iz,1,is] = pdf.ion.norm[ivpa,ivperp,iz,1,is]
+        rboundary_ion[ivpa,ivperp,iz,end,is] = pdf.ion.norm[ivpa,ivperp,iz,end,is]
     end
     if n_neutral_species > 0
         begin_sn_z_region() #do not parallelise r here
@@ -1124,7 +1096,7 @@ function init_rboundary_pdfs!(rboundary_charged, rboundary_neutral, pdf::pdf_str
             rboundary_neutral[ivz,ivr,ivzeta,iz,end,isn] = pdf.neutral.norm[ivz,ivr,ivzeta,iz,end,isn]
         end
     end
-    return rboundary_charged, rboundary_neutral
+    return rboundary_ion, rboundary_neutral
 end
 
 """
@@ -1141,914 +1113,24 @@ function create_boundary_distributions(vz, vr, vzeta, vpa, vperp, z, composition
     #depends on T_wall, which has already been set
     init_knudsen_cosine!(knudsen_cosine, vz, vr, vzeta, vpa, vperp, composition, zero)
     #initialise fixed-in-time radial boundary condition based on initial condition values
-    pdf_rboundary_charged = allocate_shared_float(vpa.n, vperp.n, z.n, 2,
+    pdf_rboundary_ion = allocate_shared_float(vpa.n, vperp.n, z.n, 2,
                                                   composition.n_ion_species)
     pdf_rboundary_neutral =  allocate_shared_float(vz.n, vr.n, vzeta.n, z.n, 2,
                                                    composition.n_neutral_species)
 
-    return boundary_distributions_struct(knudsen_cosine, pdf_rboundary_charged, pdf_rboundary_neutral)
+    return boundary_distributions_struct(knudsen_cosine, pdf_rboundary_ion, pdf_rboundary_neutral)
 end
 
 function init_boundary_distributions!(boundary_distributions, pdf, vz, vr, vzeta, vpa, vperp, z, r, composition)
     #initialise fixed-in-time radial boundary condition based on initial condition values
-    init_rboundary_pdfs!(boundary_distributions.pdf_rboundary_charged,
+    init_rboundary_pdfs!(boundary_distributions.pdf_rboundary_ion,
                          boundary_distributions.pdf_rboundary_neutral, pdf, vz, vr, vzeta,
                          vpa, vperp, z, r, composition)
     return nothing
 end
-"""
-enforce boundary conditions in vpa and z on the evolved pdf;
-also enforce boundary conditions in z on all separately evolved velocity space moments of the pdf
-"""
-function enforce_boundary_conditions!(f, f_r_bc, density, upar, ppar, moments, vpa_bc,
-        z_bc, r_bc, vpa, vperp, z, r, vpa_spectral, vperp_spectral, vpa_adv, vperp_adv, z_adv, r_adv, composition, scratch_dummy,
-        r_diffusion, vpa_diffusion, vperp_diffusion)
-    if vpa.n > 1
-        begin_s_r_z_vperp_region()
-        @loop_s_r_z_vperp is ir iz ivperp begin
-            # enforce the vpa BC
-            # use that adv.speed independent of vpa 
-            @views enforce_v_boundary_condition_local!(f[:,ivperp,iz,ir,is], vpa_bc,
-                             vpa_adv[is].speed[:,ivperp,iz,ir], vpa_diffusion,
-                             vpa, vpa_spectral)
-        end
-    end
-    if vperp.n > 1
-        begin_s_r_z_vpa_region()
-        @views enforce_vperp_boundary_condition!(f, vperp.bc, vperp, vperp_spectral,
-                             vperp_adv, vperp_diffusion)
-    end
-    if z.n > 1
-        begin_s_r_vperp_vpa_region()
-        # enforce the z BC on the evolved velocity space moments of the pdf
-        @views enforce_z_boundary_condition_moments!(density, moments, z_bc)
-        @views enforce_z_boundary_condition!(f, density, upar, ppar, moments, z_bc, z_adv, z,
-                                             vperp, vpa, composition,
-                                             scratch_dummy.buffer_vpavperprs_1, scratch_dummy.buffer_vpavperprs_2,
-                                             scratch_dummy.buffer_vpavperprs_3, scratch_dummy.buffer_vpavperprs_4)
-                                              
-    end
-    if r.n > 1
-        begin_s_z_vperp_vpa_region()
-        @views enforce_r_boundary_condition!(f, f_r_bc, r_bc, r_adv, vpa, vperp, z, r, composition,
-            scratch_dummy.buffer_vpavperpzs_1, scratch_dummy.buffer_vpavperpzs_2,
-            scratch_dummy.buffer_vpavperpzs_3, scratch_dummy.buffer_vpavperpzs_4,
-            r_diffusion)
-    end
-end
-function enforce_boundary_conditions!(fvec_out::scratch_pdf, moments, f_r_bc, vpa_bc,
-        z_bc, r_bc, vpa, vperp, z, r, vpa_spectral, vperp_spectral, vpa_adv, vperp_adv, z_adv, r_adv, composition, scratch_dummy,
-        r_diffusion, vpa_diffusion, vperp_diffusion)
-    enforce_boundary_conditions!(fvec_out.pdf, f_r_bc, fvec_out.density, fvec_out.upar,
-        fvec_out.ppar, moments, vpa_bc, z_bc, r_bc, vpa, vperp, z, r, 
-        vpa_spectral, vperp_spectral, vpa_adv, vperp_adv, z_adv,
-        r_adv, composition, scratch_dummy, r_diffusion, vpa_diffusion, vperp_diffusion)
-end
-
-"""
-enforce boundary conditions on f in r
-"""
-function enforce_r_boundary_condition!(f::AbstractArray{mk_float,5}, f_r_bc, bc::String,
-        adv, vpa, vperp, z, r, composition, end1::AbstractArray{mk_float,4},
-        end2::AbstractArray{mk_float,4}, buffer1::AbstractArray{mk_float,4},
-        buffer2::AbstractArray{mk_float,4}, r_diffusion::Bool)
-
-    nr = r.n
-
-    if r.nelement_global > r.nelement_local
-        # reconcile internal element boundaries across processes
-        # & enforce periodicity and external boundaries if needed
-        @loop_s_z_vperp_vpa is iz ivperp ivpa begin
-            end1[ivpa,ivperp,iz,is] = f[ivpa,ivperp,iz,1,is]
-            end2[ivpa,ivperp,iz,is] = f[ivpa,ivperp,iz,nr,is]
-        end
-        @views reconcile_element_boundaries_MPI!(f,
-            end1, end2,	buffer1, buffer2, r)
-    end
-
-    # 'periodic' BC enforces periodicity by taking the average of the boundary points
-    # enforce the condition if r is local
-    if bc == "periodic" && r.nelement_global == r.nelement_local
-        @loop_s_z_vperp_vpa is iz ivperp ivpa begin
-            f[ivpa,ivperp,iz,1,is] = 0.5*(f[ivpa,ivperp,iz,nr,is]+f[ivpa,ivperp,iz,1,is])
-            f[ivpa,ivperp,iz,nr,is] = f[ivpa,ivperp,iz,1,is]
-        end
-    end
-    if bc == "Dirichlet"
-        zero = 1.0e-10
-        # use the old distribution to force the new distribution to have
-        # consistant-in-time values at the boundary
-        # with bc = "Dirichlet" and r_diffusion = false
-        # impose bc for incoming parts of velocity space only (Hyperbolic PDE)
-        # with bc = "Dirichlet" and r_diffusion = true
-        # impose bc on both sides of the domain to accomodate a diffusion operator d^2 / d r^2
-        @loop_s_z_vperp_vpa is iz ivperp ivpa begin
-            ir = 1 # r = -L/2 -- check that the point is on lowest rank
-            if r.irank == 0 && (r_diffusion || adv[is].speed[ir,ivpa,ivperp,iz] > zero)
-                f[ivpa,ivperp,iz,ir,is] = f_r_bc[ivpa,ivperp,iz,1,is]
-            end
-            ir = r.n # r = L/2 -- check that the point is on highest rank
-            if r.irank == r.nrank - 1 && (r_diffusion || adv[is].speed[ir,ivpa,ivperp,iz] < -zero)
-                f[ivpa,ivperp,iz,ir,is] = f_r_bc[ivpa,ivperp,iz,end,is]
-            end
-        end
-    end
-end
-
-"""
-enforce boundary conditions on charged particle f in z
-"""
-function enforce_z_boundary_condition!(pdf, density, upar, ppar, moments, bc::String, adv,
-                                       z, vperp, vpa, composition, end1::AbstractArray{mk_float,4},
-                                       end2::AbstractArray{mk_float,4}, buffer1::AbstractArray{mk_float,4},
-                                       buffer2::AbstractArray{mk_float,4})
-    # this block ensures periodic BC can be supported with distributed memory MPI
-    if z.nelement_global > z.nelement_local
-        # reconcile internal element boundaries across processes
-        # & enforce periodicity and external boundaries if needed
-        nz = z.n
-        @loop_s_r_vperp_vpa is ir ivperp ivpa begin
-            end1[ivpa,ivperp,ir,is] = pdf[ivpa,ivperp,1,ir,is]
-            end2[ivpa,ivperp,ir,is] = pdf[ivpa,ivperp,nz,ir,is]
-        end
-        # check on periodic bc happens inside this call below
-        @views reconcile_element_boundaries_MPI!(pdf,
-            end1, end2,	buffer1, buffer2, z)
-    end
-    # define a zero that accounts for finite precision
-    zero = 1.0e-14
-    # 'constant' BC is time-independent f at upwind boundary
-    # and constant f beyond boundary 
-    if bc == "constant"
-        begin_s_r_vperp_vpa_region()
-        density_offset = 1.0
-        vwidth = 1.0
-        if z.irank == 0
-            @loop_s_r_vperp_vpa is ir ivperp ivpa begin
-                if adv[is].speed[ivpa,1,ir] > 0.0
-                    pdf[ivpa,ivperp,1,ir,is] = density_offset * exp(-(vpa.grid[ivpa]^2 + vperp.grid[ivperp]^2)/vwidth^2) / sqrt(pi)
-                end
-            end
-        end
-        if z.irank == z.nrank - 1
-            @loop_s_r_vperp_vpa is ir ivperp ivpa begin
-                if adv[is].speed[ivpa,end,ir] > 0.0
-                    pdf[ivpa,ivperp,end,ir,is] = density_offset * exp(-(vpa.grid[ivpa]^2 + vperp.grid[ivperp]^2)/vwidth^2) / sqrt(pi)
-                end
-            end
-        end
-    # 'periodic' BC enforces periodicity by taking the average of the boundary points
-    elseif bc == "periodic" && z.nelement_global == z.nelement_local
-        begin_s_r_vperp_vpa_region()
-        @loop_s_r_vperp_vpa is ir ivperp ivpa begin
-            pdf[ivpa,ivperp,1,ir,is] = 0.5*(pdf[ivpa,ivperp,z.n,ir,is]+pdf[ivpa,ivperp,1,ir,is])
-            pdf[ivpa,ivperp,z.n,ir,is] = pdf[ivpa,ivperp,1,ir,is]
-        end
-    # 'wall' BC enforces wall boundary conditions
-    elseif bc == "wall"
-        # Need integrals over vpa at wall boundaries in z, so cannot parallelize over z
-        # or vpa.
-        begin_s_r_region()
-        @loop_s is begin
-            # zero incoming BC for ions, as they recombine at the wall
-            if moments.evolve_upar
-                @loop_r ir begin
-                    @views enforce_zero_incoming_bc!(
-                        pdf[:,:,:,ir,is], z, vpa, density[:,ir,is], upar[:,ir,is],
-                        ppar[:,ir,is], moments.evolve_upar, moments.evolve_ppar, zero)
-                end
-            else
-                @loop_r ir begin
-                    @views enforce_zero_incoming_bc!(pdf[:,:,:,ir,is],
-                                                     adv[is].speed[:,:,:,ir], z, zero)
-                end
-            end
-        end
-    end
-end
-
-"""
-enforce boundary conditions on neutral particle distribution function
-"""
-function enforce_neutral_boundary_conditions!(f_neutral, f_charged,
-        boundary_distributions, density_neutral, uz_neutral, pz_neutral, moments,
-        density_ion, upar_ion, Er, vzeta_spectral, vr_spectral, vz_spectral, r_adv, z_adv,
-        vzeta_adv, vr_adv, vz_adv, r, z, vzeta, vr, vz, composition, geometry,
-        scratch_dummy, r_diffusion, vz_diffusion)
-
-    # without acceleration of neutrals bc on vz vr vzeta should not be required as no
-    # advection or diffusion in these coordinates
-
-    if vzeta_adv !== nothing && vzeta.n_global > 1 && vzeta.bc != "none"
-        begin_sn_r_z_vr_vz_region()
-        @loop_sn_r_z_vr_vz isn ir iz ivr ivz begin
-            # enforce the vz BC
-            @views enforce_v_boundary_condition_local!(f_neutral[ivz,ivr,:,iz,ir,isn],
-                                                       vzeta.bc,
-                                                       vzeta_adv[isn].speed[ivz,ivr,:,iz,ir],
-                                                       false, vzeta, vzeta_spectral)
-        end
-    end
-    if vr_adv !== nothing && vr.n_global > 1 && vr.bc != "none"
-        begin_sn_r_z_vzeta_vz_region()
-        @loop_sn_r_z_vzeta_vz isn ir iz ivzeta ivz begin
-            # enforce the vz BC
-            @views enforce_v_boundary_condition_local!(f_neutral[ivz,:,ivzeta,iz,ir,isn],
-                                                       vr.bc,
-                                                       vr_adv[isn].speed[ivz,:,ivzeta,iz,ir],
-                                                       false, vr, vr_spectral)
-        end
-    end
-    if vz_adv !== nothing && vz.n_global > 1 && vz.bc != "none"
-        begin_sn_r_z_vzeta_vr_region()
-        @loop_sn_r_z_vzeta_vr isn ir iz ivzeta ivr begin
-            # enforce the vz BC
-            @views enforce_v_boundary_condition_local!(f_neutral[:,ivr,ivzeta,iz,ir,isn],
-                                                       vz.bc,
-                                                       vz_adv[isn].speed[:,ivr,ivzeta,iz,ir],
-                                                       vz_diffusion, vz, vz_spectral)
-        end
-    end
-    # f_initial contains the initial condition for enforcing a fixed-boundary-value condition
-    if z.n > 1
-        begin_sn_r_vzeta_vr_vz_region()
-        @views enforce_neutral_z_boundary_condition!(f_neutral, density_neutral, uz_neutral,
-            pz_neutral, moments, density_ion, upar_ion, Er, boundary_distributions,
-            z_adv, z, vzeta, vr, vz, composition, geometry, 
-            scratch_dummy.buffer_vzvrvzetarsn_1, scratch_dummy.buffer_vzvrvzetarsn_2,
-            scratch_dummy.buffer_vzvrvzetarsn_3, scratch_dummy.buffer_vzvrvzetarsn_4)
-    end
-    if r.n > 1
-        begin_sn_z_vzeta_vr_vz_region()
-        @views enforce_neutral_r_boundary_condition!(f_neutral, boundary_distributions.pdf_rboundary_neutral,
-                                    r_adv, vz, vr, vzeta, z, r, composition,
-                                    scratch_dummy.buffer_vzvrvzetazsn_1, scratch_dummy.buffer_vzvrvzetazsn_2,
-                                    scratch_dummy.buffer_vzvrvzetazsn_3, scratch_dummy.buffer_vzvrvzetazsn_4,
-                                    r_diffusion)
-    end
-end
-
-function enforce_neutral_r_boundary_condition!(f::AbstractArray{mk_float,6},
-        f_r_bc::AbstractArray{mk_float,6}, adv, vz, vr, vzeta, z, r, composition,
-        end1::AbstractArray{mk_float,5}, end2::AbstractArray{mk_float,5},
-        buffer1::AbstractArray{mk_float,5}, buffer2::AbstractArray{mk_float,5},
-        r_diffusion) #f_initial,
-
-    bc = r.bc
-    nr = r.n
-
-    if r.nelement_global > r.nelement_local
-        # reconcile internal element boundaries across processes
-        # & enforce periodicity and external boundaries if needed
-        @loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
-            end1[ivz,ivr,ivzeta,iz,isn] = f[ivz,ivr,ivzeta,iz,1,isn]
-            end2[ivz,ivr,ivzeta,iz,isn] = f[ivz,ivr,ivzeta,iz,nr,isn]
-        end
-        @views reconcile_element_boundaries_MPI!(f,
-            end1, end2,	buffer1, buffer2, r)
-    end
-    # 'periodic' BC enforces periodicity by taking the average of the boundary points
-    # local case only when no communication required
-    if bc == "periodic" && r.nelement_global == r.nelement_local
-        @loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
-            f[ivz,ivr,ivzeta,iz,1,isn] = 0.5*(f[ivz,ivr,ivzeta,iz,1,isn]+f[ivz,ivr,ivzeta,iz,nr,isn])
-            f[ivz,ivr,ivzeta,iz,nr,isn] = f[ivz,ivr,ivzeta,iz,1,isn]
-        end
-    end
-    # Dirichlet boundary condition for external endpoints
-    if bc == "Dirichlet"
-        zero = 1.0e-10
-        # use the old distribution to force the new distribution to have
-        # consistant-in-time values at the boundary
-        # impose bc for incoming parts of velocity space only (Hyperbolic PDE)
-        @loop_sn_z_vzeta_vr_vz isn iz ivzeta ivr ivz begin
-            ir = 1 # r = -L/2
-            # incoming particles and on lowest rank
-            if r.irank == 0 && (r_diffusion || adv[isn].speed[ir,ivz,ivr,ivzeta,iz] > zero)
-                f[ivz,ivr,ivzeta,iz,ir,isn] = f_r_bc[ivz,ivr,ivzeta,iz,1,isn]
-            end
-            ir = nr # r = L/2
-            # incoming particles and on highest rank
-            if r.irank == r.nrank - 1 && (r_diffusion || adv[isn].speed[ir,ivz,ivr,ivzeta,iz] < -zero)
-                f[ivz,ivr,ivzeta,iz,ir,isn] = f_r_bc[ivz,ivr,ivzeta,iz,end,isn]
-            end
-        end
-    end
-end
-
-"""
-enforce boundary conditions on neutral particle f in z
-"""
-function enforce_neutral_z_boundary_condition!(pdf, density, uz, pz, moments, density_ion,
-                                               upar_ion, Er, boundary_distributions, adv,
-                                               z, vzeta, vr, vz, composition, geometry,
-                                               end1::AbstractArray{mk_float,5}, end2::AbstractArray{mk_float,5},
-                                               buffer1::AbstractArray{mk_float,5}, buffer2::AbstractArray{mk_float,5})
-    
-
-    if z.nelement_global > z.nelement_local
-        # reconcile internal element boundaries across processes
-        # & enforce periodicity and external boundaries if needed
-        nz = z.n
-        @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
-            end1[ivz,ivr,ivzeta,ir,isn] = pdf[ivz,ivr,ivzeta,1,ir,isn]
-            end2[ivz,ivr,ivzeta,ir,isn] = pdf[ivz,ivr,ivzeta,nz,ir,isn]
-        end
-        # check on periodic bc occurs within this call below
-        @views reconcile_element_boundaries_MPI!(pdf,
-            end1, end2,	buffer1, buffer2, z)
-    end
-
-    zero = 1.0e-14
-    # 'constant' BC is time-independent f at upwind boundary
-    # and constant f beyond boundary
-    if z.bc == "constant"
-        begin_sn_r_vzeta_vr_vz_region()
-        density_offset = 1.0
-        vwidth = 1.0
-        if z.irank == 0
-            @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
-                if adv[isn].speed[ivz,ivr,ivzeta,1,ir] > 0.0
-                    pdf[ivz,ivr,ivzeta,1,ir,is] = density_offset *
-                        exp(-(vzeta.grid[ivzeta]^2 + vr.grid[ivr] + vz.grid[ivz])/vwidth^2) /
-                        sqrt(pi)
-                end
-            end
-        end
-        if z.irank == z.nrank - 1
-            @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
-                if adv[isn].speed[ivz,ivr,ivzeta,end,ir] > 0.0
-                    pdf[ivz,ivr,ivzeta,end,ir,is] = density_offset *
-                        exp(-(vzeta.grid[ivzeta]^2 + vr.grid[ivr] + vz.grid[ivz])/vwidth^2) /
-                        sqrt(pi)
-                end
-            end
-        end
-    # 'periodic' BC enforces periodicity by taking the average of the boundary points
-    elseif z.bc == "periodic" && z.nelement_global == z.nelement_local
-        begin_sn_r_vzeta_vr_vz_region()
-        @loop_sn_r_vzeta_vr_vz isn ir ivzeta ivr ivz begin
-            pdf[ivz,ivr,ivzeta,1,ir,isn] = 0.5*(pdf[ivz,ivr,ivzeta,1,ir,isn] +
-                                                pdf[ivz,ivr,ivzeta,end,ir,isn])
-            pdf[ivz,ivr,ivzeta,end,ir,isn] = pdf[ivz,ivr,ivzeta,1,ir,isn]
-        end
-    # 'wall' BC enforces wall boundary conditions
-    elseif z.bc == "wall"
-        # Need integrals over vpa at wall boundaries in z, so cannot parallelize over z
-        # or vpa.
-        begin_sn_r_region()
-        @loop_sn isn begin
-            # BC for neutrals
-            @loop_r ir begin
-                # define vtfac to avoid repeated computation below
-                vtfac = sqrt(composition.T_wall * composition.mn_over_mi)
-                # Assume for now that the ion species index corresponding to this neutral
-                # species is the same as the neutral species index.
-                # Note, have already calculated moments of ion distribution function(s),
-                # so can use the moments here to get the flux
-                if z.irank == 0
-                    ion_flux_0 = -density_ion[1,ir,isn] * (upar_ion[1,ir,isn]*geometry.bzed[1,ir] - 0.5*geometry.rhostar*Er[1,ir])
-                else
-                    ion_flux_0 = NaN
-                end
-                if z.irank == z.nrank - 1
-                    ion_flux_L = density_ion[end,ir,isn] * (upar_ion[end,ir,isn]*geometry.bzed[end,ir] - 0.5*geometry.rhostar*Er[end,ir])
-                else
-                    ion_flux_L = NaN
-                end
-                # enforce boundary condition on the neutral pdf that all ions and neutrals
-                # that leave the domain re-enter as neutrals
-                @views enforce_neutral_wall_bc!(
-                    pdf[:,:,:,:,ir,isn], z, vzeta, vr, vz, pz[:,ir,isn], uz[:,ir,isn],
-                    density[:,ir,isn], ion_flux_0, ion_flux_L, boundary_distributions,
-                    vtfac, composition.recycling_fraction, moments.evolve_ppar,
-                    moments.evolve_upar, moments.evolve_density, zero)
-            end
-        end
-    end
-end
 
 """
-enforce a zero incoming BC in z for given species pdf at each radial location
-"""
-function enforce_zero_incoming_bc!(pdf, speed, z, zero)
-    nvpa = size(pdf,1)
-    # no parallel BC should be enforced for dz/dt = 0
-    # note that the parallel velocity coordinate vpa may be dz/dt or
-    # some version of the peculiar velocity (dz/dt - upar),
-    # so use advection speed below instead of vpa
-    if z.irank == 0
-        @loop_vperp_vpa ivperp ivpa begin
-            # for left boundary in zed (z = -Lz/2), want
-            # f(z=-Lz/2, v_parallel > 0) = 0
-            if speed[1,ivpa,ivperp] > zero
-                pdf[ivpa,ivperp,1] = 0.0
-            end
-        end
-    end
-    if z.irank == z.nrank - 1
-        @loop_vperp_vpa ivperp ivpa begin
-            # for right boundary in zed (z = Lz/2), want
-            # f(z=Lz/2, v_parallel < 0) = 0
-            if speed[end,ivpa,ivperp] < -zero
-                pdf[ivpa,ivperp,end] = 0.0
-            end
-        end
-    end
-end
-function enforce_zero_incoming_bc!(pdf, z::coordinate, vpa::coordinate, density, upar,
-                                   ppar, evolve_upar, evolve_ppar, zero)
-    if z.irank != 0 && z.irank != z.nrank - 1
-        # No z-boundary in this block
-        return nothing
-    end
-    nvpa, nvperp, nz = size(pdf)
-    # no parallel BC should be enforced for dz/dt = 0
-    # note that the parallel velocity coordinate vpa may be dz/dt or
-    # some version of the peculiar velocity (dz/dt - upar),
-    # so use advection speed below instead of vpa
-
-    # absolute velocity at left boundary
-    if z.irank == 0
-        @. vpa.scratch = vpagrid_to_dzdt(vpa.grid, sqrt(2.0*(ppar[1]/density[1])),
-                                         upar[1], evolve_ppar, evolve_upar)
-        @loop_vpa ivpa begin
-            # for left boundary in zed (z = -Lz/2), want
-            # f(z=-Lz/2, v_parallel > 0) = 0
-            if vpa.scratch[ivpa] > zero
-                pdf[ivpa,:,1] .= 0.0
-            end
-        end
-    end
-    # absolute velocity at right boundary
-    if z.irank == z.nrank - 1
-        @. vpa.scratch2 = vpagrid_to_dzdt(vpa.grid, sqrt(2.0*(ppar[end]/density[end])),
-                                          upar[end], evolve_ppar, evolve_upar)
-        @loop_vpa ivpa begin
-            # for right boundary in zed (z = Lz/2), want
-            # f(z=Lz/2, v_parallel < 0) = 0
-            if vpa.scratch2[ivpa] < -zero
-                pdf[ivpa,:,end] .= 0.0
-            end
-        end
-    end
-
-    # Special constraint-forcing code that tries to keep the modifications smooth at
-    # v_parallel=0.
-    if z.irank == 0 && z.irank == z.nrank - 1
-        # Both z-boundaries in this block
-        z_range = (1,nz)
-    elseif z.irank == 0
-        z_range = (1,)
-    elseif z.irank == z.nrank - 1
-        z_range = (nz,)
-    else
-        error("No boundary in this block, should have returned already")
-    end
-    for iz ∈ z_range
-        # moment-kinetic approach only implemented for 1V case so far
-        @boundscheck size(pdf,2) == 1
-
-        f = @view pdf[:,1,iz]
-        if evolve_ppar && evolve_upar
-            I0 = integrate_over_vspace(f, vpa.wgts)
-            I1 = integrate_over_vspace(f, vpa.grid, vpa.wgts)
-            I2 = integrate_over_vspace(f, vpa.grid, 2, vpa.wgts)
-
-            # Store v_parallel with upar shift removed in vpa.scratch
-            vth = sqrt(2.0*ppar[iz]/density[iz])
-            @. vpa.scratch = vpa.grid + upar[iz]/vth
-            # Introduce factor to ensure corrections go smoothly to zero near
-            # v_parallel=0
-            @. vpa.scratch2 = f * abs(vpa.scratch) / (1.0 + abs(vpa.scratch))
-            J1 = integrate_over_vspace(vpa.scratch2, vpa.grid, vpa.wgts)
-            J2 = integrate_over_vspace(vpa.scratch2, vpa.grid, 2, vpa.wgts)
-            J3 = integrate_over_vspace(vpa.scratch2, vpa.grid, 3, vpa.wgts)
-            J4 = integrate_over_vspace(vpa.scratch2, vpa.grid, 4, vpa.wgts)
-
-            A = (J3^2 - J2*J4 + 0.5*(J2^2 - J1*J3)) /
-                (I0*(J3^2 - J2*J4) + I1*(J1*J4 - J2*J3) + I2*(J2^2 - J1*J3))
-            B = (0.5*J3 + A*(I1*J4 - I2*J3)) / (J3^2 - J2*J4)
-            C = (0.5 - A*I2 -B*J3) / J4
-
-            @. f = A*f + B*vpa.grid*vpa.scratch2 + C*vpa.grid*vpa.grid*vpa.scratch2
-        elseif evolve_upar
-            I0 = integrate_over_vspace(f, vpa.wgts)
-            I1 = integrate_over_vspace(f, vpa.grid, vpa.wgts)
-
-            # Store v_parallel with upar shift removed in vpa.scratch
-            @. vpa.scratch = vpa.grid + upar[iz]
-            # Introduce factor to ensure corrections go smoothly to zero near
-            # v_parallel=0
-            @. vpa.scratch2 = f * abs(vpa.scratch) / (1.0 + abs(vpa.scratch))
-            J1 = integrate_over_vspace(vpa.scratch2, vpa.grid, vpa.wgts)
-            J2 = integrate_over_vspace(vpa.scratch2, vpa.grid, 2, vpa.wgts)
-
-            A = 1.0 / (I0 - I1*J1/J2)
-            B = -A*I1/J2
-
-            @. f = A*f + B*vpa.grid*vpa.scratch2
-        elseif evolve_density
-            I0 = integrate_over_vspace(f, vpa.wgts)
-            @. f = f / I0
-        end
-    end
-end
-
-"""
-Set up an initial condition that tries to be smoothly compatible with the sheath
-boundary condition for ions, by setting f(±(v_parallel-u0)<0) where u0=0 at the sheath
-boundaries and for z<0 increases linearly to u0=vpa.L at z=0, while for z>0 increases
-from u0=-vpa.L at z=0 to zero at the z=z.L/2 sheath.
-
-To be applied to 'full-f' distribution function on v_parallel grid (not w_parallel
-grid).
-"""
-function enforce_initial_tapered_zero_incoming!(pdf, z::coordinate, vpa::coordinate)
-    nvpa = size(pdf,1)
-    zero = 1.0e-14
-    # no parallel BC should be enforced for dz/dt = 0
-    # note that the parallel velocity coordinate vpa may be dz/dt or
-    # some version of the peculiar velocity (dz/dt - upar),
-    # so use advection speed below instead of vpa
-
-    for iz ∈ 1:z.n
-        u0 = (2.0*z.grid[iz]/z.L - sign(z.grid[iz])) * vpa.L / 2.0
-        if z.grid[iz] < -zero
-            for ivpa ∈ 1:nvpa
-                if vpa.grid[ivpa] > u0 + zero
-                    pdf[ivpa,iz] = 0.0
-                end
-            end
-        elseif z.grid[iz] > zero
-            for ivpa ∈ 1:nvpa
-                if vpa.grid[ivpa] < u0 - zero
-                    pdf[ivpa,iz] = 0.0
-                end
-            end
-        end
-    end
-end
-
-"""
-enforce the wall boundary condition on neutrals;
-i.e., the incoming flux of neutrals equals the sum of the ion/neutral outgoing fluxes
-"""
-function enforce_neutral_wall_bc!(pdf, z, vzeta, vr, vz, pz, uz, density, wall_flux_0,
-                                  wall_flux_L, boundary_distributions, vtfac,
-                                  recycling_fraction, evolve_ppar, evolve_upar,
-                                  evolve_density, zero)
-
-    # Reduce the ion flux by `recycling_fraction` to account for ions absorbed by the
-    # wall.
-    wall_flux_0 *= recycling_fraction
-    wall_flux_L *= recycling_fraction
-
-    if !evolve_density && !evolve_upar
-        knudsen_cosine = boundary_distributions.knudsen
-
-        if z.irank == 0
-            ## treat z = -Lz/2 boundary ##
-
-            # add the neutral species's contribution to the combined ion/neutral particle
-            # flux out of the domain at z=-Lz/2
-            @views wall_flux_0 += integrate_over_negative_vz(abs.(vz.grid) .* pdf[:,:,:,1], vz.grid, vz.wgts, vz.scratch, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-
-            # for left boundary in zed (z = -Lz/2), want
-            # f_n(z=-Lz/2, v_parallel > 0) = Γ_0 * f_KW(v_parallel)
-            @loop_vz ivz begin
-                if vz.grid[ivz] >= -zero
-                    @views @. pdf[ivz,:,:,1] = wall_flux_0 * knudsen_cosine[ivz,:,:]
-                end
-            end
-        end
-
-        if z.irank == z.nrank - 1
-            ## treat the right boundary at z = Lz/2 ##
-
-            # add the neutral species's contribution to the combined ion/neutral particle
-            # flux out of the domain at z=-Lz/2
-            @views wall_flux_L += integrate_over_positive_vz(abs.(vz.grid) .* pdf[:,:,:,end], vz.grid, vz.wgts, vz.scratch, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-
-            # for right boundary in zed (z = Lz/2), want
-            # f_n(z=Lz/2, v_parallel < 0) = Γ_Lz * f_KW(v_parallel)
-            @loop_vz ivz begin
-                if vz.grid[ivz] <= zero
-                    @views @. pdf[ivz,:,:,end] = wall_flux_L * knudsen_cosine[ivz,:,:]
-                end
-            end
-        end
-    elseif !evolve_upar
-        # Evolving density case
-        knudsen_cosine = boundary_distributions.knudsen
-
-        if z.irank == 0
-            ## treat z = -Lz/2 boundary ##
-
-            # Note the numerical integrol of knudsen_cosine was forced to be 1 (to machine
-            # precision) when it was initialised.
-            @views pdf_integral_0 = integrate_over_negative_vz(pdf[:,:,:,1], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            @views pdf_integral_1 = integrate_over_negative_vz(vz.grid .* pdf[:,:,:,1], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            knudsen_integral_0 = integrate_over_positive_vz(knudsen_cosine, vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            knudsen_integral_1 = 1.0 # This is enforced in initialization
-
-            # Calculate normalisation factors N_in for the incoming and N_out for the
-            # Knudsen parts of the distirbution so that ∫dvpa F = 1 and ∫dvpa vpa F = uz
-            # Note wall_flux_0 is the ion flux into the wall (reduced by the recycling
-            # fraction), and the neutral flux should be out of the wall (i.e. uz>0) so
-            # n*uz = |n*uz| = wall_flux_0
-            # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
-            #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = uz
-            uz = wall_flux_0 / density[1]
-            N_in = (1 - uz * knudsen_integral_0 / knudsen_integral_1) /
-                   (pdf_integral_0
-                    - pdf_integral_1 / knudsen_integral_1 * knudsen_integral_0)
-            N_out = (uz - N_in * pdf_integral_1) / knudsen_integral_1
-
-            @loop_vz ivz begin
-                if vz.grid[ivz] >= -zero
-                    @views @. pdf[ivz,:,:,1] = N_out * knudsen_cosine[ivz,:,:]
-                else
-                    @views @. pdf[ivz,:,:,1] *= N_in
-                end
-            end
-        end
-
-        if z.irank == z.nrank - 1
-            ## treat the right boundary at z = Lz/2 ##
-
-            # Note the numerical integrol of knudsen_cosine was forced to be 1 (to machine
-            # precision) when it was initialised.
-            @views pdf_integral_0 = integrate_over_positive_vz(pdf[:,:,:,end], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            @views pdf_integral_1 = integrate_over_positive_vz(vz.grid .* pdf[:,:,:,end], vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            knudsen_integral_0 = integrate_over_negative_vz(knudsen_cosine, vz.grid, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            knudsen_integral_1 = -1.0 # This is enforced in initialization
-
-            # Calculate normalisation factors N_in for the incoming and N_out for the
-            # Knudsen parts of the distirbution so that ∫dvpa F = 1 and ∫dvpa vpa F = uz
-            # Note wall_flux_L is the ion flux into the wall (reduced by the recycling
-            # fraction), and the neutral flux should be out of the wall (i.e. uz<0) so
-            # -n*uz = |n*uz| = wall_flux_L
-            # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
-            #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = uz
-            uz = -wall_flux_L / density[end]
-            N_in = (1 - uz * knudsen_integral_0 / knudsen_integral_1) /
-                   (pdf_integral_0
-                    - pdf_integral_1 / knudsen_integral_1 * knudsen_integral_0)
-            N_out = (uz - N_in * pdf_integral_1) / knudsen_integral_1
-
-            @loop_vz ivz begin
-                if vz.grid[ivz] <= zero
-                    @views @. pdf[ivz,:,:,end] = N_out * knudsen_cosine[ivz,:,:]
-                else
-                    @views @. pdf[ivz,:,:,end] *= N_in
-                end
-            end
-        end
-    else
-        if z.irank == 0
-            ## treat z = -Lz/2 boundary ##
-            # populate vz.scratch2 array with dz/dt values at z = -Lz/2
-            if evolve_ppar
-                vth = sqrt(2.0*pz[1]/density[1])
-            else
-                vth = nothing
-            end
-            @. vz.scratch2 = vpagrid_to_dzdt(vz.grid, vth, uz[1], evolve_ppar, evolve_upar)
-
-            # First apply boundary condition that total neutral outflux is equal to ion
-            # influx to uz
-            uz[1] = wall_flux_0 / density[1]
-            #would setting density work better??
-            #density[1] = - wall_flux_0 / uz[1]
-
-            # Create normalised Knudsen cosine distribution, to use for positive v_parallel
-            # at z = -Lz/2
-            # Note this only makes sense for the 1V case with vr.n=vzeta.n=1
-            @. vz.scratch = (3.0*pi/vtfac^3)*abs(vz.scratch2)*erfc(abs(vz.scratch2)/vtfac)
-
-            # The v_parallel>0 part of the pdf is replaced by the Knudsen cosine
-            # distribution. To ensure the constraints ∫dwpa wpa^m F = 0 are satisfied when
-            # necessary, calculate a normalisation factor for the Knudsen distribution (in
-            # vz.scratch) and correction terms for the incoming pdf similar to
-            # enforce_moment_constraints!().
-            #
-            # Note that it seems to be important that this boundary condition not be
-            # modified by the moment constraints, as that could cause numerical instability.
-            # By ensuring that the constraints are satisfied already here,
-            # enforce_moment_constraints!() will not change the pdf at the boundary. For
-            # ions this is not an issue, because points set to 0 by the bc are not modified
-            # from 0 by enforce_moment_constraints!().
-            knudsen_integral_0 = integrate_over_positive_vz(vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            knudsen_integral_1 = integrate_over_positive_vz(vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-
-            @views pdf_integral_0 = integrate_over_negative_vz(pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            @views pdf_integral_1 = integrate_over_negative_vz(vz.grid .* pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            if !evolve_ppar
-                # Calculate normalisation factors N_in for the incoming and N_out for the
-                # Knudsen parts of the distirbution so that ∫dwpa F = 1 and ∫dwpa wpa F = 0
-                # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
-                #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = 0
-                N_in = 1.0 / (pdf_integral_0 - pdf_integral_1/knudsen_integral_1*knudsen_integral_0)
-                N_out = -N_in * pdf_integral_1 / knudsen_integral_1
-
-                zero_vz_ind = 0
-                for ivz ∈ 1:vz.n
-                    if vz.scratch2[ivz] <= -zero
-                        pdf[ivz,:,:,1] .= N_in*pdf[ivz,:,:,1]
-                    else
-                        zero_vz_ind = ivz
-                        if abs(vz.scratch2[ivz]) < zero
-                            # v_z = 0 point, half contribution from original pdf and half
-                            # from Knudsen cosine distribution, to be consistent with weights
-                            # used in
-                            # integrate_over_positive_vz()/integrate_over_negative_vz().
-                            @. pdf[ivz,:,:,1] = 0.5*(N_in*pdf[ivz,:,:,1] + N_out*vz.scratch[ivz])
-                        else
-                            pdf[ivz,:,:,1] .= N_out*vz.scratch[ivz]
-                        end
-                        break
-                    end
-                end
-                for ivz ∈ zero_vz_ind+1:vz.n
-                    pdf[ivz,:,:,1] .= N_out*vz.scratch[ivz]
-                end
-            else
-                knudsen_integral_2 = integrate_over_positive_vz(vz.grid .* vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-                @views pdf_integral_2 = integrate_over_negative_vz(vz.grid .* vz.grid .* pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-                @views pdf_integral_3 = integrate_over_negative_vz(vz.grid .* vz.grid .* vz.grid .* pdf[:,:,:,1], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-                # Calculate normalisation factor N_out for the Knudsen part of the
-                # distirbution and normalisation factor N_in and correction term C*wpa*F_in
-                # for the incoming distribution so that ∫dwpa F = 1, ∫dwpa wpa F = 0, and
-                # ∫dwpa wpa^2 F = 1/2
-                # ⇒ N_in*pdf_integral_0 + C*pdf_integral_1 + N_out*knudsen_integral_0 = 1
-                #   N_in*pdf_integral_1 + C*pdf_integral_2 + N_out*knudsen_integral_1 = 0
-                #   N_in*pdf_integral_2 + C*pdf_integral_3 + N_out*knudsen_integral_2 = 1/2
-                N_in = (0.5*knudsen_integral_0*pdf_integral_2 +
-                        knudsen_integral_1*(pdf_integral_3 - 0.5*pdf_integral_1) -
-                        knudsen_integral_2*pdf_integral_2) /
-                       (knudsen_integral_0*(pdf_integral_2^2 - pdf_integral_1*pdf_integral_3) +
-                        knudsen_integral_1*(pdf_integral_0*pdf_integral_3 - pdf_integral_1*pdf_integral_2) +
-                        knudsen_integral_2*(pdf_integral_1^2 - pdf_integral_0*pdf_integral_2))
-                N_out = -(N_in*(pdf_integral_1*pdf_integral_3 - pdf_integral_2^2) + 0.5*pdf_integral_2) /
-                         (knudsen_integral_1*pdf_integral_3 - knudsen_integral_2*pdf_integral_2)
-                C = (0.5 - N_out*knudsen_integral_2 - N_in*pdf_integral_2)/pdf_integral_3
-
-                zero_vz_ind = 0
-                for ivz ∈ 1:vz.n
-                    if vz.scratch2[ivz] <= -zero
-                        @views @. pdf[ivz,:,:,1] = N_in*pdf[ivz,:,:,1] + C*vz.grid[ivz]*pdf[ivz,:,:,1]
-                    else
-                        zero_vz_ind = ivz
-                        if abs(vz.scratch2[ivz]) < zero
-                            # v_parallel = 0 point, half contribution from original pdf and half
-                            # from Knudsen cosine distribution, to be consistent with weights
-                            # used in
-                            # integrate_over_positive_vz()/integrate_over_negative_vz().
-                            @views @. pdf[ivz,:,:,1] = 0.5*(N_in*pdf[ivz,:,:,1] +
-                                                            C*vz.grid[ivz]*pdf[ivz,:,:,1] +
-                                                            N_out*vz.scratch[ivz])
-                        else
-                            @. pdf[ivz,:,:,1] = N_out*vz.scratch[ivz]
-                        end
-                        break
-                    end
-                end
-                for ivz ∈ zero_vz_ind+1:vz.n
-                    @. pdf[ivz,:,:,1] = N_out*vz.scratch[ivz]
-                end
-            end
-        end
-
-        if z.irank == z.nrank - 1
-            ## treat the right boundary at z = Lz/2 ##
-            # populate vz.scratch2 array with dz/dt values at z = Lz/2
-            if evolve_ppar
-                vth = sqrt(2.0*pz[end]/density[end])
-            else
-                vth = nothing
-            end
-            @. vz.scratch2 = vpagrid_to_dzdt(vz.grid, vth, uz[end], evolve_ppar, evolve_upar)
-
-            # First apply boundary condition that total neutral outflux is equal to ion
-            # influx to uz
-            uz[end] = - wall_flux_L / density[end]
-            #would setting density work better??
-            #density[end] = - wall_flux_L / upar[end]
-
-            # obtain the Knudsen cosine distribution at z = Lz/2
-            # the z-dependence is only introduced if the peculiiar velocity is used as vz
-            # Note this only makes sense for the 1V case with vr.n=vzeta.n=1
-            @. vz.scratch = (3.0*pi/vtfac^3)*abs(vz.scratch2)*erfc(abs(vz.scratch2)/vtfac)
-
-            # The v_parallel<0 part of the pdf is replaced by the Knudsen cosine
-            # distribution. To ensure the constraint ∫dwpa wpa F = 0 is satisfied, multiply
-            # the Knudsen distribution (in vz.scratch) by a normalisation factor given by
-            # the integral (over negative v_parallel) of the outgoing Knudsen distribution
-            # and (over positive v_parallel) of the incoming pdf.
-            knudsen_integral_0 = integrate_over_negative_vz(vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            knudsen_integral_1 = integrate_over_negative_vz(vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-
-            @views pdf_integral_0 = integrate_over_positive_vz(pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-            @views pdf_integral_1 = integrate_over_positive_vz(vz.grid .* pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-
-            if !evolve_ppar
-                # Calculate normalisation factors N_in for the incoming and N_out for the
-                # Knudsen parts of the distirbution so that ∫dwpa F = 1 and ∫dwpa wpa F = 0
-                # ⇒ N_in*pdf_integral_0 + N_out*knudsen_integral_0 = 1
-                #   N_in*pdf_integral_1 + N_out*knudsen_integral_1 = 0
-                N_in = 1.0 / (pdf_integral_0 - pdf_integral_1/knudsen_integral_1*knudsen_integral_0)
-                N_out = -N_in * pdf_integral_1 / knudsen_integral_1
-
-                zero_vz_ind = 0
-                for ivz ∈ vz.n:-1:1
-                    if vz.scratch2[ivz] >= zero
-                        @views @. pdf[ivz,:,:,end] = N_in*pdf[ivz,:,:,end]
-                    else
-                        zero_vz_ind = ivz
-                        if abs(vz.scratch2[ivz]) < zero
-                            # v_parallel = 0 point, half contribution from original pdf and half
-                            # from Knudsen cosine distribution, to be consistent with weights
-                            # used in
-                            # integrate_over_positive_vz()/integrate_over_negative_vz().
-                            @views @. pdf[ivz,:,:,end] = 0.5*(N_in*pdf[ivz,:,:,end] + N_out*vz.scratch[ivz])
-                        else
-                            @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
-                        end
-                        break
-                    end
-                end
-                for ivz ∈ 1:zero_vz_ind-1
-                    @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
-                end
-            else
-                knudsen_integral_2 = integrate_over_negative_vz(vz.grid .* vz.grid .* vz.scratch, vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-                @views pdf_integral_2 = integrate_over_positive_vz(vz.grid .* vz.grid .* pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-                @views pdf_integral_3 = integrate_over_positive_vz(vz.grid .* vz.grid .* vz.grid .* pdf[:,:,:,end], vz.scratch2, vz.wgts, vz.scratch3, vr.grid, vr.wgts, vzeta.grid, vzeta.wgts)
-                # Calculate normalisation factor N_out for the Knudsen part of the
-                # distirbution and normalisation factor N_in and correction term C*wpa*F_in
-                # for the incoming distribution so that ∫dwpa F = 1, ∫dwpa wpa F = 0, and
-                # ∫dwpa wpa^2 F = 1/2
-                # ⇒ N_in*pdf_integral_0 + C*pdf_integral_1 + N_out*knudsen_integral_0 = 1
-                #   N_in*pdf_integral_1 + C*pdf_integral_2 + N_out*knudsen_integral_1 = 0
-                #   N_in*pdf_integral_2 + C*pdf_integral_3 + N_out*knudsen_integral_2 = 1/2
-                N_in = (0.5*knudsen_integral_0*pdf_integral_2 +
-                        knudsen_integral_1*(pdf_integral_3 - 0.5*pdf_integral_1) -
-                        knudsen_integral_2*pdf_integral_2) /
-                       (knudsen_integral_0*(pdf_integral_2^2 - pdf_integral_1*pdf_integral_3) +
-                        knudsen_integral_1*(pdf_integral_0*pdf_integral_3 - pdf_integral_1*pdf_integral_2) +
-                        knudsen_integral_2*(pdf_integral_1^2 - pdf_integral_0*pdf_integral_2))
-                N_out = -(N_in*(pdf_integral_1*pdf_integral_3 - pdf_integral_2^2) + 0.5*pdf_integral_2) /
-                         (knudsen_integral_1*pdf_integral_3 - knudsen_integral_2*pdf_integral_2)
-                C = (0.5 - N_out*knudsen_integral_2 - N_in*pdf_integral_2)/pdf_integral_3
-
-                zero_vz_ind = 0
-                for ivz ∈ vz.n:-1:1
-                    if vz.scratch2[ivz] >= zero
-                        @views @. pdf[ivz,:,:,end] = N_in*pdf[ivz,:,:,end] + C*vz.grid[ivz]*pdf[ivz,:,:,end]
-                    else
-                        zero_vz_ind = ivz
-                        if abs(vz.scratch2[ivz]) < zero
-                            # v_parallel = 0 point, half contribution from original pdf and half
-                            # from Knudsen cosine distribution, to be consistent with weights
-                            # used in
-                            # integrate_over_positive_vz()/integrate_over_negative_vz().
-                            @views @. pdf[ivz,:,:,end] = 0.5*(N_in*pdf[ivz,:,:,end] +
-                                                              C*vz.grid[ivz]*pdf[ivz,:,:,end] +
-                                                              N_out*vz.scratch[ivz])
-                        else
-                            @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
-                        end
-                        break
-                    end
-                end
-                for ivz ∈ 1:zero_vz_ind-1
-                    @. pdf[ivz,:,:,end] = N_out*vz.scratch[ivz]
-                end
-            end
-        end
-    end
-end
-
-"""
-create an array of dz/dt values corresponding to the given vpagrid values
-"""
-function vpagrid_to_dzdt(vpagrid, vth, upar, evolve_ppar, evolve_upar)
-    if evolve_ppar
-        if evolve_upar
-            return vpagrid .* vth .+ upar
-        else
-            return vpagrid .* vth
-        end
-    elseif evolve_upar
-        return vpagrid .+ upar
-    else
-        return vpagrid
-    end
-end
-
-"""
-Take the full charged-particle distribution function, calculate the moments, then
+Take the full ion distribution function, calculate the moments, then
 normalise and shift to the moment-kinetic grid.
 
 Uses input value of `f` and modifies in place to the normalised distribution functions.
@@ -2057,7 +1139,7 @@ the moments of `f`.
 
 Inputs/outputs depend on z, vperp, and vpa (should be inside loops over species, r)
 """
-function convert_full_f_charged_to_normalised!(f, density, upar, ppar, vth, vperp, vpa,
+function convert_full_f_ion_to_normalised!(f, density, upar, ppar, vth, vperp, vpa,
         vpa_spectral, evolve_density, evolve_upar, evolve_ppar)
 
     @loop_z iz begin
@@ -2146,91 +1228,4 @@ function convert_full_f_neutral_to_normalised!(f, density, uz, pz, vth, vzeta, v
     return nothing
 end
 
-"""
-enforce the z boundary condition on the evolved velocity space moments of f
-"""
-function enforce_z_boundary_condition_moments!(density, moments, bc::String)
-    ## TODO: parallelise
-    #begin_serial_region()
-    #@serial_region begin
-    #    # enforce z boundary condition on density if it is evolved separately from f
-    #	if moments.evolve_density
-    #        # TODO: extend to 'periodic' BC case, as this requires further code modifications to be consistent
-    #        # with finite difference derivatives (should be fine for Chebyshev)
-    #        if bc == "wall"
-    #            @loop_s_r is ir begin
-    #                density[1,ir,is] = 0.5*(density[1,ir,is] + density[end,ir,is])
-    #                density[end,ir,is] = density[1,ir,is]
-    #        	end
-    #        end
-    #    end
-    #end
-end
-
-"""
-"""
-function enforce_v_boundary_condition_local!(f, bc, speed, v_diffusion, v, v_spectral)
-    if bc == "zero"
-        if v_diffusion || speed[1] > 0.0
-            # 'upwind' boundary
-            f[1] = 0.0
-        end
-        if v_diffusion || speed[end] < 0.0
-            # 'upwind' boundary
-            f[end] = 0.0
-        end
-    elseif bc == "both_zero"
-        f[1] = 0.0
-        f[end] = 0.0
-    elseif bc == "zero_gradient"
-        D0 = v_spectral.lobatto.Dmat[1,:]
-        # adjust F(vpa = -L/2) so that d F / d vpa = 0 at vpa = -L/2
-        f[1] = -sum(D0[2:v.ngrid].*f[2:v.ngrid])/D0[1]
-
-        D0 = v_spectral.lobatto.Dmat[end,:]
-        # adjust F(vpa = L/2) so that d F / d vpa = 0 at vpa = L/2
-        f[end] = -sum(D0[1:ngrid-1].*f[end-v.ngrid+1:end-1])/D0[v.ngrid]
-    elseif bc == "periodic"
-        f[1] = 0.5*(f[1]+f[end])
-        f[end] = f[1]
-    else
-        error("Unsupported boundary condition option '$bc' for $(v.name)")
-    end
-end
-
-"""
-enforce zero boundary condition at vperp -> infinity
-"""
-function enforce_vperp_boundary_condition!(f, bc, vperp, vperp_spectral, vperp_advect, diffusion)
-    if bc == "zero"
-        nvperp = vperp.n
-        ngrid = vperp.ngrid
-        # set zero boundary condition
-        @loop_s_r_z_vpa is ir iz ivpa begin
-            if diffusion || vperp_advect[is].speed[nvperp,ivpa,iz,ir] < 0.0
-                f[ivpa,nvperp,iz,ir,is] = 0.0
-            end
-        end
-        # set regularity condition d F / d vperp = 0 at vperp = 0
-        if vperp.discretization == "gausslegendre_pseudospectral" || vperp.discretization == "chebyshev_pseudospectral"
-            D0 = vperp_spectral.radau.D0
-            buffer = @view vperp.scratch[1:ngrid-1]
-            @loop_s_r_z_vpa is ir iz ivpa begin
-                if diffusion || vperp_advect[is].speed[1,ivpa,iz,ir] > 0.0
-                    # adjust F(vperp = 0) so that d F / d vperp = 0 at vperp = 0
-                    @views @. buffer = D0[2:ngrid] * f[ivpa,2:ngrid,iz,ir,is]
-                    f[ivpa,1,iz,ir,is] = -sum(buffer)/D0[1]
-                end
-            end
-        else
-            println("vperp.bc=\"$bc\" not supported by discretization "
-                    * "$(vperp.discretization)")
-        end
-    elseif bc == "none"
-        # Do nothing
-    else
-        error("Unsupported boundary condition option '$bc' for vperp")
-    end
-end
-
 end
diff --git a/moment_kinetics/src/input_structs.jl b/moment_kinetics/src/input_structs.jl
index 2b716a172..fe7661e9a 100644
--- a/moment_kinetics/src/input_structs.jl
+++ b/moment_kinetics/src/input_structs.jl
@@ -2,6 +2,7 @@
 """
 module input_structs
 
+export advance_info
 export evolve_moments_options
 export time_info
 export advection_input, advection_input_mutable
@@ -91,7 +92,7 @@ mutable struct advance_info
     ionization_collisions::Bool
     ionization_collisions_1V::Bool
     ionization_source::Bool
-    krook_collisions::Bool
+    krook_collisions_ii::Bool
     explicit_weakform_fp_collisions::Bool
     external_source::Bool
     numerical_dissipation::Bool
@@ -348,8 +349,8 @@ end
 """
 Base.@kwdef struct krook_collisions_input
     use_krook::Bool
-    # Coulomb collision rate at the reference density and temperature
-    krook_collision_frequency_prefactor::mk_float#
+    # Ion-ion Coulomb collision rate at the reference density and temperature
+    nuii0::mk_float
     # Setting to switch between different options for Krook collision operator
     frequency_option::String # "reference_parameters" # "manual", 
 end
@@ -425,6 +426,7 @@ Base.@kwdef struct io_input
     ascii_output::Bool
     binary_format::binary_format_type
     parallel_io::Bool
+    run_id::String
 end
 
 """
diff --git a/moment_kinetics/src/ionization.jl b/moment_kinetics/src/ionization.jl
index 91a8d1d4b..a4e7ac3f1 100644
--- a/moment_kinetics/src/ionization.jl
+++ b/moment_kinetics/src/ionization.jl
@@ -95,7 +95,7 @@ function ionization_collisions_1V!(f_out, f_neutral_out, fvec_in, vz, vpa, vperp
             if moments.evolve_ppar
                 # will need the ratio of thermal speeds both to interpolate between vpa grids
                 # for different species and to account for different normalizations of each species' pdf
-                vth_ratio = moments.charged.vth[iz,ir,is]/moments.neutral.vth[iz,ir,isn]
+                vth_ratio = moments.ion.vth[iz,ir,is]/moments.neutral.vth[iz,ir,isn]
             else
                 vth_ratio = 1.0
             end
@@ -129,7 +129,7 @@ function ionization_collisions_1V!(f_out, f_neutral_out, fvec_in, vz, vpa, vperp
                     # to get f_{s'}(wpahat_s), need to obtain wpahat_s grid locations
                     # in terms of the wpahat_{s'} coordinate:
                     # (wpahat_{s'})_j = ((wpahat_{s})_j * vth_{s} + upar_{s} - upar_{s'}) / vth_{s'}
-                    @. vpa.scratch = (vpa.grid * moments.charged.vth[iz,ir,is] + fvec_in.upar[iz,ir,is] - fvec_in.uz_neutral[iz,ir,isn]) / moments.neutral.vth[iz,ir,isn]
+                    @. vpa.scratch = (vpa.grid * moments.ion.vth[iz,ir,is] + fvec_in.upar[iz,ir,is] - fvec_in.uz_neutral[iz,ir,isn]) / moments.neutral.vth[iz,ir,isn]
                 end
                 # interpolate to the new grid (passed in as vpa.scratch)
                 # and return interpolated values in vpa.scratch2
diff --git a/moment_kinetics/src/krook_collisions.jl b/moment_kinetics/src/krook_collisions.jl
index d487c195d..dce34db29 100644
--- a/moment_kinetics/src/krook_collisions.jl
+++ b/moment_kinetics/src/krook_collisions.jl
@@ -2,12 +2,11 @@
 """
 module krook_collisions
 
-export setup_krook_collisions_input, get_collision_frequency, krook_collisions!
+export setup_krook_collisions_input, get_collision_frequency_ii, krook_collisions!
 
-using ..constants: epsilon0, proton_charge
 using ..looping
 using ..input_structs: krook_collisions_input, set_defaults_and_check_section!
-using ..reference_parameters: get_reference_collision_frequency
+using ..reference_parameters: get_reference_collision_frequency_ii
 
 
 """
@@ -21,18 +20,18 @@ frequency_option = "manual"
 """
 function setup_krook_collisions_input(toml_input::Dict, reference_params)
     # get reference collision frequency
-    nuii_krook_default = get_reference_collision_frequency(reference_params)
+    nuii_krook_default = get_reference_collision_frequency_ii(reference_params)
     # read the input toml and specify a sensible default    
     input_section = input_section = set_defaults_and_check_section!(toml_input, "krook_collisions",
        # begin default inputs (as kwargs)
        use_krook = false,
-       krook_collision_frequency_prefactor = -1.0,
+       nuii0 = -1.0,
        frequency_option = "reference_parameters")
        
     # ensure that the collision frequency is consistent with the input option
     frequency_option = input_section["frequency_option"]
     if frequency_option == "reference_parameters"
-        input_section["krook_collision_frequency_prefactor"] = nuii_krook_default
+        input_section["nuii0"] = nuii_krook_default
     elseif frequency_option == "manual" 
         # use the frequency from the input file
         # do nothing
@@ -43,7 +42,7 @@ function setup_krook_collisions_input(toml_input::Dict, reference_params)
     # finally, ensure prefactor < 0 if use_krook is false
     # so that prefactor > 0 is the only check required in the rest of the code
     if !input_section["use_krook"]
-        input_section["krook_collision_frequency_prefactor"] = -1.0
+        input_section["nuii0"] = -1.0
     end
     input = Dict(Symbol(k)=>v for (k,v) in input_section)
     #println(input)
@@ -51,21 +50,21 @@ function setup_krook_collisions_input(toml_input::Dict, reference_params)
 end
 
 """
-    get_collision_frequency(collisions, n, vth)
+    get_collision_frequency_ii(collisions, n, vth)
 
-Calculate the collision frequency, depending on the settings/parameters in `collisions`,
-for the given density `n` and thermal speed `vth`.
+Calculate the ion-ion collision frequency, depending on the settings/parameters in
+`collisions`, for the given density `n` and thermal speed `vth`.
 
 `n` and `vth` may be scalars or arrays, but should have shapes that can be broadcasted
 together.
 """
-function get_collision_frequency(collisions, n, vth)
+function get_collision_frequency_ii(collisions, n, vth)
     # extract krook options from collisions struct
     colk = collisions.krook
-    krook_collision_frequency_prefactor = colk.krook_collision_frequency_prefactor
+    nuii0 = colk.nuii0
     frequency_option = colk.frequency_option
     if frequency_option == "reference_parameters"
-        return @. krook_collision_frequency_prefactor * n * vth^(-3)
+        return @. nuii0 * n * vth^(-3)
     elseif frequency_option == "manual"
         # Include 0.0*n so that the result gets promoted to an array if n is an array,
         # which hopefully means this function will have a fixed return type given the
@@ -98,8 +97,8 @@ function krook_collisions!(pdf_out, fvec_in, moments, composition, collisions, v
         # through by vth, remembering pdf is already multiplied by vth
         @loop_s_r_z is ir iz begin
             n = fvec_in.density[iz,ir,is]
-            vth = moments.charged.vth[iz,ir,is]
-            nu_ii = get_collision_frequency(collisions, n, vth)
+            vth = moments.ion.vth[iz,ir,is]
+            nu_ii = get_collision_frequency_ii(collisions, n, vth)
             @loop_vperp_vpa ivperp ivpa begin
                 pdf_out[ivpa,ivperp,iz,ir,is] -= dt * nu_ii *
                     (fvec_in.pdf[ivpa,ivperp,iz,ir,is]
@@ -111,8 +110,8 @@ function krook_collisions!(pdf_out, fvec_in, moments, composition, collisions, v
         # is already multiplied by vth, and grid is already normalized by vth
         @loop_s_r_z is ir iz begin
             n = fvec_in.density[iz,ir,is]
-            vth = moments.charged.vth[iz,ir,is]
-            nu_ii = get_collision_frequency(collisions, n, vth)
+            vth = moments.ion.vth[iz,ir,is]
+            nu_ii = get_collision_frequency_ii(collisions, n, vth)
             @loop_vperp_vpa ivperp ivpa begin
                 pdf_out[ivpa,ivperp,iz,ir,is] -= dt * nu_ii *
                     (fvec_in.pdf[ivpa,ivperp,iz,ir,is]
@@ -124,8 +123,8 @@ function krook_collisions!(pdf_out, fvec_in, moments, composition, collisions, v
         # Compared to evolve_density version, grid is already shifted by upar
         @loop_s_r_z is ir iz begin
             n = fvec_in.density[iz,ir,is]
-            vth = moments.charged.vth[iz,ir,is]
-            nu_ii = get_collision_frequency(collisions, n, vth)
+            vth = moments.ion.vth[iz,ir,is]
+            nu_ii = get_collision_frequency_ii(collisions, n, vth)
             @loop_vperp_vpa ivperp ivpa begin
                 pdf_out[ivpa,ivperp,iz,ir,is] -= dt * nu_ii *
                     (fvec_in.pdf[ivpa,ivperp,iz,ir,is]
@@ -138,8 +137,8 @@ function krook_collisions!(pdf_out, fvec_in, moments, composition, collisions, v
         # that pdf is already normalized by density
         @loop_s_r_z is ir iz begin
             n = fvec_in.density[iz,ir,is]
-            vth = moments.charged.vth[iz,ir,is]
-            nu_ii = get_collision_frequency(collisions, n, vth)
+            vth = moments.ion.vth[iz,ir,is]
+            nu_ii = get_collision_frequency_ii(collisions, n, vth)
             @loop_vperp_vpa ivperp ivpa begin
                 pdf_out[ivpa,ivperp,iz,ir,is] -= dt * nu_ii *
                 (fvec_in.pdf[ivpa,ivperp,iz,ir,is]
@@ -151,13 +150,13 @@ function krook_collisions!(pdf_out, fvec_in, moments, composition, collisions, v
     else
         @loop_s_r_z is ir iz begin
             n = fvec_in.density[iz,ir,is]
-            vth = moments.charged.vth[iz,ir,is]
+            vth = moments.ion.vth[iz,ir,is]
             if vperp.n == 1
                 vth_prefactor = 1.0 / vth
             else
                 vth_prefactor = 1.0 / vth^3
             end
-            nu_ii = get_collision_frequency(collisions, n, vth)
+            nu_ii = get_collision_frequency_ii(collisions, n, vth)
             @loop_vperp_vpa ivperp ivpa begin
                 pdf_out[ivpa,ivperp,iz,ir,is] -= dt * nu_ii *
                     (fvec_in.pdf[ivpa,ivperp,iz,ir,is]
diff --git a/moment_kinetics/src/load_data.jl b/moment_kinetics/src/load_data.jl
index 2ce2a5546..91992e9c6 100644
--- a/moment_kinetics/src/load_data.jl
+++ b/moment_kinetics/src/load_data.jl
@@ -4,7 +4,7 @@ module load_data
 
 export open_readonly_output_file
 export load_fields_data
-export load_charged_particle_moments_data
+export load_ion_particle_moments_data
 export load_neutral_particle_moments_data
 export load_pdf_data
 export load_neutral_pdf_data
@@ -17,12 +17,12 @@ export read_distributed_zr_data!
 
 using ..array_allocation: allocate_float, allocate_int
 using ..calculus: derivative!
-using ..communication: setup_distributed_memory_MPI
+using ..communication
 using ..coordinates: coordinate, define_coordinate
 using ..file_io: check_io_implementation, get_group, get_subgroup_keys, get_variable_keys
-using ..krook_collisions: get_collision_frequency
-using ..input_structs: advection_input, grid_input, hdf5, netcdf
+using ..input_structs
 using ..interpolation: interpolate_to_grid_1d!
+using ..krook_collisions
 using ..looping
 using ..moment_kinetics_input: mk_input
 using ..neutral_vz_advection: update_speed_neutral_vz!
@@ -45,7 +45,7 @@ const timestep_diagnostic_variables = ("time_for_run", "step_counter", "dt",
 const em_variables = ("phi", "Er", "Ez")
 const ion_moment_variables = ("density", "parallel_flow", "parallel_pressure",
                               "thermal_speed", "temperature", "parallel_heat_flux",
-                              "collision_frequency", "sound_speed", "mach_number")
+                              "collision_frequency_ii", "sound_speed", "mach_number")
 const neutral_moment_variables = ("density_neutral", "uz_neutral", "pz_neutral",
                                   "thermal_speed_neutral", "temperature_neutral",
                                   "qz_neutral")
@@ -186,7 +186,8 @@ function load_input(fid)
 end
 
 """
-    load_coordinate_data(fid, name; printout=false, irank=nothing, nrank=nothing)
+    load_coordinate_data(fid, name; printout=false, irank=nothing, nrank=nothing,
+                         run_directory=nothing, ignore_MPI=true)
 
 Load data for the coordinate `name` from a file-handle `fid`.
 
@@ -199,6 +200,10 @@ If `printout` is set to `true` a message will be printed when this function is c
 If `irank` and `nrank` are passed, then the `coord` and `spectral` objects returned will
 be set up for the parallelisation specified by `irank` and `nrank`, rather than the one
 implied by the output file.
+
+Unless `ignore_MPI=false` is passed, the returned coordinates will be created without
+shared memory scratch arrays (`ignore_MPI=true` will be passed through to
+[`define_coordinate`](@ref)).
 """
 function load_coordinate_data(fid, name; printout=false, irank=nothing, nrank=nothing,
                               run_directory=nothing, ignore_MPI=true)
@@ -209,7 +214,12 @@ function load_coordinate_data(fid, name; printout=false, irank=nothing, nrank=no
     overview = get_group(fid, "overview")
     parallel_io = load_variable(overview, "parallel_io")
 
-    coord_group = get_group(get_group(fid, "coords"), name)
+    coords_group = get_group(fid, "coords")
+    if name ∈ get_subgroup_keys(coords_group)
+        coord_group = get_group(coords_group, name)
+    else
+        return nothing, nothing, nothing
+    end
 
     ngrid = load_variable(coord_group, "ngrid")
     n_local = load_variable(coord_group, "n_local")
@@ -290,7 +300,8 @@ function load_coordinate_data(fid, name; printout=false, irank=nothing, nrank=no
                        advection_input("default", 0.0, 0.0, 0.0), MPI.COMM_NULL,
                        element_spacing_option)
 
-    coord, spectral = define_coordinate(input, parallel_io; ignore_MPI=ignore_MPI)
+    coord, spectral = define_coordinate(input, parallel_io; run_directory=run_directory,
+                                        ignore_MPI=ignore_MPI)
 
     return coord, spectral, chunk_size
 end
@@ -441,33 +452,33 @@ end
 
 """
 """
-function load_charged_particle_moments_data(fid; printout=false, extended_moments = false)
+function load_ion_moments_data(fid; printout=false, extended_moments = false)
     if printout
-        print("Loading charged particle velocity moments data...")
+        print("Loading ion velocity moments data...")
     end
 
     group = get_group(fid, "dynamic_data")
 
-    # Read charged species density
+    # Read ion species density
     density = load_variable(group, "density")
 
-    # Read charged species parallel flow
+    # Read ion species parallel flow
     parallel_flow = load_variable(group, "parallel_flow")
 
-    # Read charged species parallel pressure
+    # Read ion species parallel pressure
     parallel_pressure = load_variable(group, "parallel_pressure")
 
-    # Read charged_species parallel heat flux
+    # Read ion_species parallel heat flux
     parallel_heat_flux = load_variable(group, "parallel_heat_flux")
 
-    # Read charged species thermal speed
+    # Read ion species thermal speed
     thermal_speed = load_variable(group, "thermal_speed")
 
     if extended_moments
-        # Read charged species perpendicular pressure
+        # Read ion species perpendicular pressure
         perpendicular_pressure = load_variable(group, "perpendicular_pressure")
 
-        # Read charged species entropy_production
+        # Read ion species entropy_production
         entropy_production = load_variable(group, "entropy_production")
     end
 
@@ -475,7 +486,7 @@ function load_charged_particle_moments_data(fid; printout=false, extended_moment
         println("done.")
     end
     if extended_moments
-        density, parallel_flow, parallel_pressure, perpendicular_pressure, parallel_heat_flux, thermal_speed, entropy_production
+        return density, parallel_flow, parallel_pressure, perpendicular_pressure, parallel_heat_flux, thermal_speed, entropy_production
     else
         return density, parallel_flow, parallel_pressure, parallel_heat_flux, thermal_speed
     end
@@ -514,12 +525,12 @@ end
 """
 function load_pdf_data(fid; printout=false)
     if printout
-        print("Loading charged particle distribution function data...")
+        print("Loading ion particle distribution function data...")
     end
 
     group = get_group(fid, "dynamic_data")
 
-    # Read charged distribution function
+    # Read ion distribution function
     pdf = load_variable(group, "f")
 
     if printout
@@ -574,86 +585,26 @@ function reload_evolving_fields!(pdf, moments, boundary_distributions,
             previous_runs_info = load_run_info_history(fid)
 
             restart_n_ion_species, restart_n_neutral_species = load_species_data(fid)
-            if parallel_io
-                restart_z, restart_z_spectral, _ =
-                    load_coordinate_data(fid, "z"; irank=z.irank, nrank=z.nrank)
-                restart_r, restart_r_spectral, _ =
-                    load_coordinate_data(fid, "r"; irank=r.irank, nrank=r.nrank)
-                restart_vperp, restart_vperp_spectral, _ =
-                    load_coordinate_data(fid, "vperp"; irank=vperp.irank,
-                                         nrank=vperp.nrank)
-                restart_vpa, restart_vpa_spectral, _ =
-                    load_coordinate_data(fid, "vpa"; irank=vpa.irank, nrank=vpa.nrank)
-                restart_vzeta, restart_vzeta_spectral, _ =
-                    load_coordinate_data(fid, "vzeta"; irank=vzeta.irank,
-                                         nrank=vzeta.nrank)
-                restart_vr, restart_vr_spectral, _ =
-                    load_coordinate_data(fid, "vr"; irank=vr.irank, nrank=vr.nrank)
-                restart_vz, restart_vz_spectral, _ =
-                    load_coordinate_data(fid, "vz"; irank=vz.irank, nrank=vz.nrank)
-            else
-                restart_z, restart_z_spectral, _ =
-                    load_coordinate_data(fid, "z")
-                restart_r, restart_r_spectral, _ =
-                    load_coordinate_data(fid, "r")
-                restart_vperp, restart_vperp_spectral, _ =
-                    load_coordinate_data(fid, "vperp")
-                restart_vpa, restart_vpa_spectral, _ =
-                    load_coordinate_data(fid, "vpa")
-                restart_vzeta, restart_vzeta_spectral, _ =
-                    load_coordinate_data(fid, "vzeta")
-                restart_vr, restart_vr_spectral, _ =
-                    load_coordinate_data(fid, "vr")
-                restart_vz, restart_vz_spectral, _ =
-                    load_coordinate_data(fid, "vz")
-
-                if restart_r.nrank != r.nrank
-                    error("Not using parallel I/O, and distributed MPI layout has "
-                          * "changed: now r.nrank=$(r.nrank), but we are trying to "
-                          * "restart from files ith restart_r.nrank=$(restart_r.nrank).")
-                end
-                if restart_z.nrank != z.nrank
-                    error("Not using parallel I/O, and distributed MPI layout has "
-                          * "changed: now z.nrank=$(z.nrank), but we are trying to "
-                          * "restart from files ith restart_z.nrank=$(restart_z.nrank).")
-                end
-                if restart_vperp.nrank != vperp.nrank
-                    error("Not using parallel I/O, and distributed MPI layout has "
-                          * "changed: now vperp.nrank=$(vperp.nrank), but we are trying to "
-                          * "restart from files ith restart_vperp.nrank=$(restart_vperp.nrank).")
-                end
-                if restart_vpa.nrank != vpa.nrank
-                    error("Not using parallel I/O, and distributed MPI layout has "
-                          * "changed: now vpa.nrank=$(vpa.nrank), but we are trying to "
-                          * "restart from files ith restart_vpa.nrank=$(restart_vpa.nrank).")
-                end
-                if restart_vzeta.nrank != vzeta.nrank
-                    error("Not using parallel I/O, and distributed MPI layout has "
-                          * "changed: now vzeta.nrank=$(vzeta.nrank), but we are trying to "
-                          * "restart from files ith restart_vzeta.nrank=$(restart_vzeta.nrank).")
-                end
-                if restart_vr.nrank != vr.nrank
-                    error("Not using parallel I/O, and distributed MPI layout has "
-                          * "changed: now vr.nrank=$(vr.nrank), but we are trying to "
-                          * "restart from files ith restart_vr.nrank=$(restart_vr.nrank).")
-                end
-                if restart_vz.nrank != vz.nrank
-                    error("Not using parallel I/O, and distributed MPI layout has "
-                          * "changed: now vz.nrank=$(vz.nrank), but we are trying to "
-                          * "restart from files ith restart_vz.nrank=$(restart_vz.nrank).")
-                end
-            end
+            restart_r, restart_r_spectral, restart_z, restart_z_spectral, restart_vperp,
+                restart_vperp_spectral, restart_vpa, restart_vpa_spectral, restart_vzeta,
+                restart_vzeta_spectral, restart_vr,restart_vr_spectral, restart_vz,
+                restart_vz_spectral = load_restart_coordinates(fid, r, z, vperp, vpa,
+                                                               vzeta, vr, vz, parallel_io)
 
             # Test whether any interpolation is needed
             interpolation_needed = Dict(
-                x.name => x.n != restart_x.n || !all(isapprox.(x.grid, restart_x.grid))
+                x.name => (restart_x !== nothing
+                           && (x.n != restart_x.n
+                               || !all(isapprox.(x.grid, restart_x.grid))))
                 for (x, restart_x) ∈ ((z, restart_z), (r, restart_r),
                                       (vperp, restart_vperp), (vpa, restart_vpa),
                                       (vzeta, restart_vzeta), (vr, restart_vr),
                                       (vz, restart_vz)))
 
             neutral_1V = (vzeta.n_global == 1 && vr.n_global == 1)
-            restart_neutral_1V = (restart_vzeta.n_global == 1 && restart_vr.n_global == 1)
+            restart_neutral_1V = ((restart_vzeta === nothing
+                                   || restart_vzeta.n_global == 1)
+                                  && (restart_vr === nothing || restart_vr.n_global == 1))
             if any(geometry.bzeta .!= 0.0) && ((neutral_1V && !restart_neutral_1V) ||
                                                (!neutral_1V && restart_neutral_1V))
                 # One but not the other of the run being restarted from and this run are
@@ -666,614 +617,184 @@ function reload_evolving_fields!(pdf, moments, boundary_distributions,
 
             code_time = load_slice(dynamic, "time", time_index)
 
-            if parallel_io
-                function get_range(coord)
-                    if coord.irank == coord.nrank - 1
-                        return coord.global_io_range
-                    else
-                        # Need to modify the range to load the end-point that is duplicated on
-                        # the next process
-                        this_range = coord.global_io_range
-                        return this_range.start:(this_range.stop+1)
-                    end
+            r_range, z_range, vperp_range, vpa_range, vzeta_range, vr_range, vz_range =
+                get_reload_ranges(parallel_io, restart_r, restart_z, restart_vperp,
+                                  restart_vpa, restart_vzeta, restart_vr, restart_vz)
+
+            moments.ion.dens .= reload_moment("density", dynamic, time_index, r, z,
+                                              r_range, z_range, restart_r,
+                                              restart_r_spectral, restart_z,
+                                              restart_z_spectral, interpolation_needed)
+            moments.ion.dens_updated .= true
+            moments.ion.upar .= reload_moment("parallel_flow", dynamic, time_index, r, z,
+                                              r_range, z_range, restart_r,
+                                              restart_r_spectral, restart_z,
+                                              restart_z_spectral, interpolation_needed)
+            moments.ion.upar_updated .= true
+            moments.ion.ppar .= reload_moment("parallel_pressure", dynamic, time_index, r,
+                                              z, r_range, z_range, restart_r,
+                                              restart_r_spectral, restart_z,
+                                              restart_z_spectral, interpolation_needed)
+            moments.ion.ppar_updated .= true
+            moments.ion.qpar .= reload_moment("parallel_heat_flux", dynamic, time_index,
+                                              r, z, r_range, z_range, restart_r,
+                                              restart_r_spectral, restart_z,
+                                              restart_z_spectral, interpolation_needed)
+            moments.ion.qpar_updated .= true
+            moments.ion.vth .= reload_moment("thermal_speed", dynamic, time_index, r, z,
+                                             r_range, z_range, restart_r,
+                                             restart_r_spectral, restart_z,
+                                             restart_z_spectral, interpolation_needed)
+            moments.ion.dSdt .= reload_moment("entropy_production", dynamic, time_index,
+                                              r, z, r_range, z_range, restart_r,
+                                              restart_r_spectral, restart_z,
+                                              restart_z_spectral, interpolation_needed)
+            if moments.evolve_density || moments.evolve_upar || moments.evolve_ppar
+                if "ion_constraints_A_coefficient" ∈ keys(dynamic)
+                    moments.ion.constraints_A_coefficient .=
+                        reload_moment("ion_constraints_A_coefficient", dynamic,
+                                      time_index, r, z, r_range, z_range, restart_r,
+                                      restart_r_spectral, restart_z, restart_z_spectral,
+                                      interpolation_needed)
+                elseif moments.ion.constraints_A_coefficient !== nothing
+                    moments.ion.constraints_A_coefficient .= 0.0
                 end
-                r_range = get_range(restart_r)
-                z_range = get_range(restart_z)
-                vperp_range = get_range(restart_vperp)
-                vpa_range = get_range(restart_vpa)
-                vzeta_range = get_range(restart_vzeta)
-                vr_range = get_range(restart_vr)
-                vz_range = get_range(restart_vz)
-            else
-                r_range = (:)
-                z_range = (:)
-                vperp_range = (:)
-                vpa_range = (:)
-                vzeta_range = (:)
-                vr_range = (:)
-                vz_range = (:)
-            end
-
-            function load_moment(var_name)
-                moment = load_slice(dynamic, var_name, z_range, r_range, :, time_index)
-                orig_nz, orig_nr, nspecies = size(moment)
-                if interpolation_needed["r"]
-                    new_moment = allocate_float(orig_nz, r.n, nspecies)
-                    for is ∈ 1:nspecies, iz ∈ 1:orig_nz
-                        @views interpolate_to_grid_1d!(new_moment[iz,:,is], r.grid,
-                                                       moment[iz,:,is], restart_r,
-                                                       restart_r_spectral)
-                    end
-                    moment = new_moment
+                if "ion_constraints_B_coefficient" ∈ keys(dynamic)
+                    moments.ion.constraints_B_coefficient .=
+                        reload_moment("ion_constraints_B_coefficient", dynamic,
+                                      time_index, r, z, r_range, z_range, restart_r,
+                                      restart_r_spectral, restart_z, restart_z_spectral,
+                                      interpolation_needed)
+                elseif moments.ion.constraints_B_coefficient !== nothing
+                    moments.ion.constraints_B_coefficient .= 0.0
                 end
-                if interpolation_needed["z"]
-                    new_moment = allocate_float(z.n, r.n, nspecies)
-                    for is ∈ 1:nspecies, ir ∈ 1:r.n
-                        @views interpolate_to_grid_1d!(new_moment[:,ir,is], z.grid,
-                                                       moment[:,ir,is], restart_z,
-                                                       restart_z_spectral)
-                    end
-                    moment = new_moment
+                if "ion_constraints_C_coefficient" ∈ keys(dynamic)
+                    moments.ion.constraints_C_coefficient .=
+                        reload_moment("ion_constraints_C_coefficient", dynamic,
+                                      time_index, r, z, r_range, z_range, restart_r,
+                                      restart_r_spectral, restart_z, restart_z_spectral,
+                                      interpolation_needed)
+                elseif moments.ion.constraints_C_coefficient !== nothing
+                    moments.ion.constraints_C_coefficient .= 0.0
                 end
-                return moment
             end
-
-            moments.charged.dens .= load_moment("density")
-            moments.charged.dens_updated .= true
-            moments.charged.upar .= load_moment("parallel_flow")
-            moments.charged.upar_updated .= true
-            moments.charged.ppar .= load_moment("parallel_pressure")
-            moments.charged.ppar_updated .= true
-            moments.charged.qpar .= load_moment("parallel_heat_flux")
-            moments.charged.qpar_updated .= true
-            moments.charged.vth .= load_moment("thermal_speed")
             if z.irank == 0
                 if "chodura_integral_lower" ∈ keys(dynamic)
-                    moments.charged.chodura_integral_lower .= load_slice(dynamic, "chodura_integral_lower",
-                                                                         r_range, :, time_index)
+                    moments.ion.chodura_integral_lower .= load_slice(dynamic, "chodura_integral_lower",
+                                                                     r_range, :, time_index)
                 else
-                    moments.charged.chodura_integral_lower .= 0.0
+                    moments.ion.chodura_integral_lower .= 0.0
                 end
             end
             if z.irank == z.nrank - 1
                 if "chodura_integral_upper" ∈ keys(dynamic)
-                    moments.charged.chodura_integral_upper .= load_slice(dynamic, "chodura_integral_upper",
-                                                                         r_range, :, time_index)
+                    moments.ion.chodura_integral_upper .= load_slice(dynamic, "chodura_integral_upper",
+                                                                     r_range, :, time_index)
                 else
-                    moments.charged.chodura_integral_upper .= 0.0
+                    moments.ion.chodura_integral_upper .= 0.0
                 end
             end
 
             if "external_source_controller_integral" ∈ get_variable_keys(dynamic) &&
-                    length(moments.charged.external_source_controller_integral) == 1
-                moments.charged.external_source_controller_integral .=
+                    length(moments.ion.external_source_controller_integral) == 1
+                moments.ion.external_source_controller_integral .=
                     load_slice(dynamic, "external_source_controller_integral", time_index)
-            elseif length(moments.charged.external_source_controller_integral) > 1
-                moments.charged.external_source_controller_integral .=
-                    load_moment("external_source_controller_integral")
+            elseif length(moments.ion.external_source_controller_integral) > 1
+                moments.ion.external_source_controller_integral .=
+                    reload_moment("external_source_controller_integral", dynamic,
+                                  time_index, r, z, r_range, z_range, restart_r,
+                                  restart_r_spectral, restart_z, restart_z_spectral,
+                                  interpolation_needed)
             end
 
-            function load_charged_pdf()
-                this_pdf = load_slice(dynamic, "f", vpa_range, vperp_range, z_range,
-                                      r_range, :, time_index)
-                orig_nvpa, orig_nvperp, orig_nz, orig_nr, nspecies = size(this_pdf)
-                if interpolation_needed["r"]
-                    new_pdf = allocate_float(orig_nvpa, orig_nvperp, orig_nz, r.n, nspecies)
-                    for is ∈ 1:nspecies, iz ∈ 1:orig_nz, ivperp ∈ 1:orig_nvperp,
-                            ivpa ∈ 1:orig_nvpa
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[ivpa,ivperp,iz,:,is], r.grid,
-                            this_pdf[ivpa,ivperp,iz,:,is], restart_r,
-                            restart_r_spectral)
-                    end
-                    this_pdf = new_pdf
-                end
-                if interpolation_needed["z"]
-                    new_pdf = allocate_float(orig_nvpa, orig_nvperp, z.n, r.n, nspecies)
-                    for is ∈ 1:nspecies, ir ∈ 1:r.n, ivperp ∈ 1:orig_nvperp,
-                            ivpa ∈ 1:orig_nvpa
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[ivpa,ivperp,:,ir,is], z.grid,
-                            this_pdf[ivpa,ivperp,:,ir,is], restart_z,
-                            restart_z_spectral)
-                    end
-                    this_pdf = new_pdf
-                end
-
-                # Current moment-kinetic implementation is only 1V, so no need to handle a
-                # normalised vperp coordinate. This will need to change when 2V
-                # moment-kinetics is implemented.
-                if interpolation_needed["vperp"]
-                    new_pdf = allocate_float(orig_nvpa, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivpa ∈ 1:orig_nvpa
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[ivpa,:,iz,ir,is], vperp.grid,
-                            this_pdf[ivpa,:,iz,ir,is], restart_vperp,
-                            restart_vperp_spectral)
-                    end
-                    this_pdf = new_pdf
-                end
-
-                if (
-                    (moments.evolve_density == restart_evolve_density &&
-                     moments.evolve_upar == restart_evolve_upar && moments.evolve_ppar ==
-                     restart_evolve_ppar)
-                    || (!moments.evolve_upar && !restart_evolve_upar &&
-                        !moments.evolve_ppar && !restart_evolve_ppar)
-                   )
-                    # No chages to velocity-space coordinates, so just interpolate from
-                    # one grid to the other
-                    if interpolation_needed["vpa"]
-                        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                        for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivperp,iz,ir,is], vpa.grid,
-                                this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                                restart_vpa_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-                elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                        restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa = old_wpa + upar
-                    # => old_wpa = new_wpa - upar
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .- moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                        !restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa = old_wpa*vth
-                    # => old_wpa = new_wpa/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid ./ moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                        restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa = old_wpa*vth + upar
-                    # => old_wpa = (new_wpa - upar)/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. (vpa.grid - moments.charged.upar[iz,ir,is]) /
-                               moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                        !restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa + upar = old_wpa
-                    # => old_wpa = new_wpa + upar
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .+ moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                        !restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa + upar = old_wpa*vth
-                    # => old_wpa = (new_wpa + upar)/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. (vpa.grid + moments.charged.upar[iz,ir,is]) /
-                               moments.charged.vth
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                        restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa + upar = old_wpa*vth + upar
-                    # => old_wpa = new_wpa/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid ./ moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                        !restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth = old_wpa
-                    # => old_wpa = new_wpa*vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .* moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                        restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth = old_wpa + upar
-                    # => old_wpa = new_wpa*vth - upar/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = @. vpa.grid * moments.charged.vth[iz,ir,is] -
-                                              moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                        restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa*vth = old_wpa*vth + upar
-                    # => old_wpa = new_wpa - upar/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. vpa.grid -
-                               moments.charged.upar[iz,ir,is]/moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && moments.evolve_ppar &&
-                        !restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth + upar = old_wpa
-                    # => old_wpa = new_wpa*vth + upar
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = @. vpa.grid * moments.charged.vth[iz,ir,is] +
-                                              moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && moments.evolve_ppar &&
-                        restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth + upar = old_wpa + upar
-                    # => old_wpa = new_wpa*vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .* moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && moments.evolve_ppar &&
-                        !restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa*vth + upar = old_wpa*vth
-                    # => old_wpa = new_wpa + upar/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. vpa.grid +
-                               moments.charged.upar[iz,ir,is] / moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,ir,is], restart_vpa,
-                            restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                else
-                    # This should never happen, as all combinations of evolve_* options
-                    # should be handled above.
-                    error("Unsupported combination of moment-kinetic options:"
-                          * " evolve_density=", moments.evolve_density
-                          * " evolve_upar=", moments.evolve_upar
-                          * " evolve_ppar=", moments.evolve_ppar
-                          * " restart_evolve_density=", restart_evolve_density
-                          * " restart_evolve_upar=", restart_evolve_upar
-                          * " restart_evolve_ppar=", restart_evolve_ppar)
-                end
-                if moments.evolve_density && !restart_evolve_density
-                    # Need to normalise by density
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,ir,is] ./= moments.charged.dens[iz,ir,is]
-                    end
-                elseif !moments.evolve_density && restart_evolve_density
-                    # Need to unnormalise by density
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,ir,is] .*= moments.charged.dens[iz,ir,is]
-                    end
-                end
-                if moments.evolve_ppar && !restart_evolve_ppar
-                    # Need to normalise by vth
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,ir,is] .*= moments.charged.vth[iz,ir,is]
-                    end
-                elseif !moments.evolve_ppar && restart_evolve_ppar
-                    # Need to unnormalise by vth
-                    for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,ir,is] ./= moments.charged.vth[iz,ir,is]
-                    end
-                end
-
-                return this_pdf
-            end
-
-            pdf.charged.norm .= load_charged_pdf()
+            pdf.ion.norm .= reload_ion_pdf(dynamic, time_index, moments, r, z, vperp, vpa, r_range,
+                                           z_range, vperp_range, vpa_range, restart_r,
+                                           restart_r_spectral, restart_z,
+                                           restart_z_spectral, restart_vperp,
+                                           restart_vperp_spectral, restart_vpa,
+                                           restart_vpa_spectral, interpolation_needed,
+                                           restart_evolve_density, restart_evolve_upar,
+                                           restart_evolve_ppar)
             boundary_distributions_io = get_group(fid, "boundary_distributions")
 
-            function load_charged_boundary_pdf(var_name, ir)
-                this_pdf = load_slice(boundary_distributions_io, var_name, vpa_range,
-                                      vperp_range, z_range, :)
-                orig_nvpa, orig_nvperp, orig_nz, nspecies = size(this_pdf)
-                if interpolation_needed["z"]
-                    new_pdf = allocate_float(orig_nvpa, orig_nvperp, z.n, nspecies)
-                    for is ∈ 1:nspecies, ivperp ∈ 1:orig_nvperp,
-                            ivpa ∈ 1:orig_nvpa
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[ivpa,ivperp,:,is], z.grid,
-                            this_pdf[ivpa,ivperp,:,is], restart_z,
-                            restart_z_spectral)
-                    end
-                    this_pdf = new_pdf
-                end
-
-                # Current moment-kinetic implementation is only 1V, so no need to handle a
-                # normalised vperp coordinate. This will need to change when 2V
-                # moment-kinetics is implemented.
-                if interpolation_needed["vperp"]
-                    new_pdf = allocate_float(orig_nvpa, vperp.n, z.n, nspecies)
-                    for is ∈ 1:nspecies, iz ∈ 1:z.n, ivpa ∈ 1:orig_nvpa
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[ivpa,:,iz,is], vperp.grid,
-                            this_pdf[ivpa,:,iz,is], restart_vperp,
-                            restart_vperp_spectral)
-                    end
-                    this_pdf = new_pdf
-                end
-
-                if (
-                    (moments.evolve_density == restart_evolve_density &&
-                     moments.evolve_upar == restart_evolve_upar && moments.evolve_ppar ==
-                     restart_evolve_ppar)
-                    || (!moments.evolve_upar && !restart_evolve_upar &&
-                        !moments.evolve_ppar && !restart_evolve_ppar)
-                   )
-                    # No chages to velocity-space coordinates, so just interpolate from
-                    # one grid to the other
-                    if interpolation_needed["vpa"]
-                        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                        for is ∈ 1:nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivperp,iz,is], vpa.grid,
-                                this_pdf[:,ivperp,iz,is], restart_vpa,
-                                restart_vpa_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-                elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                        restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa = old_wpa + upar
-                    # => old_wpa = new_wpa - upar
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .- moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                        !restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa = old_wpa*vth
-                    # => old_wpa = new_wpa/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid ./ moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                        restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa = old_wpa*vth + upar
-                    # => old_wpa = (new_wpa - upar)/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. (vpa.grid - moments.charged.upar[iz,ir,is]) /
-                               moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                        !restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa + upar = old_wpa
-                    # => old_wpa = new_wpa + upar
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .+ moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                        !restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa + upar = old_wpa*vth
-                    # => old_wpa = (new_wpa + upar)/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. (vpa.grid + moments.charged.upar[iz,ir,is]) /
-                               moments.charged.vth
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                        restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa + upar = old_wpa*vth + upar
-                    # => old_wpa = new_wpa/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid ./ moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                        !restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth = old_wpa
-                    # => old_wpa = new_wpa*vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .* moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                        restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth = old_wpa + upar
-                    # => old_wpa = new_wpa*vth - upar/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = @. vpa.grid * moments.charged.vth[iz,ir,is] -
-                                              moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                        restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa*vth = old_wpa*vth + upar
-                    # => old_wpa = new_wpa - upar/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. vpa.grid -
-                               moments.charged.upar[iz,ir,is]/moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && moments.evolve_ppar &&
-                        !restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth + upar = old_wpa
-                    # => old_wpa = new_wpa*vth + upar
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = @. vpa.grid * moments.charged.vth[iz,ir,is] +
-                                              moments.charged.upar[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && moments.evolve_ppar &&
-                        restart_evolve_upar && !restart_evolve_ppar)
-                    # vpa = new_wpa*vth + upar = old_wpa + upar
-                    # => old_wpa = new_wpa*vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals = vpa.grid .* moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                elseif (moments.evolve_upar && moments.evolve_ppar &&
-                        !restart_evolve_upar && restart_evolve_ppar)
-                    # vpa = new_wpa*vth + upar = old_wpa*vth
-                    # => old_wpa = new_wpa + upar/vth
-                    new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
-                    for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
-                        restart_vpa_vals =
-                            @. vpa.grid +
-                               moments.charged.upar[iz,ir,is] / moments.charged.vth[iz,ir,is]
-                        @views interpolate_to_grid_1d!(
-                            new_pdf[:,ivperp,iz,is], restart_vpa_vals,
-                            this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
-                    end
-                    this_pdf = new_pdf
-                else
-                    # This should never happen, as all combinations of evolve_* options
-                    # should be handled above.
-                    error("Unsupported combination of moment-kinetic options:"
-                          * " evolve_density=", moments.evolve_density
-                          * " evolve_upar=", moments.evolve_upar
-                          * " evolve_ppar=", moments.evolve_ppar
-                          * " restart_evolve_density=", restart_evolve_density
-                          * " restart_evolve_upar=", restart_evolve_upar
-                          * " restart_evolve_ppar=", restart_evolve_ppar)
-                end
-                if moments.evolve_density && !restart_evolve_density
-                    # Need to normalise by density
-                    for is ∈ nspecies, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,is] ./= moments.charged.dens[iz,ir,is]
-                    end
-                elseif !moments.evolve_density && restart_evolve_density
-                    # Need to unnormalise by density
-                    for is ∈ nspecies, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,is] .*= moments.charged.dens[iz,ir,is]
-                    end
-                end
-                if moments.evolve_ppar && !restart_evolve_ppar
-                    # Need to normalise by vth
-                    for is ∈ nspecies, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,is] .*= moments.charged.vth[iz,ir,is]
-                    end
-                elseif !moments.evolve_ppar && restart_evolve_ppar
-                    # Need to unnormalise by vth
-                    for is ∈ nspecies, iz ∈ 1:z.n
-                        this_pdf[:,:,iz,is] ./= moments.charged.vth[iz,ir,is]
-                    end
-                end
-
-                return this_pdf
-            end
-
-            boundary_distributions.pdf_rboundary_charged[:,:,:,1,:] .=
-                load_charged_boundary_pdf("pdf_rboundary_charged_left", 1)
-            boundary_distributions.pdf_rboundary_charged[:,:,:,2,:] .=
-                load_charged_boundary_pdf("pdf_rboundary_charged_right", r.n)
+            boundary_distributions.pdf_rboundary_ion[:,:,:,1,:] .=
+                reload_ion_boundary_pdf(boundary_distributions_io,
+                                        "pdf_rboundary_ion_left", 1, moments, z, vperp,
+                                        vpa, z_range, vperp_range, vpa_range, restart_z,
+                                        restart_z_spectral, restart_vperp,
+                                        restart_vperp_spectral, restart_vpa,
+                                        restart_vpa_spectral, interpolation_needed,
+                                        restart_evolve_density, restart_evolve_upar,
+                                        restart_evolve_ppar)
+            boundary_distributions.pdf_rboundary_ion[:,:,:,2,:] .=
+                reload_ion_boundary_pdf(boundary_distributions_io,
+                                        "pdf_rboundary_ion_right", r.n, moments, z, vperp,
+                                        vpa, z_range, vperp_range, vpa_range, restart_z,
+                                        restart_z_spectral, restart_vperp,
+                                        restart_vperp_spectral, restart_vpa,
+                                        restart_vpa_spectral, interpolation_needed,
+                                        restart_evolve_density, restart_evolve_upar,
+                                        restart_evolve_ppar)
 
             if composition.n_neutral_species > 0
-                moments.neutral.dens .= load_moment("density_neutral")
+                moments.neutral.dens .= reload_moment("density_neutral", dynamic,
+                                                      time_index, r, z, r_range, z_range,
+                                                      restart_r, restart_r_spectral,
+                                                      restart_z, restart_z_spectral,
+                                                      interpolation_needed)
                 moments.neutral.dens_updated .= true
-                moments.neutral.uz .= load_moment("uz_neutral")
+                moments.neutral.uz .= reload_moment("uz_neutral", dynamic, time_index, r,
+                                                    z, r_range, z_range, restart_r,
+                                                    restart_r_spectral, restart_z,
+                                                    restart_z_spectral,
+                                                    interpolation_needed)
                 moments.neutral.uz_updated .= true
-                moments.neutral.pz .= load_moment("pz_neutral")
+                moments.neutral.pz .= reload_moment("pz_neutral", dynamic, time_index, r,
+                                                    z, r_range, z_range, restart_r,
+                                                    restart_r_spectral, restart_z,
+                                                    restart_z_spectral,
+                                                    interpolation_needed)
                 moments.neutral.pz_updated .= true
-                moments.neutral.qz .= load_moment("qz_neutral")
+                moments.neutral.qz .= reload_moment("qz_neutral", dynamic, time_index, r,
+                                                    z, r_range, z_range, restart_r,
+                                                    restart_r_spectral, restart_z,
+                                                    restart_z_spectral,
+                                                    interpolation_needed)
                 moments.neutral.qz_updated .= true
-                moments.neutral.vth .= load_moment("thermal_speed_neutral")
+                moments.neutral.vth .= reload_moment("thermal_speed_neutral", dynamic,
+                                                     time_index, r, z, r_range, z_range,
+                                                     restart_r, restart_r_spectral,
+                                                     restart_z, restart_z_spectral,
+                                                     interpolation_needed)
+                if moments.evolve_density || moments.evolve_upar || moments.evolve_ppar
+                    if "neutral_constraints_A_coefficient" ∈ keys(dynamic)
+                        moments.neutral.constraints_A_coefficient .=
+                            reload_moment("neutral_constraints_A_coefficient", dynamic,
+                                          time_index, r, z, r_range, z_range, restart_r,
+                                          restart_r_spectral, restart_z, restart_z_spectral,
+                                          interpolation_needed)
+                    elseif moments.neutral.constraints_A_coefficient !== nothing
+                        moments.neutral.constraints_A_coefficient .= 0.0
+                    end
+                    if "neutral_constraints_B_coefficient" ∈ keys(dynamic)
+                        moments.neutral.constraints_B_coefficient .=
+                            reload_moment("neutral_constraints_B_coefficient", dynamic,
+                                          time_index, r, z, r_range, z_range, restart_r,
+                                          restart_r_spectral, restart_z, restart_z_spectral,
+                                          interpolation_needed)
+                    elseif moments.neutral.constraints_B_coefficient !== nothing
+                        moments.neutral.constraints_B_coefficient .= 0.0
+                    end
+                    if "neutral_constraints_C_coefficient" ∈ keys(dynamic)
+                        moments.neutral.constraints_C_coefficient .=
+                            reload_moment("neutral_constraints_C_coefficient", dynamic,
+                                          time_index, r, z, r_range, z_range, restart_r,
+                                          restart_r_spectral, restart_z, restart_z_spectral,
+                                          interpolation_needed)
+                    elseif moments.neutral.constraints_C_coefficient !== nothing
+                        moments.neutral.constraints_C_coefficient .= 0.0
+                    end
+                end
 
                 if "external_source_neutral_controller_integral" ∈ get_variable_keys(dynamic) &&
                         length(moments.neutral.external_source_controller_integral) == 1
@@ -1283,579 +804,46 @@ function reload_evolving_fields!(pdf, moments, boundary_distributions,
                                    time_index)
                 elseif length(moments.neutral.external_source_controller_integral) > 1
                     moments.neutral.external_source_controller_integral .=
-                        load_moment("external_source_neutral_controller_integral")
-                end
-
-                function load_neutral_pdf()
-                    this_pdf = load_slice(dynamic, "f_neutral", vz_range, vr_range,
-                                          vzeta_range, z_range, r_range, :, time_index)
-                    orig_nvz, orig_nvr, orig_nvzeta, orig_nz, orig_nr, nspecies =
-                        size(this_pdf)
-                    if interpolation_needed["r"]
-                        new_pdf = allocate_float(orig_nvz, orig_nvr, orig_nvzeta, orig_nz,
-                                                 r.n, nspecies)
-                        for is ∈ 1:nspecies, iz ∈ 1:orig_nz, ivzeta ∈ 1:orig_nvzeta,
-                                ivr ∈ 1:orig_nvr, ivz ∈ 1:orig_nvz
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[ivz,ivr,ivzeta,iz,:,is], r.grid,
-                                this_pdf[ivz,ivr,ivzeta,iz,:,is], restart_r,
-                                restart_r_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-                    if interpolation_needed["z"]
-                        new_pdf = allocate_float(orig_nvz, orig_nvr, orig_nvzeta, z.n,
-                                                 r.n, nspecies)
-                        for is ∈ 1:nspecies, ir ∈ 1:r.n, ivzeta ∈ 1:orig_nvzeta,
-                                ivr ∈ 1:orig_nvr, ivz ∈ 1:orig_nvz
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[ivz,ivr,ivzeta,:,ir,is], z.grid,
-                                this_pdf[ivz,ivr,ivzeta,:,ir,is], restart_z,
-                                restart_z_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-
-                    # Current moment-kinetic implementation is only 1V, so no need
-                    # to handle normalised vzeta or vr coordinates. This will need
-                    # to change when/if 3V moment-kinetics is implemented.
-                    if interpolation_needed["vzeta"]
-                        new_pdf = allocate_float(orig_nvz, orig_nvr, vzeta.n, z.n, r.n,
-                                                 nspecies)
-                        for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:orig_nvr,
-                                ivz ∈ 1:orig_nvz
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[ivz,ivr,:,iz,ir,is], vzeta.grid,
-                                this_pdf[ivz,ivr,:,iz,ir,is], restart_vzeta,
-                                restart_vzeta_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-                    if interpolation_needed["vr"]
-                        new_pdf = allocate_float(orig_nvz, vr.n, vzeta.n, z.n, r.n,
-                                                 nspecies)
-                        for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n,
-                                ivzeta ∈ 1:vzeta.n, ivz ∈ 1:orig_nvz
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[ivz,:,ivzeta,iz,ir,is], vr.grid,
-                                this_pdf[ivz,:,ivzeta,iz,ir,is], restart_vr,
-                                restart_vr_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-
-                    if (
-                        (moments.evolve_density == restart_evolve_density &&
-                         moments.evolve_upar == restart_evolve_upar &&
-                         moments.evolve_ppar == restart_evolve_ppar)
-                        || (!moments.evolve_upar && !restart_evolve_upar &&
-                            !moments.evolve_ppar && !restart_evolve_ppar)
-                       )
-                        # No chages to velocity-space coordinates, so just interpolate from
-                        # one grid to the other
-                        if interpolation_needed["vz"]
-                            new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                            for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                    ivzeta ∈ 1:vzeta.n
-                                @views interpolate_to_grid_1d!(
-                                    new_pdf[:,ivr,ivzeta,iz,ir,is], vz.grid,
-                                    this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                    restart_vz_spectral)
-                            end
-                            this_pdf = new_pdf
-                        end
-                    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                            restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa = old_wpa + upar
-                        # => old_wpa = new_wpa - upar
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivzeta ∈ 1:vzeta.n,
-                                ivr ∈ 1:vr.n
-                            restart_vz_vals = vz.grid .- moments.neutral.uz[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                            !restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa = old_wpa*vth
-                        # => old_wpa = new_wpa/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                            restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa = old_wpa*vth + upar
-                        # => old_wpa = (new_wpa - upar)/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. (vz.grid - moments.neutral.uz[iz,ir,is]) /
-                                   moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                            !restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa + upar = old_wpa
-                        # => old_wpa = new_wpa + upar
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid .+ moments.neutral.uz[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz, restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                            !restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa + upar = old_wpa*vth
-                        # => old_wpa = (new_wpa + upar)/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. (vz.grid + moments.neutral.uz[iz,ir,is]) /
-                                    moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                            restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa + upar = old_wpa*vth + upar
-                        # => old_wpa = new_wpa/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                            !restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth = old_wpa
-                        # => old_wpa = new_wpa*vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid .* moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                            restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth = old_wpa + upar
-                        # => old_wpa = new_wpa*vth - upar/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid * moments.neutral.vth[iz,ir,is] -
-                                   moments.neutral.upar[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                            restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa*vth = old_wpa*vth + upar
-                        # => old_wpa = new_wpa - upar/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid -
-                                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && moments.evolve_ppar &&
-                            !restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth + upar = old_wpa
-                        # => old_wpa = new_wpa*vth + upar
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid * moments.neutral.vth[iz,ir,is] +
-                                   moments.neutral.uz[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && moments.evolve_ppar &&
-                            restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth + upar = old_wpa + upar
-                        # => old_wpa = new_wpa*vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid .* moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && moments.evolve_ppar &&
-                            !restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa*vth + upar = old_wpa*vth
-                        # => old_wpa = new_wpa + upar/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid +
-                                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    else
-                        # This should never happen, as all combinations of evolve_* options
-                        # should be handled above.
-                        error("Unsupported combination of moment-kinetic options:"
-                              * " evolve_density=", moments.evolve_density
-                              * " evolve_upar=", moments.evolve_upar
-                              * " evolve_ppar=", moments.evolve_ppar
-                              * " restart_evolve_density=", restart_evolve_density
-                              * " restart_evolve_upar=", restart_evolve_upar
-                              * " restart_evolve_ppar=", restart_evolve_ppar)
-                    end
-                    if moments.evolve_density && !restart_evolve_density
-                        # Need to normalise by density
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,ir,is] ./= moments.neutral.dens[iz,ir,is]
-                        end
-                    elseif !moments.evolve_density && restart_evolve_density
-                        # Need to unnormalise by density
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,ir,is] .*= moments.neutral.dens[iz,ir,is]
-                        end
-                    end
-                    if moments.evolve_ppar && !restart_evolve_ppar
-                        # Need to normalise by vth
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,ir,is] .*= moments.neutral.vth[iz,ir,is]
-                        end
-                    elseif !moments.evolve_ppar && restart_evolve_ppar
-                        # Need to unnormalise by vth
-                        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,ir,is] ./= moments.neutral.vth[iz,ir,is]
-                        end
-                    end
-
-                    return this_pdf
+                        reload_moment("external_source_neutral_controller_integral",
+                                      dynamic, time_index, r, z, r_range, z_range,
+                                      restart_r, restart_r_spectral, restart_z,
+                                      restart_z_spectral, interpolation_needed)
                 end
 
-                pdf.neutral.norm .= load_neutral_pdf()
-
-                function load_neutral_boundary_pdf(var_name, ir)
-                    this_pdf = load_slice(boundary_distributions_io, var_name, vz_range,
-                                          vr_range, vzeta_range, z_range, :)
-                    orig_nvz, orig_nvr, orig_nvzeta, orig_nz, nspecies = size(this_pdf)
-                    if interpolation_needed["z"]
-                        new_pdf = allocate_float(orig_nvz, orig_nvr, orig_nvzeta, z.n,
-                                                 nspecies)
-                        for is ∈ 1:nspecies, ivzeta ∈ 1:orig_nvzeta, ivr ∈ 1:orig_nvr,
-                                ivz ∈ 1:orig_nvz
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[ivz,ivr,ivzeta,:,is], z.grid,
-                                this_pdf[ivz,ivr,ivzeta,:,is], restart_z,
-                                restart_z_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-
-                    # Current moment-kinetic implementation is only 1V, so no need
-                    # to handle normalised vzeta or vr coordinates. This will need
-                    # to change when/if 3V moment-kinetics is implemented.
-                    if interpolation_needed["vzeta"]
-                        new_pdf = allocate_float(orig_nvz, orig_nvr, vzeta.n, z.n,
-                                                 nspecies)
-                        for is ∈ 1:nspecies, iz ∈ 1:z.n, ivr ∈ 1:orig_nvr,
-                                ivz ∈ 1:orig_nvz
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[ivz,ivr,:,iz,is], vzeta.grid,
-                                this_pdf[ivz,ivr,:,iz,is], restart_vzeta,
-                                restart_vzeta_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-                    if interpolation_needed["vr"]
-                        new_pdf = allocate_float(orig_nvz, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ 1:nspecies, iz ∈ 1:z.n, ivzeta ∈ 1:vzeta.n,
-                                ivz ∈ 1:orig_nvz
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[ivz,:,ivzeta,iz,is], vr.grid,
-                                this_pdf[ivz,:,ivzeta,iz,is], restart_vr,
-                                restart_vr_spectral)
-                        end
-                        this_pdf = new_pdf
-                    end
-
-                    if (
-                        (moments.evolve_density == restart_evolve_density &&
-                         moments.evolve_upar == restart_evolve_upar && moments.evolve_ppar ==
-                         restart_evolve_ppar)
-                        || (!moments.evolve_upar && !restart_evolve_upar &&
-                            !moments.evolve_ppar && !restart_evolve_ppar)
-                       )
-                        # No chages to velocity-space coordinates, so just interpolate from
-                        # one grid to the other
-                        if interpolation_needed["vz"]
-                            new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                            for is ∈ 1:nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
-                                    ivzeta ∈ 1:vzeta.n
-                                @views interpolate_to_grid_1d!(
-                                    new_pdf[:,ivr,ivzeta,iz,is], vz.grid,
-                                    this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                    restart_vz_spectral)
-                            end
-                            this_pdf = new_pdf
-                        end
-                    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                            restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa = old_wpa + upar
-                        # => old_wpa = new_wpa - upar
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivzeta ∈ 1:vzeta.n, ivr ∈ 1:vr.n
-                            restart_vz_vals = vz.grid .- moments.neutral.uz[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                            !restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa = old_wpa*vth
-                        # => old_wpa = new_wpa/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
-                            restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa = old_wpa*vth + upar
-                        # => old_wpa = (new_wpa - upar)/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. (vz.grid - moments.neutral.uz[iz,ir,is]) /
-                                   moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                            !restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa + upar = old_wpa
-                        # => old_wpa = new_wpa + upar
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid .+
-                                              moments.neutral.uz[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                            !restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa + upar = old_wpa*vth
-                        # => old_wpa = (new_wpa + upar)/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. (vz.grid + moments.neutral.uz[iz,ir,is]) /
-                                   moments.neutral.vth
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && !moments.evolve_ppar &&
-                            restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa + upar = old_wpa*vth + upar
-                        # => old_wpa = new_wpa/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                            !restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth = old_wpa
-                        # => old_wpa = new_wpa*vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid .*
-                                              moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                            restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth = old_wpa + upar
-                        # => old_wpa = new_wpa*vth - upar/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid * moments.neutral.vth[iz,ir,is] -
-                                   moments.neutral.upar[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (!moments.evolve_upar && moments.evolve_ppar &&
-                            restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa*vth = old_wpa*vth + upar
-                        # => old_wpa = new_wpa - upar/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid -
-                                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && moments.evolve_ppar &&
-                            !restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth + upar = old_wpa
-                        # => old_wpa = new_wpa*vth + upar
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid * moments.neutral.vth[iz,ir,is] +
-                                   moments.neutral.uz[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && moments.evolve_ppar &&
-                            restart_evolve_upar && !restart_evolve_ppar)
-                        # vpa = new_wpa*vth + upar = old_wpa + upar
-                        # => old_wpa = new_wpa*vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals = vz.grid .* moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                        this_pdf = new_pdf
-                    elseif (moments.evolve_upar && moments.evolve_ppar &&
-                            !restart_evolve_upar && restart_evolve_ppar)
-                        # vpa = new_wpa*vth + upar = old_wpa*vth
-                        # => old_wpa = new_wpa + upar/vth
-                        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
-                        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
-                            restart_vz_vals =
-                                @. vz.grid +
-                                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
-                            @views interpolate_to_grid_1d!(
-                                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
-                                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
-                                restart_vz_spectral)
-                        end
-                    else
-                        # This should never happen, as all combinations of evolve_* options
-                        # should be handled above.
-                        error("Unsupported combination of moment-kinetic options:"
-                              * " evolve_density=", moments.evolve_density
-                              * " evolve_upar=", moments.evolve_upar
-                              * " evolve_ppar=", moments.evolve_ppar
-                              * " restart_evolve_density=", restart_evolve_density
-                              * " restart_evolve_upar=", restart_evolve_upar
-                              * " restart_evolve_ppar=", restart_evolve_ppar)
-                    end
-                    if moments.evolve_density && !restart_evolve_density
-                        # Need to normalise by density
-                        for is ∈ nspecies, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,is] ./= moments.neutral.dens[iz,ir,is]
-                        end
-                    elseif !moments.evolve_density && restart_evolve_density
-                        # Need to unnormalise by density
-                        for is ∈ nspecies, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,is] .*= moments.neutral.dens[iz,ir,is]
-                        end
-                    end
-                    if moments.evolve_ppar && !restart_evolve_ppar
-                        # Need to normalise by vth
-                        for is ∈ nspecies, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,is] .*= moments.neutral.vth[iz,ir,is]
-                        end
-                    elseif !moments.evolve_ppar && restart_evolve_ppar
-                        # Need to unnormalise by vth
-                        for is ∈ nspecies, iz ∈ 1:z.n
-                            this_pdf[:,:,:,iz,is] ./= moments.neutral.vth[iz,ir,is]
-                        end
-                    end
-
-                    return this_pdf
-                end
+                pdf.neutral.norm .=
+                    reload_neutral_pdf(dynamic, time_index, moments, r, z, vzeta, vr, vz,
+                                       r_range, z_range, vzeta_range, vr_range, vz_range,
+                                       restart_r, restart_r_spectral, restart_z,
+                                       restart_z_spectral, restart_vzeta,
+                                       restart_vzeta_spectral, restart_vr,
+                                       restart_vr_spectral, restart_vz,
+                                       restart_vz_spectral, interpolation_needed,
+                                       restart_evolve_density, restart_evolve_upar,
+                                       restart_evolve_ppar)
 
                 boundary_distributions.pdf_rboundary_neutral[:,:,:,:,1,:] .=
-                    load_neutral_boundary_pdf("pdf_rboundary_neutral_left", 1)
+                    reload_neutral_boundary_pdf(boundary_distributions_io,
+                                                "pdf_rboundary_neutral_left", 1, moments,
+                                                z, vzeta, vr, vz, z_range, vzeta_range,
+                                                vr_range, vz_range, restart_z,
+                                                restart_z_spectral, restart_vzeta,
+                                                restart_vzeta_spectral, restart_vr,
+                                                restart_vr_spectral, restart_vz,
+                                                restart_vz_spectral, interpolation_needed,
+                                                restart_evolve_density,
+                                                restart_evolve_upar, restart_evolve_ppar)
                 boundary_distributions.pdf_rboundary_neutral[:,:,:,:,2,:] .=
-                    load_neutral_boundary_pdf("pdf_rboundary_neutral_right", r.n)
+                    reload_neutral_boundary_pdf(boundary_distributions_io,
+                                                "pdf_rboundary_neutral_right", r.n,
+                                                moments, z, vzeta, vr, vz, z_range,
+                                                vzeta_range, vr_range, vz_range,
+                                                restart_z, restart_z_spectral,
+                                                restart_vzeta, restart_vzeta_spectral,
+                                                restart_vr, restart_vr_spectral,
+                                                restart_vz, restart_vz_spectral,
+                                                interpolation_needed,
+                                                restart_evolve_density,
+                                                restart_evolve_upar, restart_evolve_ppar)
             end
 
             if "dt" ∈ keys(dynamic)
@@ -1870,7 +858,7 @@ function reload_evolving_fields!(pdf, moments, boundary_distributions,
                 # timestep, so just leave the value of "dt_before_last_fail" from
                 # the input file.
                 dt_before_last_fail = load_slice(dynamic, "dt_before_last_fail",
-                                                 time_index)
+                                                time_index)
             end
         finally
             close(fid)
@@ -1880,6 +868,1220 @@ function reload_evolving_fields!(pdf, moments, boundary_distributions,
     return code_time, dt, dt_before_last_fail, previous_runs_info, time_index
 end
 
+function load_restart_coordinates(fid, r, z, vperp, vpa, vzeta, vr, vz, parallel_io)
+    if parallel_io
+        restart_z, restart_z_spectral, _ =
+            load_coordinate_data(fid, "z"; irank=z.irank, nrank=z.nrank)
+        restart_r, restart_r_spectral, _ =
+            load_coordinate_data(fid, "r"; irank=r.irank, nrank=r.nrank)
+        restart_vperp, restart_vperp_spectral, _ =
+            load_coordinate_data(fid, "vperp"; irank=vperp.irank, nrank=vperp.nrank)
+        restart_vpa, restart_vpa_spectral, _ =
+            load_coordinate_data(fid, "vpa"; irank=vpa.irank, nrank=vpa.nrank)
+        restart_vzeta, restart_vzeta_spectral, _ =
+            load_coordinate_data(fid, "vzeta"; irank=vzeta.irank, nrank=vzeta.nrank)
+        restart_vr, restart_vr_spectral, _ =
+            load_coordinate_data(fid, "vr"; irank=vr.irank, nrank=vr.nrank)
+        restart_vz, restart_vz_spectral, _ =
+            load_coordinate_data(fid, "vz"; irank=vz.irank, nrank=vz.nrank)
+    else
+        restart_z, restart_z_spectral, _ = load_coordinate_data(fid, "z")
+        restart_r, restart_r_spectral, _ = load_coordinate_data(fid, "r")
+        restart_vperp, restart_vperp_spectral, _ =
+            load_coordinate_data(fid, "vperp")
+        restart_vpa, restart_vpa_spectral, _ = load_coordinate_data(fid, "vpa")
+        restart_vzeta, restart_vzeta_spectral, _ =
+            load_coordinate_data(fid, "vzeta")
+        restart_vr, restart_vr_spectral, _ = load_coordinate_data(fid, "vr")
+        restart_vz, restart_vz_spectral, _ = load_coordinate_data(fid, "vz")
+
+        if restart_r.nrank != r.nrank
+            error("Not using parallel I/O, and distributed MPI layout has "
+                  * "changed: now r.nrank=$(r.nrank), but we are trying to "
+                  * "restart from files ith restart_r.nrank=$(restart_r.nrank).")
+        end
+        if restart_z.nrank != z.nrank
+            error("Not using parallel I/O, and distributed MPI layout has "
+                  * "changed: now z.nrank=$(z.nrank), but we are trying to "
+                  * "restart from files ith restart_z.nrank=$(restart_z.nrank).")
+        end
+        if restart_vperp.nrank != vperp.nrank
+            error("Not using parallel I/O, and distributed MPI layout has "
+                  * "changed: now vperp.nrank=$(vperp.nrank), but we are trying to "
+                  * "restart from files ith restart_vperp.nrank=$(restart_vperp.nrank).")
+        end
+        if restart_vpa.nrank != vpa.nrank
+            error("Not using parallel I/O, and distributed MPI layout has "
+                  * "changed: now vpa.nrank=$(vpa.nrank), but we are trying to "
+                  * "restart from files ith restart_vpa.nrank=$(restart_vpa.nrank).")
+        end
+        if restart_vzeta.nrank != vzeta.nrank
+            error("Not using parallel I/O, and distributed MPI layout has "
+                  * "changed: now vzeta.nrank=$(vzeta.nrank), but we are trying to "
+                  * "restart from files ith restart_vzeta.nrank=$(restart_vzeta.nrank).")
+        end
+        if restart_vr.nrank != vr.nrank
+            error("Not using parallel I/O, and distributed MPI layout has "
+                  * "changed: now vr.nrank=$(vr.nrank), but we are trying to "
+                  * "restart from files ith restart_vr.nrank=$(restart_vr.nrank).")
+        end
+        if restart_vz.nrank != vz.nrank
+            error("Not using parallel I/O, and distributed MPI layout has "
+                  * "changed: now vz.nrank=$(vz.nrank), but we are trying to "
+                  * "restart from files ith restart_vz.nrank=$(restart_vz.nrank).")
+        end
+    end
+
+    return restart_r, restart_r_spectral, restart_z, restart_z_spectral, restart_vperp,
+           restart_vperp_spectral, restart_vpa, restart_vpa_spectral, restart_vzeta,
+           restart_vzeta_spectral, restart_vr,restart_vr_spectral, restart_vz,
+           restart_vz_spectral
+end
+
+function get_reload_ranges(parallel_io, restart_r, restart_z, restart_vperp, restart_vpa,
+                           restart_vzeta, restart_vr, restart_vz)
+    if parallel_io
+        function get_range(coord)
+            if coord === nothing
+                return 1:0
+            elseif coord.irank == coord.nrank - 1
+                return coord.global_io_range
+            else
+                # Need to modify the range to load the end-point that is duplicated on
+                # the next process
+                this_range = coord.global_io_range
+                return this_range.start:(this_range.stop+1)
+            end
+        end
+        r_range = get_range(restart_r)
+        z_range = get_range(restart_z)
+        vperp_range = get_range(restart_vperp)
+        vpa_range = get_range(restart_vpa)
+        vzeta_range = get_range(restart_vzeta)
+        vr_range = get_range(restart_vr)
+        vz_range = get_range(restart_vz)
+    else
+        r_range = (:)
+        z_range = (:)
+        vperp_range = (:)
+        vpa_range = (:)
+        vzeta_range = (:)
+        vr_range = (:)
+        vz_range = (:)
+    end
+    return r_range, z_range, vperp_range, vpa_range, vzeta_range, vr_range, vz_range
+end
+
+function reload_moment(var_name, dynamic, time_index, r, z, r_range, z_range, restart_r,
+                       restart_r_spectral, restart_z, restart_z_spectral,
+                       interpolation_needed)
+    moment = load_slice(dynamic, var_name, z_range, r_range, :, time_index)
+    orig_nz, orig_nr, nspecies = size(moment)
+    if interpolation_needed["r"]
+        new_moment = allocate_float(orig_nz, r.n, nspecies)
+        for is ∈ 1:nspecies, iz ∈ 1:orig_nz
+            @views interpolate_to_grid_1d!(new_moment[iz,:,is], r.grid,
+                                           moment[iz,:,is], restart_r,
+                                           restart_r_spectral)
+        end
+        moment = new_moment
+    end
+    if interpolation_needed["z"]
+        new_moment = allocate_float(z.n, r.n, nspecies)
+        for is ∈ 1:nspecies, ir ∈ 1:r.n
+            @views interpolate_to_grid_1d!(new_moment[:,ir,is], z.grid,
+                                           moment[:,ir,is], restart_z,
+                                           restart_z_spectral)
+        end
+        moment = new_moment
+    end
+    return moment
+end
+
+function reload_ion_pdf(dynamic, time_index, moments, r, z, vperp, vpa, r_range, z_range,
+                        vperp_range, vpa_range, restart_r, restart_r_spectral, restart_z,
+                        restart_z_spectral, restart_vperp, restart_vperp_spectral,
+                        restart_vpa, restart_vpa_spectral, interpolation_needed,
+                        restart_evolve_density, restart_evolve_upar, restart_evolve_ppar)
+
+    this_pdf = load_slice(dynamic, "f", vpa_range, vperp_range, z_range,
+        r_range, :, time_index)
+    orig_nvpa, orig_nvperp, orig_nz, orig_nr, nspecies = size(this_pdf)
+    if interpolation_needed["r"]
+        new_pdf = allocate_float(orig_nvpa, orig_nvperp, orig_nz, r.n, nspecies)
+        for is ∈ 1:nspecies, iz ∈ 1:orig_nz, ivperp ∈ 1:orig_nvperp,
+            ivpa ∈ 1:orig_nvpa
+            @views interpolate_to_grid_1d!(
+                       new_pdf[ivpa,ivperp,iz,:,is], r.grid,
+                       this_pdf[ivpa,ivperp,iz,:,is], restart_r,
+                       restart_r_spectral)
+        end
+        this_pdf = new_pdf
+    end
+    if interpolation_needed["z"]
+        new_pdf = allocate_float(orig_nvpa, orig_nvperp, z.n, r.n, nspecies)
+        for is ∈ 1:nspecies, ir ∈ 1:r.n, ivperp ∈ 1:orig_nvperp,
+            ivpa ∈ 1:orig_nvpa
+            @views interpolate_to_grid_1d!(
+                       new_pdf[ivpa,ivperp,:,ir,is], z.grid,
+                       this_pdf[ivpa,ivperp,:,ir,is], restart_z,
+                       restart_z_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    # Current moment-kinetic implementation is only 1V, so no need to handle a
+    # normalised vperp coordinate. This will need to change when 2V
+    # moment-kinetics is implemented.
+    if interpolation_needed["vperp"]
+        new_pdf = allocate_float(orig_nvpa, vperp.n, z.n, r.n, nspecies)
+        for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivpa ∈ 1:orig_nvpa
+            @views interpolate_to_grid_1d!(
+                       new_pdf[ivpa,:,iz,ir,is], vperp.grid,
+                       this_pdf[ivpa,:,iz,ir,is], restart_vperp,
+                       restart_vperp_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    if (
+        (moments.evolve_density == restart_evolve_density &&
+         moments.evolve_upar == restart_evolve_upar && moments.evolve_ppar ==
+         restart_evolve_ppar)
+        || (!moments.evolve_upar && !restart_evolve_upar &&
+            !moments.evolve_ppar && !restart_evolve_ppar)
+       )
+        # No chages to velocity-space coordinates, so just interpolate from
+        # one grid to the other
+        if interpolation_needed["vpa"]
+            new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+            for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+                @views interpolate_to_grid_1d!(
+                           new_pdf[:,ivperp,iz,ir,is], vpa.grid,
+                           this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                           restart_vpa_spectral)
+            end
+            this_pdf = new_pdf
+        end
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa + upar
+        # => old_wpa = new_wpa - upar
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .- moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid ./ moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth + upar
+        # => old_wpa = (new_wpa - upar)/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. (vpa.grid - moments.ion.upar[iz,ir,is]) / moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa
+        # => old_wpa = new_wpa + upar
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .+ moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth
+        # => old_wpa = (new_wpa + upar)/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. (vpa.grid + moments.ion.upar[iz,ir,is]) / moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth + upar
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid ./ moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .* moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa + upar
+        # => old_wpa = new_wpa*vth - upar/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = @. vpa.grid * moments.ion.vth[iz,ir,is] - moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa*vth + upar
+        # => old_wpa = new_wpa - upar/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. vpa.grid - moments.ion.upar[iz,ir,is]/moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa
+        # => old_wpa = new_wpa*vth + upar
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = @. vpa.grid * moments.ion.vth[iz,ir,is] + moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa + upar
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .* moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa*vth
+        # => old_wpa = new_wpa + upar/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. vpa.grid + moments.ion.upar[iz,ir,is] / moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                       new_pdf[:,ivperp,iz,ir,is], restart_vpa_vals,
+                       this_pdf[:,ivperp,iz,ir,is], restart_vpa,
+                       restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    else
+        # This should never happen, as all combinations of evolve_* options
+        # should be handled above.
+        error("Unsupported combination of moment-kinetic options:"
+              * " evolve_density=", moments.evolve_density
+              * " evolve_upar=", moments.evolve_upar
+              * " evolve_ppar=", moments.evolve_ppar
+              * " restart_evolve_density=", restart_evolve_density
+              * " restart_evolve_upar=", restart_evolve_upar
+              * " restart_evolve_ppar=", restart_evolve_ppar)
+    end
+    if moments.evolve_density && !restart_evolve_density
+        # Need to normalise by density
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,iz,ir,is] ./= moments.ion.dens[iz,ir,is]
+        end
+    elseif !moments.evolve_density && restart_evolve_density
+        # Need to unnormalise by density
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,iz,ir,is] .*= moments.ion.dens[iz,ir,is]
+        end
+    end
+    if moments.evolve_ppar && !restart_evolve_ppar
+        # Need to normalise by vth
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,iz,ir,is] .*= moments.ion.vth[iz,ir,is]
+        end
+    elseif !moments.evolve_ppar && restart_evolve_ppar
+        # Need to unnormalise by vth
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,iz,ir,is] ./= moments.ion.vth[iz,ir,is]
+        end
+    end
+
+    return this_pdf
+end
+
+function reload_ion_boundary_pdf(boundary_distributions_io, var_name, ir, moments, z,
+                                 vperp, vpa, z_range, vperp_range, vpa_range, restart_z,
+                                 restart_z_spectral, restart_vperp,
+                                 restart_vperp_spectral, restart_vpa,
+                                 restart_vpa_spectral, interpolation_needed,
+                                 restart_evolve_density, restart_evolve_upar,
+                                 restart_evolve_ppar)
+    this_pdf = load_slice(boundary_distributions_io, var_name, vpa_range,
+        vperp_range, z_range, :)
+    orig_nvpa, orig_nvperp, orig_nz, nspecies = size(this_pdf)
+    if interpolation_needed["z"]
+        new_pdf = allocate_float(orig_nvpa, orig_nvperp, z.n, nspecies)
+        for is ∈ 1:nspecies, ivperp ∈ 1:orig_nvperp,
+            ivpa ∈ 1:orig_nvpa
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[ivpa,ivperp,:,is], z.grid,
+                                           this_pdf[ivpa,ivperp,:,is], restart_z,
+                                           restart_z_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    # Current moment-kinetic implementation is only 1V, so no need to handle a
+    # normalised vperp coordinate. This will need to change when 2V
+    # moment-kinetics is implemented.
+    if interpolation_needed["vperp"]
+        new_pdf = allocate_float(orig_nvpa, vperp.n, z.n, nspecies)
+        for is ∈ 1:nspecies, iz ∈ 1:z.n, ivpa ∈ 1:orig_nvpa
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[ivpa,:,iz,is], vperp.grid,
+                                           this_pdf[ivpa,:,iz,is], restart_vperp,
+                                           restart_vperp_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    if (
+        (moments.evolve_density == restart_evolve_density &&
+         moments.evolve_upar == restart_evolve_upar && moments.evolve_ppar ==
+         restart_evolve_ppar)
+        || (!moments.evolve_upar && !restart_evolve_upar &&
+            !moments.evolve_ppar && !restart_evolve_ppar)
+       )
+        # No chages to velocity-space coordinates, so just interpolate from
+        # one grid to the other
+        if interpolation_needed["vpa"]
+            new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+            for is ∈ 1:nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+                @views interpolate_to_grid_1d!(
+                                               new_pdf[:,ivperp,iz,is], vpa.grid,
+                                               this_pdf[:,ivperp,iz,is], restart_vpa,
+                                               restart_vpa_spectral)
+            end
+            this_pdf = new_pdf
+        end
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa + upar
+        # => old_wpa = new_wpa - upar
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .- moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid ./ moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth + upar
+        # => old_wpa = (new_wpa - upar)/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. (vpa.grid - moments.ion.upar[iz,ir,is]) /
+            moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa
+        # => old_wpa = new_wpa + upar
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .+ moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth
+        # => old_wpa = (new_wpa + upar)/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. (vpa.grid + moments.ion.upar[iz,ir,is]) /
+            moments.ion.vth
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth + upar
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid ./ moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .* moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa + upar
+        # => old_wpa = new_wpa*vth - upar/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = @. vpa.grid * moments.ion.vth[iz,ir,is] -
+            moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa*vth + upar
+        # => old_wpa = new_wpa - upar/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. vpa.grid -
+            moments.ion.upar[iz,ir,is]/moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa
+        # => old_wpa = new_wpa*vth + upar
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = @. vpa.grid * moments.ion.vth[iz,ir,is] +
+            moments.ion.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa + upar
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals = vpa.grid .* moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa*vth
+        # => old_wpa = new_wpa + upar/vth
+        new_pdf = allocate_float(vpa.n, vperp.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivperp ∈ 1:vperp.n
+            restart_vpa_vals =
+            @. vpa.grid +
+            moments.ion.upar[iz,ir,is] / moments.ion.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                                           new_pdf[:,ivperp,iz,is], restart_vpa_vals,
+                                           this_pdf[:,ivperp,iz,is], restart_vpa, restart_vpa_spectral)
+        end
+        this_pdf = new_pdf
+    else
+        # This should never happen, as all combinations of evolve_* options
+        # should be handled above.
+        error("Unsupported combination of moment-kinetic options:"
+              * " evolve_density=", moments.evolve_density
+              * " evolve_upar=", moments.evolve_upar
+              * " evolve_ppar=", moments.evolve_ppar
+              * " restart_evolve_density=", restart_evolve_density
+              * " restart_evolve_upar=", restart_evolve_upar
+              * " restart_evolve_ppar=", restart_evolve_ppar)
+    end
+    if moments.evolve_density && !restart_evolve_density
+        # Need to normalise by density
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,iz,is] ./= moments.ion.dens[iz,ir,is]
+        end
+    elseif !moments.evolve_density && restart_evolve_density
+        # Need to unnormalise by density
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,iz,is] .*= moments.ion.dens[iz,ir,is]
+        end
+    end
+    if moments.evolve_ppar && !restart_evolve_ppar
+        # Need to normalise by vth
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,iz,is] .*= moments.ion.vth[iz,ir,is]
+        end
+    elseif !moments.evolve_ppar && restart_evolve_ppar
+        # Need to unnormalise by vth
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,iz,is] ./= moments.ion.vth[iz,ir,is]
+        end
+    end
+
+    return this_pdf
+end
+
+function reload_neutral_pdf(dynamic, time_index, moments, r, z, vzeta, vr, vz, r_range,
+                            z_range, vzeta_range, vr_range, vz_range, restart_r,
+                            restart_r_spectral, restart_z, restart_z_spectral,
+                            restart_vzeta, restart_vzeta_spectral, restart_vr,
+                            restart_vr_spectral, restart_vz, restart_vz_spectral,
+                            interpolation_needed, restart_evolve_density,
+                            restart_evolve_upar, restart_evolve_ppar)
+    this_pdf = load_slice(dynamic, "f_neutral", vz_range, vr_range,
+                          vzeta_range, z_range, r_range, :, time_index)
+    orig_nvz, orig_nvr, orig_nvzeta, orig_nz, orig_nr, nspecies =
+        size(this_pdf)
+    if interpolation_needed["r"]
+        new_pdf = allocate_float(orig_nvz, orig_nvr, orig_nvzeta, orig_nz,
+                                 r.n, nspecies)
+        for is ∈ 1:nspecies, iz ∈ 1:orig_nz, ivzeta ∈ 1:orig_nvzeta,
+                ivr ∈ 1:orig_nvr, ivz ∈ 1:orig_nvz
+            @views interpolate_to_grid_1d!(
+                new_pdf[ivz,ivr,ivzeta,iz,:,is], r.grid,
+                this_pdf[ivz,ivr,ivzeta,iz,:,is], restart_r,
+                restart_r_spectral)
+        end
+        this_pdf = new_pdf
+    end
+    if interpolation_needed["z"]
+        new_pdf = allocate_float(orig_nvz, orig_nvr, orig_nvzeta, z.n,
+                                 r.n, nspecies)
+        for is ∈ 1:nspecies, ir ∈ 1:r.n, ivzeta ∈ 1:orig_nvzeta,
+                ivr ∈ 1:orig_nvr, ivz ∈ 1:orig_nvz
+            @views interpolate_to_grid_1d!(
+                new_pdf[ivz,ivr,ivzeta,:,ir,is], z.grid,
+                this_pdf[ivz,ivr,ivzeta,:,ir,is], restart_z,
+                restart_z_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    # Current moment-kinetic implementation is only 1V, so no need
+    # to handle normalised vzeta or vr coordinates. This will need
+    # to change when/if 3V moment-kinetics is implemented.
+    if interpolation_needed["vzeta"]
+        new_pdf = allocate_float(orig_nvz, orig_nvr, vzeta.n, z.n, r.n,
+                                 nspecies)
+        for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:orig_nvr,
+                ivz ∈ 1:orig_nvz
+            @views interpolate_to_grid_1d!(
+                new_pdf[ivz,ivr,:,iz,ir,is], vzeta.grid,
+                this_pdf[ivz,ivr,:,iz,ir,is], restart_vzeta,
+                restart_vzeta_spectral)
+        end
+        this_pdf = new_pdf
+    end
+    if interpolation_needed["vr"]
+        new_pdf = allocate_float(orig_nvz, vr.n, vzeta.n, z.n, r.n,
+                                 nspecies)
+        for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n,
+                ivzeta ∈ 1:vzeta.n, ivz ∈ 1:orig_nvz
+            @views interpolate_to_grid_1d!(
+                new_pdf[ivz,:,ivzeta,iz,ir,is], vr.grid,
+                this_pdf[ivz,:,ivzeta,iz,ir,is], restart_vr,
+                restart_vr_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    if (
+        (moments.evolve_density == restart_evolve_density &&
+         moments.evolve_upar == restart_evolve_upar &&
+         moments.evolve_ppar == restart_evolve_ppar)
+        || (!moments.evolve_upar && !restart_evolve_upar &&
+            !moments.evolve_ppar && !restart_evolve_ppar)
+       )
+        # No chages to velocity-space coordinates, so just interpolate from
+        # one grid to the other
+        if interpolation_needed["vz"]
+            new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+            for is ∈ 1:nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                    ivzeta ∈ 1:vzeta.n
+                @views interpolate_to_grid_1d!(
+                    new_pdf[:,ivr,ivzeta,iz,ir,is], vz.grid,
+                    this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                    restart_vz_spectral)
+            end
+            this_pdf = new_pdf
+        end
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa + upar
+        # => old_wpa = new_wpa - upar
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivzeta ∈ 1:vzeta.n,
+                ivr ∈ 1:vr.n
+            restart_vz_vals = vz.grid .- moments.neutral.uz[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth + upar
+        # => old_wpa = (new_wpa - upar)/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. (vz.grid - moments.neutral.uz[iz,ir,is]) /
+                   moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa
+        # => old_wpa = new_wpa + upar
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid .+ moments.neutral.uz[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz, restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth
+        # => old_wpa = (new_wpa + upar)/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. (vz.grid + moments.neutral.uz[iz,ir,is]) /
+                    moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth + upar
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid .* moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa + upar
+        # => old_wpa = new_wpa*vth - upar/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid * moments.neutral.vth[iz,ir,is] -
+                   moments.neutral.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa*vth + upar
+        # => old_wpa = new_wpa - upar/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid -
+                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa
+        # => old_wpa = new_wpa*vth + upar
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid * moments.neutral.vth[iz,ir,is] +
+                   moments.neutral.uz[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa + upar
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid .* moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa*vth
+        # => old_wpa = new_wpa + upar/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, r.n, nspecies)
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid +
+                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,ir,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    else
+        # This should never happen, as all combinations of evolve_* options
+        # should be handled above.
+        error("Unsupported combination of moment-kinetic options:"
+              * " evolve_density=", moments.evolve_density
+              * " evolve_upar=", moments.evolve_upar
+              * " evolve_ppar=", moments.evolve_ppar
+              * " restart_evolve_density=", restart_evolve_density
+              * " restart_evolve_upar=", restart_evolve_upar
+              * " restart_evolve_ppar=", restart_evolve_ppar)
+    end
+    if moments.evolve_density && !restart_evolve_density
+        # Need to normalise by density
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,ir,is] ./= moments.neutral.dens[iz,ir,is]
+        end
+    elseif !moments.evolve_density && restart_evolve_density
+        # Need to unnormalise by density
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,ir,is] .*= moments.neutral.dens[iz,ir,is]
+        end
+    end
+    if moments.evolve_ppar && !restart_evolve_ppar
+        # Need to normalise by vth
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,ir,is] .*= moments.neutral.vth[iz,ir,is]
+        end
+    elseif !moments.evolve_ppar && restart_evolve_ppar
+        # Need to unnormalise by vth
+        for is ∈ nspecies, ir ∈ 1:r.n, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,ir,is] ./= moments.neutral.vth[iz,ir,is]
+        end
+    end
+
+    return this_pdf
+end
+
+function reload_neutral_boundary_pdf(boundary_distributions_io, var_name, ir, moments, z,
+                                     vzeta, vr, vz, z_range, vzeta_range, vr_range,
+                                     vz_range, restart_z, restart_z_spectral,
+                                     restart_vzeta, restart_vzeta_spectral, restart_vr,
+                                     restart_vr_spectral, restart_vz, restart_vz_spectral,
+                                     interpolation_needed, restart_evolve_density,
+                                     restart_evolve_upar, restart_evolve_ppar)
+    this_pdf = load_slice(boundary_distributions_io, var_name, vz_range,
+                          vr_range, vzeta_range, z_range, :)
+    orig_nvz, orig_nvr, orig_nvzeta, orig_nz, nspecies = size(this_pdf)
+    if interpolation_needed["z"]
+        new_pdf = allocate_float(orig_nvz, orig_nvr, orig_nvzeta, z.n,
+                                 nspecies)
+        for is ∈ 1:nspecies, ivzeta ∈ 1:orig_nvzeta, ivr ∈ 1:orig_nvr,
+                ivz ∈ 1:orig_nvz
+            @views interpolate_to_grid_1d!(
+                new_pdf[ivz,ivr,ivzeta,:,is], z.grid,
+                this_pdf[ivz,ivr,ivzeta,:,is], restart_z,
+                restart_z_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    # Current moment-kinetic implementation is only 1V, so no need
+    # to handle normalised vzeta or vr coordinates. This will need
+    # to change when/if 3V moment-kinetics is implemented.
+    if interpolation_needed["vzeta"]
+        new_pdf = allocate_float(orig_nvz, orig_nvr, vzeta.n, z.n,
+                                 nspecies)
+        for is ∈ 1:nspecies, iz ∈ 1:z.n, ivr ∈ 1:orig_nvr,
+                ivz ∈ 1:orig_nvz
+            @views interpolate_to_grid_1d!(
+                new_pdf[ivz,ivr,:,iz,is], vzeta.grid,
+                this_pdf[ivz,ivr,:,iz,is], restart_vzeta,
+                restart_vzeta_spectral)
+        end
+        this_pdf = new_pdf
+    end
+    if interpolation_needed["vr"]
+        new_pdf = allocate_float(orig_nvz, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ 1:nspecies, iz ∈ 1:z.n, ivzeta ∈ 1:vzeta.n,
+                ivz ∈ 1:orig_nvz
+            @views interpolate_to_grid_1d!(
+                new_pdf[ivz,:,ivzeta,iz,is], vr.grid,
+                this_pdf[ivz,:,ivzeta,iz,is], restart_vr,
+                restart_vr_spectral)
+        end
+        this_pdf = new_pdf
+    end
+
+    if (
+        (moments.evolve_density == restart_evolve_density &&
+         moments.evolve_upar == restart_evolve_upar && moments.evolve_ppar ==
+         restart_evolve_ppar)
+        || (!moments.evolve_upar && !restart_evolve_upar &&
+            !moments.evolve_ppar && !restart_evolve_ppar)
+       )
+        # No chages to velocity-space coordinates, so just interpolate from
+        # one grid to the other
+        if interpolation_needed["vz"]
+            new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+            for is ∈ 1:nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n,
+                    ivzeta ∈ 1:vzeta.n
+                @views interpolate_to_grid_1d!(
+                    new_pdf[:,ivr,ivzeta,iz,is], vz.grid,
+                    this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                    restart_vz_spectral)
+            end
+            this_pdf = new_pdf
+        end
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa + upar
+        # => old_wpa = new_wpa - upar
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivzeta ∈ 1:vzeta.n, ivr ∈ 1:vr.n
+            restart_vz_vals = vz.grid .- moments.neutral.uz[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa = old_wpa*vth + upar
+        # => old_wpa = (new_wpa - upar)/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. (vz.grid - moments.neutral.uz[iz,ir,is]) /
+                   moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa
+        # => old_wpa = new_wpa + upar
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid .+
+                              moments.neutral.uz[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth
+        # => old_wpa = (new_wpa + upar)/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. (vz.grid + moments.neutral.uz[iz,ir,is]) /
+                   moments.neutral.vth
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && !moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa + upar = old_wpa*vth + upar
+        # => old_wpa = new_wpa/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid ./ moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid .*
+                              moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa + upar
+        # => old_wpa = new_wpa*vth - upar/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid * moments.neutral.vth[iz,ir,is] -
+                   moments.neutral.upar[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (!moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth = old_wpa*vth + upar
+        # => old_wpa = new_wpa - upar/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid -
+                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa
+        # => old_wpa = new_wpa*vth + upar
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid * moments.neutral.vth[iz,ir,is] +
+                   moments.neutral.uz[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            restart_evolve_upar && !restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa + upar
+        # => old_wpa = new_wpa*vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals = vz.grid .* moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+        this_pdf = new_pdf
+    elseif (moments.evolve_upar && moments.evolve_ppar &&
+            !restart_evolve_upar && restart_evolve_ppar)
+        # vpa = new_wpa*vth + upar = old_wpa*vth
+        # => old_wpa = new_wpa + upar/vth
+        new_pdf = allocate_float(vz.n, vr.n, vzeta.n, z.n, nspecies)
+        for is ∈ nspecies, iz ∈ 1:z.n, ivr ∈ 1:vr.n, ivzeta ∈ 1:vzeta.n
+            restart_vz_vals =
+                @. vz.grid +
+                   moments.neutral.uz[iz,ir,is]/moments.neutral.vth[iz,ir,is]
+            @views interpolate_to_grid_1d!(
+                new_pdf[:,ivr,ivzeta,iz,is], restart_vz_vals,
+                this_pdf[:,ivr,ivzeta,iz,is], restart_vz,
+                restart_vz_spectral)
+        end
+    else
+        # This should never happen, as all combinations of evolve_* options
+        # should be handled above.
+        error("Unsupported combination of moment-kinetic options:"
+              * " evolve_density=", moments.evolve_density
+              * " evolve_upar=", moments.evolve_upar
+              * " evolve_ppar=", moments.evolve_ppar
+              * " restart_evolve_density=", restart_evolve_density
+              * " restart_evolve_upar=", restart_evolve_upar
+              * " restart_evolve_ppar=", restart_evolve_ppar)
+    end
+    if moments.evolve_density && !restart_evolve_density
+        # Need to normalise by density
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,is] ./= moments.neutral.dens[iz,ir,is]
+        end
+    elseif !moments.evolve_density && restart_evolve_density
+        # Need to unnormalise by density
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,is] .*= moments.neutral.dens[iz,ir,is]
+        end
+    end
+    if moments.evolve_ppar && !restart_evolve_ppar
+        # Need to normalise by vth
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,is] .*= moments.neutral.vth[iz,ir,is]
+        end
+    elseif !moments.evolve_ppar && restart_evolve_ppar
+        # Need to unnormalise by vth
+        for is ∈ nspecies, iz ∈ 1:z.n
+            this_pdf[:,:,:,iz,is] ./= moments.neutral.vth[iz,ir,is]
+        end
+    end
+
+    return this_pdf
+end
+
 """
 Read a slice of an ion distribution function
 
@@ -1888,11 +2090,11 @@ restarts (which are sequential in time), so concatenate the data from each entry
 
 The slice to take is specified by the keyword arguments.
 """
-function load_distributed_charged_pdf_slice(run_names::Tuple, nblocks::Tuple, t_range,
-                                            n_species::mk_int, r::coordinate,
-                                            z::coordinate, vperp::coordinate,
-                                            vpa::coordinate; is=nothing, ir=nothing,
-                                            iz=nothing, ivperp=nothing, ivpa=nothing)
+function load_distributed_ion_pdf_slice(run_names::Tuple, nblocks::Tuple, t_range,
+                                        n_species::mk_int, r::coordinate,
+                                        z::coordinate, vperp::coordinate,
+                                        vpa::coordinate; is=nothing, ir=nothing,
+                                        iz=nothing, ivperp=nothing, ivpa=nothing)
     # dimension of pdf is [vpa,vperp,z,r,species,t]
 
     result_dims = mk_int[]
@@ -2492,8 +2694,7 @@ function get_run_info_no_setup(run_dir::Union{AbstractString,Tuple{AbstractStrin
         load_coordinate_data(file_final_restart, "z")
     r_local, r_local_spectral, r_chunk_size =
         load_coordinate_data(file_final_restart, "r")
-    r, r_spectral, z, z_spectral = construct_global_zr_coords(r_local, z_local;
-                                                              ignore_MPI=true)
+    r, r_spectral, z, z_spectral = construct_global_zr_coords(r_local, z_local)
 
     vperp, vperp_spectral, vperp_chunk_size =
         load_coordinate_data(file_final_restart, "vperp")
@@ -2637,7 +2838,7 @@ function postproc_load_variable(run_info, variable_name; it=nothing, is=nothing,
     if ivperp === nothing
         if :vperp ∈ keys(run_info)
             # v-space coordinates only present if run_info contains distribution functions
-            nvperp = run_info.vperp.n
+            nvperp = run_info.vperp === nothing ? 1 : run_info.vperp.n
             ivperp = 1:nvperp
         else
             nvperp = nothing
@@ -2651,7 +2852,7 @@ function postproc_load_variable(run_info, variable_name; it=nothing, is=nothing,
     if ivpa === nothing
         if :vpa ∈ keys(run_info)
             # v-space coordinates only present if run_info contains distribution functions
-            nvpa = run_info.vpa.n
+            nvpa = run_info.vpa === nothing ? 1 : run_info.vpa.n
             ivpa = 1:nvpa
         else
             nvpa = nothing
@@ -2665,7 +2866,7 @@ function postproc_load_variable(run_info, variable_name; it=nothing, is=nothing,
     if ivzeta === nothing
         if :vzeta ∈ keys(run_info)
             # v-space coordinates only present if run_info contains distribution functions
-            nvzeta = run_info.vzeta.n
+            nvzeta = run_info.vzeta === nothing ? 1 : run_info.vzeta.n
             ivzeta = 1:nvzeta
         else
             nvzeta = nothing
@@ -2679,7 +2880,7 @@ function postproc_load_variable(run_info, variable_name; it=nothing, is=nothing,
     if ivr === nothing
         if :vr ∈ keys(run_info)
             # v-space coordinates only present if run_info contains distribution functions
-            nvr = run_info.vr.n
+            nvr = run_info.vr === nothing ? 1 : run_info.vr.n
             ivr = 1:nvr
         else
             nvr = nothing
@@ -2693,7 +2894,7 @@ function postproc_load_variable(run_info, variable_name; it=nothing, is=nothing,
     if ivz === nothing
         if :vz ∈ keys(run_info)
             # v-space coordinates only present if run_info contains distribution functions
-            nvz = run_info.vz.n
+            nvz = run_info.vz === nothing ? 1 : run_info.vz.n
             ivz = 1:nvz
         else
             nvz = nothing
@@ -2913,14 +3114,13 @@ function postproc_load_variable(run_info, variable_name; it=nothing, is=nothing,
                                       run_info.r_local.n, run_info.itime_skip)
             result = result[iz,ir,is,it]
         elseif nd === 6
-            result = load_distributed_charged_pdf_slice(run_info.files, run_info.nblocks,
-                                                        it, run_info.n_ion_species,
-                                                        run_info.r_local,
-                                                        run_info.z_local, run_info.vperp,
-                                                        run_info.vpa;
-                                                        is=(is === (:) ? nothing : is),
-                                                        ir=ir, iz=iz, ivperp=ivperp,
-                                                        ivpa=ivpa)
+            result = load_distributed_ion_pdf_slice(run_info.files, run_info.nblocks, it,
+                                                    run_info.n_ion_species,
+                                                    run_info.r_local, run_info.z_local,
+                                                    run_info.vperp, run_info.vpa;
+                                                    is=(is === (:) ? nothing : is),
+                                                    ir=ir, iz=iz, ivperp=ivperp,
+                                                    ivpa=ivpa)
         elseif nd === 7
             result = load_distributed_neutral_pdf_slice(run_info.files, run_info.nblocks,
                                                         it, run_info.n_ion_species,
@@ -3027,13 +3227,34 @@ function get_variable(run_info, variable_name; normalize_advection_speed_shape=t
         return variable
     end
 
+    # Get a 'per step' value from a saved 'cumulative' value. E.g. 'iterations per step'
+    # from a saved 'cumulative total iterations'
+    function get_per_step_from_cumulative_variable(run_info, varname::String; kwargs...)
+        variable = get_variable(run_info, varname; kwargs...)
+        tdim = ndims(variable)
+        for i ∈ size(variable, tdim):-1:2
+            selectdim(variable, tdim, i) .-= selectdim(variable, tdim, i-1)
+        end
+
+        # Per-step count does not make sense for the first step, so make sure element-1 is
+        # zero.
+        selectdim(variable, tdim, 1) .= zero(first(variable))
+
+        # Assume cumulative variables always increase, so if any value in the 'per-step'
+        # variable is negative, it is because there was a restart where the cumulative
+        # variable started over
+        variable .= max.(variable, zero(first(variable)))
+
+        return variable
+    end
+
     if variable_name == "temperature"
         vth = postproc_load_variable(run_info, "thermal_speed"; kwargs...)
         variable = vth.^2
-    elseif variable_name == "collision_frequency"
+    elseif variable_name == "collision_frequency_ii"
         n = postproc_load_variable(run_info, "density"; kwargs...)
         vth = postproc_load_variable(run_info, "thermal_speed"; kwargs...)
-        variable = get_collision_frequency(run_info.collisions, n, vth)
+        variable = get_collision_frequency_ii(run_info.collisions, n, vth)
     elseif variable_name == "temperature_neutral"
         vth = postproc_load_variable(run_info, "thermal_speed_neutral"; kwargs...)
         variable = vth.^2
@@ -3126,8 +3347,14 @@ function get_variable(run_info, variable_name; normalize_advection_speed_shape=t
         dqpar_dz = get_z_derivative(run_info, "parallel_heat_flux")
         if run_info.external_source_settings.ion.active
             external_source_amplitude = get_variable(run_info, "external_source_amplitude")
+            external_source_density_amplitude = get_variable(run_info, "external_source_density_amplitude")
+            external_source_momentum_amplitude = get_variable(run_info, "external_source_momentum_amplitude")
+            external_source_pressure_amplitude = get_variable(run_info, "external_source_pressure_amplitude")
         else
             external_source_amplitude = zeros(0,0,run_info.nt)
+            external_source_density_amplitude = zeros(0,0,run_info.nt)
+            external_source_momentum_amplitude = zeros(0,0,run_info.nt)
+            external_source_pressure_amplitude = zeros(0,0,run_info.nt)
         end
 
         nz, nr, nspecies, nt = size(vth)
@@ -3145,12 +3372,15 @@ function get_variable(run_info, variable_name; normalize_advection_speed_shape=t
             advect = [(speed=@view(speed[:,:,:,:,is,it]),) for is ∈ 1:nspecies]
             # Only need Ez
             fields = (Ez=@view(Ez[:,:,it]),)
-            @views moments = (charged=(dppar_dz=dppar_dz[:,:,:,it],
-                                       dupar_dz=dupar_dz[:,:,:,it],
-                                       dvth_dz=dvth_dz[:,:,:,it],
-                                       dqpar_dz=dqpar_dz[:,:,:,it],
-                                       vth=vth[:,:,:,it],
-                                       external_source_amplitude=external_source_amplitude[:,:,it]),
+            @views moments = (ion=(dppar_dz=dppar_dz[:,:,:,it],
+                                   dupar_dz=dupar_dz[:,:,:,it],
+                                   dvth_dz=dvth_dz[:,:,:,it],
+                                   dqpar_dz=dqpar_dz[:,:,:,it],
+                                   vth=vth[:,:,:,it],
+                                   external_source_amplitude=external_source_amplitude[:,:,it],
+                                   external_source_density_amplitude=external_source_density_amplitude[:,:,it],
+                                   external_source_momentum_amplitude=external_source_momentum_amplitude[:,:,it],
+                                   external_source_pressure_amplitude=external_source_pressure_amplitude[:,:,it]),
                              evolve_density=run_info.evolve_density,
                              evolve_upar=run_info.evolve_upar,
                              evolve_ppar=run_info.evolve_ppar)
@@ -3244,8 +3474,14 @@ function get_variable(run_info, variable_name; normalize_advection_speed_shape=t
         dqz_dz = get_z_derivative(run_info, "qz_neutral")
         if run_info.external_source_settings.neutral.active
             external_source_amplitude = get_variable(run_info, "external_source_neutral_amplitude")
+            external_source_density_amplitude = get_variable(run_info, "external_source_neutral_density_amplitude")
+            external_source_momentum_amplitude = get_variable(run_info, "external_source_neutral_momentum_amplitude")
+            external_source_pressure_amplitude = get_variable(run_info, "external_source_neutral_pressure_amplitude")
         else
             external_source_amplitude = zeros(0,0,run_info.nt)
+            external_source_density_amplitude = zeros(0,0,run_info.nt)
+            external_source_momentum_amplitude = zeros(0,0,run_info.nt)
+            external_source_pressure_amplitude = zeros(0,0,run_info.nt)
         end
 
         nz, nr, nspecies, nt = size(vth)
@@ -3274,7 +3510,10 @@ function get_variable(run_info, variable_name; normalize_advection_speed_shape=t
                                        dvth_dz=dvth_dz[:,:,:,it],
                                        dqz_dz=dqz_dz[:,:,:,it],
                                        vth=vth[:,:,:,it],
-                                       external_source_amplitude=external_source_amplitude[:,:,it]),
+                                       external_source_amplitude=external_source_amplitude[:,:,it],
+                                       external_source_density_amplitude=external_source_density_amplitude[:,:,it],
+                                       external_source_momentum_amplitude=external_source_momentum_amplitude[:,:,it],
+                                       external_source_pressure_amplitude=external_source_pressure_amplitude[:,:,it]),
                              evolve_density=run_info.evolve_density,
                              evolve_upar=run_info.evolve_upar,
                              evolve_ppar=run_info.evolve_ppar)
@@ -3288,29 +3527,13 @@ function get_variable(run_info, variable_name; normalize_advection_speed_shape=t
         variable = speed
         variable = select_slice_of_variable(variable; kwargs...)
     elseif variable_name == "steps_per_output"
-        steps_per_output = get_variable(run_info, "step_counter"; kwargs...)
-        for i ∈ length(steps_per_output):-1:2
-            steps_per_output[i] -= steps_per_output[i-1]
-        end
-        variable = steps_per_output
+        variable = get_per_step_from_cumulative_variable(run_info, "step_counter"; kwargs...)
     elseif variable_name == "failures_per_output"
-        failures_per_output = get_variable(run_info, "failure_counter"; kwargs...)
-        for i ∈ length(failures_per_output):-1:2
-            failures_per_output[i] -= failures_per_output[i-1]
-        end
-        variable = failures_per_output
+        variable = get_per_step_from_cumulative_variable(run_info, "failure_counter"; kwargs...)
     elseif variable_name == "failure_caused_by_per_output"
-        failure_caused_by_per_output = get_variable(run_info, "failure_caused_by"; kwargs...)
-        for i ∈ size(failure_caused_by_per_output,2):-1:2
-            failure_caused_by_per_output[:,i] .-= failure_caused_by_per_output[:,i-1]
-        end
-        variable = failure_caused_by_per_output
+        variable = get_per_step_from_cumulative_variable(run_info, "failure_caused_by"; kwargs...)
     elseif variable_name == "limit_caused_by_per_output"
-        limit_caused_by_per_output = get_variable(run_info, "limit_caused_by"; kwargs...)
-        for i ∈ size(limit_caused_by_per_output,2):-1:2
-            limit_caused_by_per_output[:,i] .-= limit_caused_by_per_output[:,i-1]
-        end
-        variable = limit_caused_by_per_output
+        variable = get_per_step_from_cumulative_variable(run_info, "limit_caused_by"; kwargs...)
     elseif variable_name == "average_successful_dt"
         steps_per_output = get_variable(run_info, "steps_per_output"; kwargs...)
         failures_per_output = get_variable(run_info, "failures_per_output"; kwargs...)
@@ -3322,6 +3545,11 @@ function get_variable(run_info, variable_name; normalize_advection_speed_shape=t
         end
 
         variable = delta_t ./ successful_steps_per_output
+        for i ∈ eachindex(successful_steps_per_output)
+            if successful_steps_per_output[i] == 0
+                variable[i] = 0.0
+            end
+        end
         if successful_steps_per_output[1] == 0
             # Don't want a meaningless Inf...
             variable[1] = 0.0
diff --git a/moment_kinetics/src/moment_constraints.jl b/moment_kinetics/src/moment_constraints.jl
index fbdf384a1..ae49821dd 100644
--- a/moment_kinetics/src/moment_constraints.jl
+++ b/moment_kinetics/src/moment_constraints.jl
@@ -6,7 +6,6 @@ function.
 module moment_constraints
 
 using ..communication: _block_synchronize
-using ..initial_conditions: enforce_zero_incoming_bc!
 using ..looping
 using ..velocity_moments: integrate_over_vspace, update_qpar!
 
@@ -69,12 +68,18 @@ function hard_force_moment_constraints!(f, moments, vpa)
         B = -A*I1/I2
 
         @. f1d = A*f1d + B*vpa.grid*f1d
+
+        C = NaN
     elseif moments.evolve_density
         I0 = integrate_over_vspace(f1d, vpa.wgts)
-        @. f1d = f1d / I0
+        A = 1.0 / I0
+        @. f1d = A * f1d
+
+        B = NaN
+        C = NaN
     end
 
-    return nothing
+    return A, B, C
 end
 
 """
@@ -113,12 +118,18 @@ function hard_force_moment_constraints_neutral!(f, moments, vz)
         B = -A*I1/I2
 
         @. f1d = A*f1d + B*vz.grid*f1d
+
+        C = NaN
     elseif moments.evolve_density
         I0 = integrate_over_vspace(f1d, vz.wgts)
-        @. f1d = f1d / I0
+        A = 1.0 / I0
+        @. f1d = A * f1d
+
+        B = NaN
+        C = NaN
     end
 
-    return nothing
+    return A, B, C
 end
 
 end
diff --git a/moment_kinetics/src/moment_kinetics.jl b/moment_kinetics/src/moment_kinetics.jl
index 5076e14ef..5e01d0885 100644
--- a/moment_kinetics/src/moment_kinetics.jl
+++ b/moment_kinetics/src/moment_kinetics.jl
@@ -41,7 +41,6 @@ include("em_fields.jl")
 include("bgk.jl")
 include("manufactured_solns.jl") # MRH Here?
 include("external_sources.jl")
-include("initial_conditions.jl")
 include("moment_constraints.jl")
 include("fokker_planck_test.jl")
 include("fokker_planck_calculus.jl")
@@ -54,6 +53,7 @@ include("vperp_advection.jl")
 include("neutral_r_advection.jl")
 include("neutral_z_advection.jl")
 include("neutral_vz_advection.jl")
+include("boundary_conditions.jl")
 include("charge_exchange.jl")
 include("ionization.jl")
 include("krook_collisions.jl")
@@ -65,8 +65,9 @@ include("numerical_dissipation.jl")
 include("moment_kinetics_input.jl")
 include("utils.jl")
 include("load_data.jl")
-include("parameter_scans.jl")
 include("analysis.jl")
+include("initial_conditions.jl")
+include("parameter_scans.jl")
 include("time_advance.jl")
 
 using TimerOutputs
@@ -76,15 +77,14 @@ using Primes
 
 using .file_io: setup_file_io, finish_file_io
 using .file_io: write_data_to_ascii
-using .file_io: write_moments_data_to_binary, write_dfns_data_to_binary
+using .file_io: write_all_moments_data_to_binary, write_all_dfns_data_to_binary
 using .command_line_options: get_options
 using .communication
 using .communication: _block_synchronize
 using .debugging
 using .external_sources
 using .input_structs
-using .initial_conditions: allocate_pdf_and_moments, init_pdf_and_moments!,
-                           enforce_boundary_conditions!
+using .initial_conditions: allocate_pdf_and_moments, init_pdf_and_moments!
 using .load_data: reload_evolving_fields!
 using .looping
 using .moment_constraints: hard_force_moment_constraints!
@@ -92,7 +92,11 @@ using .looping: debug_setup_loop_ranges_split_one_combination!
 using .moment_kinetics_input: mk_input, read_input_file
 using .time_advance: setup_time_advance!, time_advance!
 using .type_definitions: mk_int
-using .utils: to_minutes
+using .utils: to_minutes, get_default_restart_filename,
+              get_prefix_iblock_and_move_existing_file
+using .em_fields: setup_em_fields
+using .time_advance: setup_dummy_and_buffer_arrays
+using .time_advance: allocate_advection_structs
 
 @debug_detect_redundant_block_synchronize using ..communication: debug_detect_redundant_is_active
 
@@ -191,75 +195,6 @@ function run_moment_kinetics()
                         restart_time_index=restart_time_index)
 end
 
-"""
-Append a number to the filename, to get a new, non-existing filename to backup the file
-to.
-"""
-function get_backup_filename(filename)
-    if !isfile(filename)
-        error("Requested to restart from $filename, but this file does not exist")
-    end
-    counter = 1
-    temp, extension = splitext(filename)
-    extension = extension[2:end]
-    temp, iblock_or_type = splitext(temp)
-    iblock_or_type = iblock_or_type[2:end]
-    iblock = nothing
-    basename = nothing
-    type = nothing
-    if iblock_or_type == "dfns"
-        iblock = nothing
-        type = iblock_or_type
-        basename = temp
-        parallel_io = true
-    else
-        # Filename had an iblock, so we are not using parallel I/O, but actually want to
-        # use the iblock for this block, not necessarily for the exact file that was
-        # passed.
-        iblock = iblock_index[]
-        basename, type = splitext(temp)
-        type = type[2:end]
-        parallel_io = false
-    end
-    if type != "dfns"
-        error("Must pass the '.dfns.h5' output file for restarting. Got $filename.")
-    end
-    backup_dfns_filename = ""
-    if parallel_io
-        # Using parallel I/O
-        while true
-            backup_dfns_filename = "$(basename)_$(counter).$(type).$(extension)"
-            if !isfile(backup_dfns_filename)
-                break
-            end
-            counter += 1
-        end
-        # Create dfns_filename here even though it is the filename passed in, as
-        # parallel_io=false branch needs to get the right `iblock` for this block.
-        dfns_filename = "$(basename).dfns.$(extension)"
-        moments_filename = "$(basename).moments.$(extension)"
-        backup_moments_filename = "$(basename)_$(counter).moments.$(extension)"
-    else
-        while true
-            backup_dfns_filename = "$(basename)_$(counter).$(type).$(iblock).$(extension)"
-            if !isfile(backup_dfns_filename)
-                break
-            end
-            counter += 1
-        end
-        # Create dfns_filename here even though it is almost the filename passed in, in
-        # order to get the right `iblock` for this block.
-        dfns_filename = "$(basename).dfns.$(iblock).$(extension)"
-        moments_filename = "$(basename).moments.$(iblock).$(extension)"
-        backup_moments_filename = "$(basename)_$(counter).moments.$(iblock).$(extension)"
-    end
-    backup_dfns_filename == "" && error("Failed to find a name for backup file.")
-    backup_prefix_iblock = ("$(basename)_$(counter)", iblock)
-    original_prefix_iblock = (basename, iblock)
-    return dfns_filename, backup_dfns_filename, parallel_io, moments_filename,
-           backup_moments_filename, backup_prefix_iblock, original_prefix_iblock
-end
-
 """
 Perform all the initialization steps for a run.
 
@@ -313,12 +248,28 @@ function setup_moment_kinetics(input_dict::AbstractDict;
             vperp=vperp.n, vpa=vpa.n, vzeta=vzeta.n, vr=vr.n, vz=vz.n)
     end
 
+    # create the "fields" structure that contains arrays
+    # for the electrostatic potential phi and the electromagnetic fields
+    fields = setup_em_fields(vperp.n, z.n, r.n, composition.n_ion_species,
+                             drive_input.force_phi, drive_input.amplitude,
+                             drive_input.frequency, drive_input.force_Er_zero_at_wall)
+
     # Allocate arrays and create the pdf and moments structs
     pdf, moments, boundary_distributions =
         allocate_pdf_and_moments(composition, r, z, vperp, vpa, vzeta, vr, vz,
                                  evolve_moments, collisions, external_source_settings,
                                  num_diss_params)
 
+    # create structs containing the information needed to treat advection in z, r, vpa, vperp, and vz
+    # for ions, electrons and neutrals
+    # NB: the returned advection_structs are yet to be initialized
+    advection_structs = allocate_advection_structs(composition, z, r, vpa, vperp, vz, vr, vzeta)
+
+    # setup dummy arrays & buffer arrays for z r MPI                             
+    n_neutral_species_alloc = max(1, composition.n_neutral_species)
+    scratch_dummy = setup_dummy_and_buffer_arrays(r.n, z.n, vpa.n, vperp.n, vz.n, vr.n, vzeta.n, 
+        composition.n_ion_species, n_neutral_species_alloc)
+
     if restart === false
         restarting = false
         # initialize f(z,vpa) and the lowest three v-space moments (density(z), upar(z) and ppar(z)),
@@ -335,55 +286,14 @@ function setup_moment_kinetics(input_dict::AbstractDict;
     else
         restarting = true
 
-        run_name = input_dict["run_name"]
-        base_directory = get(input_dict, "base_directory", "runs")
-        output_dir = joinpath(base_directory, run_name)
         if restart === true
-            run_name = input_dict["run_name"]
-            io_settings = get(input_dict, "output", Dict{String,Any}())
-            binary_format = get(io_settings, "binary_format", hdf5)
-            if binary_format === hdf5
-                ext = "h5"
-            elseif binary_format === netcdf
-                ext = "cdf"
-            else
-                error("Unrecognized binary_format '$binary_format'")
-            end
-            restart_filename_pattern = joinpath(output_dir, run_name * ".dfns*." * ext)
-            restart_filename_glob = glob(restart_filename_pattern)
-            if length(restart_filename_glob) == 0
-                error("No output file to restart from found matching the pattern "
-                      * "$restart_filename_pattern")
-            end
-            restart_filename = restart_filename_glob[1]
+            restart_filename = get_default_restart_filename(io_input, "dfns")
         else
             restart_filename = restart
         end
 
-        # Move the output file being restarted from to make sure it doesn't get
-        # overwritten.
-        dfns_filename, backup_dfns_filename, parallel_io, moments_filename,
-        backup_moments_filename, backup_prefix_iblock, original_prefix_iblock =
-            get_backup_filename(restart_filename)
-
-        # Ensure every process got the filenames and checked files exist before moving
-        # files
-        MPI.Barrier(comm_world)
-
-        if abspath(output_dir) == abspath(dirname(dfns_filename))
-            # Only move the file if it is in our current run directory. Otherwise we are
-            # restarting from another run, and will not be overwriting the file.
-            if (parallel_io && global_rank[] == 0) || (!parallel_io && block_rank[] == 0)
-                mv(dfns_filename, backup_dfns_filename)
-                mv(moments_filename, backup_moments_filename)
-            end
-        else
-            # Reload from dfns_filename without moving the file
-            backup_prefix_iblock = original_prefix_iblock
-        end
-
-        # Ensure files have been moved before any process tries to read from them
-        MPI.Barrier(comm_world)
+        backup_prefix_iblock = get_prefix_iblock_and_move_existing_file(restart_filename,
+                                                                        io_input.output_dir)
 
         # Reload pdf and moments from an existing output file
         code_time, dt, dt_before_last_fail, previous_runs_info, restart_time_index =
@@ -399,17 +309,22 @@ function setup_moment_kinetics(input_dict::AbstractDict;
 
         _block_synchronize()
     end
+
+    # Broadcast code_time from the root process of each shared-memory block (on which it
+    # might have been loaded from a restart file).
+    code_time = MPI.Bcast(code_time, 0, comm_block[])
+
     # create arrays and do other work needed to setup
     # the main time advance loop -- including normalisation of f by density if requested
 
-    moments, fields, spectral_objects, advect_objects,
-    scratch, advance, t_params, fp_arrays, gyroavs, scratch_dummy, manufactured_source_list =
-        setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz_spectral,
-            vr_spectral, vzeta_spectral, vpa_spectral, vperp_spectral, z_spectral,
-            r_spectral, composition, drive_input, moments, t_input, code_time, dt,
+    moments, spectral_objects, scratch, advance, t_params, fp_arrays, gyroavs,
+    manufactured_source_list =
+        setup_time_advance!(pdf, fields, vz, vr, vzeta, vpa, vperp, z, r, gyrophase,
+            vz_spectral, vr_spectral, vzeta_spectral, vpa_spectral, vperp_spectral,
+            z_spectral, r_spectral, composition, moments, t_input, code_time, dt,
             dt_before_last_fail, collisions, species, geometry, boundary_distributions,
             external_source_settings, num_diss_params, manufactured_solns_input,
-            restarting)
+            advection_structs, scratch_dummy, restarting)
 
     # This is the closest we can get to the end time of the setup before writing it to the
     # output file
@@ -421,20 +336,21 @@ function setup_moment_kinetics(input_dict::AbstractDict;
         moments.evolve_upar, moments.evolve_ppar, external_source_settings, input_dict,
         restart_time_index, previous_runs_info, time_for_setup)
     # write initial data to ascii files
-    write_data_to_ascii(moments, fields, vpa, vperp, z, r, code_time,
+    write_data_to_ascii(pdf, moments, fields, vpa, vperp, z, r, code_time,
         composition.n_ion_species, composition.n_neutral_species, ascii_io)
     # write initial data to binary files
 
-    write_moments_data_to_binary(moments, fields, code_time, composition.n_ion_species,
-        composition.n_neutral_species, io_moments, 1, 0.0, t_params, r, z)
-    write_dfns_data_to_binary(pdf.charged.norm, pdf.neutral.norm, moments, fields,
-         code_time, composition.n_ion_species, composition.n_neutral_species, io_dfns, 1,
-         0.0, t_params, r, z, vperp, vpa, vzeta, vr, vz)
+    write_all_moments_data_to_binary(moments, fields, code_time,
+        composition.n_ion_species, composition.n_neutral_species, io_moments, 1, 0.0, t_params, r,
+        z)
+    write_all_dfns_data_to_binary(pdf, moments, fields, code_time,
+        composition.n_ion_species, composition.n_neutral_species, io_dfns, 1, 0.0,
+        t_params, r, z, vperp, vpa, vzeta, vr, vz)
 
     begin_s_r_z_vperp_region()
 
     return pdf, scratch, code_time, t_params, vz, vr, vzeta, vpa, vperp, gyrophase, z, r,
-           moments, fields, spectral_objects, advect_objects,
+           moments, fields, spectral_objects, advection_structs,
            composition, collisions, geometry, gyroavs, boundary_distributions,
            external_source_settings, num_diss_params, advance, fp_arrays, scratch_dummy,
            manufactured_source_list, ascii_io, io_moments, io_dfns
diff --git a/moment_kinetics/src/moment_kinetics_input.jl b/moment_kinetics/src/moment_kinetics_input.jl
index 70e60fd96..56358a27b 100644
--- a/moment_kinetics/src/moment_kinetics_input.jl
+++ b/moment_kinetics/src/moment_kinetics_input.jl
@@ -25,6 +25,7 @@ using ..geo: init_magnetic_geometry, setup_geometry_input
 using MPI
 using Quadmath
 using TOML
+using UUIDs
 
 """
 Read input from a TOML file
@@ -121,39 +122,39 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
     geometry_in = setup_geometry_input(scan_input, get_default_rhostar(reference_params))
     
     ispecies = 1
-    species.charged[1].z_IC.initialization_option = get(scan_input, "z_IC_option$ispecies", "gaussian")
-    species.charged[1].initial_density = get(scan_input, "initial_density$ispecies", 1.0)
-    species.charged[1].initial_temperature = get(scan_input, "initial_temperature$ispecies", 1.0)
-    species.charged[1].z_IC.width = get(scan_input, "z_IC_width$ispecies", 0.125)
-    species.charged[1].z_IC.wavenumber = get(scan_input, "z_IC_wavenumber$ispecies", 1)
-    species.charged[1].z_IC.density_amplitude = get(scan_input, "z_IC_density_amplitude$ispecies", 0.001)
-    species.charged[1].z_IC.density_phase = get(scan_input, "z_IC_density_phase$ispecies", 0.0)
-    species.charged[1].z_IC.upar_amplitude = get(scan_input, "z_IC_upar_amplitude$ispecies", 0.0)
-    species.charged[1].z_IC.upar_phase = get(scan_input, "z_IC_upar_phase$ispecies", 0.0)
-    species.charged[1].z_IC.temperature_amplitude = get(scan_input, "z_IC_temperature_amplitude$ispecies", 0.0)
-    species.charged[1].z_IC.temperature_phase = get(scan_input, "z_IC_temperature_phase$ispecies", 0.0)
-    species.charged[1].r_IC.initialization_option = get(scan_input, "r_IC_option$ispecies", "gaussian")
-    species.charged[1].r_IC.wavenumber = get(scan_input, "r_IC_wavenumber$ispecies", 1)
-    species.charged[1].r_IC.density_amplitude = get(scan_input, "r_IC_density_amplitude$ispecies", 0.0)
-    species.charged[1].r_IC.density_phase = get(scan_input, "r_IC_density_phase$ispecies", 0.0)
-    species.charged[1].r_IC.upar_amplitude = get(scan_input, "r_IC_upar_amplitude$ispecies", 0.0)
-    species.charged[1].r_IC.upar_phase = get(scan_input, "r_IC_upar_phase$ispecies", 0.0)
-    species.charged[1].r_IC.temperature_amplitude = get(scan_input, "r_IC_temperature_amplitude$ispecies", 0.0)
-    species.charged[1].r_IC.temperature_phase = get(scan_input, "r_IC_temperature_phase$ispecies", 0.0)
-    species.charged[1].vpa_IC.initialization_option = get(scan_input, "vpa_IC_option$ispecies", "gaussian")
-    species.charged[1].vpa_IC.density_amplitude = get(scan_input, "vpa_IC_density_amplitude$ispecies", 1.000)
-    species.charged[1].vpa_IC.width = get(scan_input, "vpa_IC_width$ispecies", 1.0)
-    species.charged[1].vpa_IC.density_phase = get(scan_input, "vpa_IC_density_phase$ispecies", 0.0)
-    species.charged[1].vpa_IC.upar_amplitude = get(scan_input, "vpa_IC_upar_amplitude$ispecies", 0.0)
-    species.charged[1].vpa_IC.upar_phase = get(scan_input, "vpa_IC_upar_phase$ispecies", 0.0)
-    species.charged[1].vpa_IC.temperature_amplitude = get(scan_input, "vpa_IC_temperature_amplitude$ispecies", 0.0)
-    species.charged[1].vpa_IC.temperature_phase = get(scan_input, "vpa_IC_temperature_phase$ispecies", 0.0)
+    species.ion[1].z_IC.initialization_option = get(scan_input, "z_IC_option$ispecies", "gaussian")
+    species.ion[1].initial_density = get(scan_input, "initial_density$ispecies", 1.0)
+    species.ion[1].initial_temperature = get(scan_input, "initial_temperature$ispecies", 1.0)
+    species.ion[1].z_IC.width = get(scan_input, "z_IC_width$ispecies", 0.125)
+    species.ion[1].z_IC.wavenumber = get(scan_input, "z_IC_wavenumber$ispecies", 1)
+    species.ion[1].z_IC.density_amplitude = get(scan_input, "z_IC_density_amplitude$ispecies", 0.001)
+    species.ion[1].z_IC.density_phase = get(scan_input, "z_IC_density_phase$ispecies", 0.0)
+    species.ion[1].z_IC.upar_amplitude = get(scan_input, "z_IC_upar_amplitude$ispecies", 0.0)
+    species.ion[1].z_IC.upar_phase = get(scan_input, "z_IC_upar_phase$ispecies", 0.0)
+    species.ion[1].z_IC.temperature_amplitude = get(scan_input, "z_IC_temperature_amplitude$ispecies", 0.0)
+    species.ion[1].z_IC.temperature_phase = get(scan_input, "z_IC_temperature_phase$ispecies", 0.0)
+    species.ion[1].r_IC.initialization_option = get(scan_input, "r_IC_option$ispecies", "gaussian")
+    species.ion[1].r_IC.wavenumber = get(scan_input, "r_IC_wavenumber$ispecies", 1)
+    species.ion[1].r_IC.density_amplitude = get(scan_input, "r_IC_density_amplitude$ispecies", 0.0)
+    species.ion[1].r_IC.density_phase = get(scan_input, "r_IC_density_phase$ispecies", 0.0)
+    species.ion[1].r_IC.upar_amplitude = get(scan_input, "r_IC_upar_amplitude$ispecies", 0.0)
+    species.ion[1].r_IC.upar_phase = get(scan_input, "r_IC_upar_phase$ispecies", 0.0)
+    species.ion[1].r_IC.temperature_amplitude = get(scan_input, "r_IC_temperature_amplitude$ispecies", 0.0)
+    species.ion[1].r_IC.temperature_phase = get(scan_input, "r_IC_temperature_phase$ispecies", 0.0)
+    species.ion[1].vpa_IC.initialization_option = get(scan_input, "vpa_IC_option$ispecies", "gaussian")
+    species.ion[1].vpa_IC.density_amplitude = get(scan_input, "vpa_IC_density_amplitude$ispecies", 1.000)
+    species.ion[1].vpa_IC.width = get(scan_input, "vpa_IC_width$ispecies", 1.0)
+    species.ion[1].vpa_IC.density_phase = get(scan_input, "vpa_IC_density_phase$ispecies", 0.0)
+    species.ion[1].vpa_IC.upar_amplitude = get(scan_input, "vpa_IC_upar_amplitude$ispecies", 0.0)
+    species.ion[1].vpa_IC.upar_phase = get(scan_input, "vpa_IC_upar_phase$ispecies", 0.0)
+    species.ion[1].vpa_IC.temperature_amplitude = get(scan_input, "vpa_IC_temperature_amplitude$ispecies", 0.0)
+    species.ion[1].vpa_IC.temperature_phase = get(scan_input, "vpa_IC_temperature_phase$ispecies", 0.0)
     ispecies += 1
     if n_neutral_species > 0
         species.neutral[1].z_IC.initialization_option = get(scan_input, "z_IC_option$ispecies", "gaussian")
         species.neutral[1].initial_density = get(scan_input, "initial_density$ispecies", 1.0)
         species.neutral[1].initial_temperature = get(scan_input, "initial_temperature$ispecies", 1.0)
-        species.neutral[1].z_IC.width = get(scan_input, "z_IC_width$ispecies", species.charged[1].z_IC.width)
+        species.neutral[1].z_IC.width = get(scan_input, "z_IC_width$ispecies", species.ion[1].z_IC.width)
         species.neutral[1].z_IC.density_amplitude = get(scan_input, "z_IC_density_amplitude$ispecies", 0.001)
         species.neutral[1].z_IC.density_phase = get(scan_input, "z_IC_density_phase$ispecies", 0.0)
         species.neutral[1].z_IC.upar_amplitude = get(scan_input, "z_IC_upar_amplitude$ispecies", 0.0)
@@ -169,7 +170,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
         species.neutral[1].r_IC.temperature_phase = get(scan_input, "r_IC_temperature_phase$ispecies", 0.0)
         species.neutral[1].vpa_IC.initialization_option = get(scan_input, "vpa_IC_option$ispecies", "gaussian")
         species.neutral[1].vpa_IC.density_amplitude = get(scan_input, "vpa_IC_density_amplitude$ispecies", 1.000)
-        species.neutral[1].vpa_IC.width = get(scan_input, "vpa_IC_width$ispecies", species.charged[1].vpa_IC.width)
+        species.neutral[1].vpa_IC.width = get(scan_input, "vpa_IC_width$ispecies", species.ion[1].vpa_IC.width)
         species.neutral[1].vpa_IC.density_phase = get(scan_input, "vpa_IC_density_phase$ispecies", 0.0)
         species.neutral[1].vpa_IC.upar_amplitude = get(scan_input, "vpa_IC_upar_amplitude$ispecies", 0.0)
         species.neutral[1].vpa_IC.upar_phase = get(scan_input, "vpa_IC_upar_phase$ispecies", 0.0)
@@ -179,7 +180,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
     end
     #################### end specification of species inputs #####################
 
-    charge_exchange = get(scan_input, "charge_exchange_frequency", 2.0*sqrt(species.charged[1].initial_temperature))
+    charge_exchange = get(scan_input, "charge_exchange_frequency", 2.0*sqrt(species.ion[1].initial_temperature))
     ionization = get(scan_input, "ionization_frequency", charge_exchange)
     constant_ionization_rate = get(scan_input, "constant_ionization_rate", false)
     # set up krook collision inputs
@@ -192,7 +193,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
     timestepping_section = set_defaults_and_check_section!(
         scan_input, "timestepping";
         nstep=5,
-        dt=0.00025/sqrt(species.charged[1].initial_temperature),
+        dt=0.00025/sqrt(species.ion[1].initial_temperature),
         CFL_prefactor=-1.0,
         nwrite=1,
         nwrite_dfns=nothing,
@@ -336,7 +337,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
 	# do not parallelise vpa with distributed-memory MPI
     vpa.nelement_local = vpa.nelement_global 
     # L is the box length in units of vthermal_species
-    vpa.L = get(scan_input, "vpa_L", 8.0*sqrt(species.charged[1].initial_temperature))
+    vpa.L = get(scan_input, "vpa_L", 8.0*sqrt(species.ion[1].initial_temperature))
     # determine the boundary condition
     # only supported option at present is "zero" and "periodic"
     vpa.bc = get(scan_input, "vpa_bc", "periodic")
@@ -354,7 +355,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
     # do not parallelise vperp with distributed-memory MPI
     vperp.nelement_local = vperp.nelement_global 
     # L is the box length in units of vthermal_species
-    vperp.L = get(scan_input, "vperp_L", 8.0*sqrt(species.charged[1].initial_temperature))
+    vperp.L = get(scan_input, "vperp_L", 8.0*sqrt(species.ion[1].initial_temperature))
     # Note vperp.bc is set below, after numerical dissipation is initialized, so that it
     # can use the numerical dissipation settings to set its default value.
     #
@@ -398,7 +399,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
         # do not parallelise vz with distributed-memory MPI
         vr.nelement_local = vr.nelement_global
         # L is the box length in units of vthermal_species
-        vr.L = get(scan_input, "vr_L", 8.0*sqrt(species.charged[1].initial_temperature))
+        vr.L = get(scan_input, "vr_L", 8.0*sqrt(species.ion[1].initial_temperature))
         # determine the boundary condition
         # only supported option at present is "zero" and "periodic"
         vr.bc = get(scan_input, "vr_bc", "none")
@@ -415,7 +416,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
         # do not parallelise vz with distributed-memory MPI
         vzeta.nelement_local = vzeta.nelement_global
         # L is the box length in units of vthermal_species
-        vzeta.L = get(scan_input, "vzeta_L", 8.0*sqrt(species.charged[1].initial_temperature))
+        vzeta.L = get(scan_input, "vzeta_L", 8.0*sqrt(species.ion[1].initial_temperature))
         # determine the boundary condition
         # only supported option at present is "zero" and "periodic"
         vzeta.bc = get(scan_input, "vzeta_bc", "none")
@@ -427,14 +428,19 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
 
     is_1V = (vperp.ngrid == vperp.nelement_global == 1 && vzeta.ngrid ==
              vzeta.nelement_global == 1 && vr.ngrid == vr.nelement_global == 1)
-    num_diss_params = setup_numerical_dissipation(
-        get(scan_input, "numerical_dissipation", Dict{String,Any}()), is_1V)
+    
+    ion_num_diss_param_dict = get(scan_input, "ion_numerical_dissipation", Dict{String,Any}())
+    electron_num_diss_param_dict = get(scan_input, "electron_numerical_dissipation", Dict{String,Any}())
+    neutral_num_diss_param_dict = get(scan_input, "neutral_numerical_dissipation", Dict{String,Any}())
+    num_diss_params = setup_numerical_dissipation(ion_num_diss_param_dict,
+                                                  electron_num_diss_param_dict,
+                                                  neutral_num_diss_param_dict, is_1V)
 
     # vperp.bc is set here (a bit out of place) so that we can use
-    # num_diss_params.vperp_dissipation_coefficient to set the default.
+    # num_diss_params.ion.vperp_dissipation_coefficient to set the default.
     vperp.bc = get(scan_input, "vperp_bc",
                    ( collisions.fkpl.nuii > 0.0 ||
-                    num_diss_params.vperp_dissipation_coefficient > 0.0) ?
+                    num_diss_params.ion.vperp_dissipation_coefficient > 0.0) ?
                     "zero" : "none")
     
     #########################################################################
@@ -518,36 +524,36 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
     vzeta_immutable = grid_input("vzeta", vzeta.ngrid, vzeta.nelement_global, vzeta.nelement_local, 1, 0, vzeta.L,
         vzeta.discretization, vzeta.fd_option, vzeta.cheb_option, vzeta.bc, vzeta_advection_immutable, MPI.COMM_NULL, vzeta.element_spacing_option)
     
-    species_charged_immutable = Array{species_parameters,1}(undef,n_ion_species)
+    species_ion_immutable = Array{species_parameters,1}(undef,n_ion_species)
     species_neutral_immutable = Array{species_parameters,1}(undef,n_neutral_species)
     
     for is ∈ 1:n_ion_species
         species_type = "ion"
         #    species_type = "electron"
-        z_IC = initial_condition_input(species.charged[is].z_IC.initialization_option,
-            species.charged[is].z_IC.width, species.charged[is].z_IC.wavenumber,
-            species.charged[is].z_IC.density_amplitude, species.charged[is].z_IC.density_phase,
-            species.charged[is].z_IC.upar_amplitude, species.charged[is].z_IC.upar_phase,
-            species.charged[is].z_IC.temperature_amplitude, species.charged[is].z_IC.temperature_phase,
-            species.charged[is].z_IC.monomial_degree, 0.0, 0.0, 0.0, 0.0)
-        r_IC = initial_condition_input(species.charged[is].r_IC.initialization_option,
-            species.charged[is].r_IC.width, species.charged[is].r_IC.wavenumber,
-            species.charged[is].r_IC.density_amplitude, species.charged[is].r_IC.density_phase,
-            species.charged[is].r_IC.upar_amplitude, species.charged[is].r_IC.upar_phase,
-            species.charged[is].r_IC.temperature_amplitude, species.charged[is].r_IC.temperature_phase,
-            species.charged[is].r_IC.monomial_degree, 0.0, 0.0, 0.0, 0.0)
-        vpa_IC = initial_condition_input(species.charged[is].vpa_IC.initialization_option,
-            species.charged[is].vpa_IC.width, species.charged[is].vpa_IC.wavenumber,
-            species.charged[is].vpa_IC.density_amplitude, species.charged[is].vpa_IC.density_phase,
-            species.charged[is].vpa_IC.upar_amplitude, species.charged[is].vpa_IC.upar_phase,
-            species.charged[is].vpa_IC.temperature_amplitude,
-            species.charged[is].vpa_IC.temperature_phase, species.charged[is].vpa_IC.monomial_degree,
+        z_IC = initial_condition_input(species.ion[is].z_IC.initialization_option,
+            species.ion[is].z_IC.width, species.ion[is].z_IC.wavenumber,
+            species.ion[is].z_IC.density_amplitude, species.ion[is].z_IC.density_phase,
+            species.ion[is].z_IC.upar_amplitude, species.ion[is].z_IC.upar_phase,
+            species.ion[is].z_IC.temperature_amplitude, species.ion[is].z_IC.temperature_phase,
+            species.ion[is].z_IC.monomial_degree, 0.0, 0.0, 0.0, 0.0)
+        r_IC = initial_condition_input(species.ion[is].r_IC.initialization_option,
+            species.ion[is].r_IC.width, species.ion[is].r_IC.wavenumber,
+            species.ion[is].r_IC.density_amplitude, species.ion[is].r_IC.density_phase,
+            species.ion[is].r_IC.upar_amplitude, species.ion[is].r_IC.upar_phase,
+            species.ion[is].r_IC.temperature_amplitude, species.ion[is].r_IC.temperature_phase,
+            species.ion[is].r_IC.monomial_degree, 0.0, 0.0, 0.0, 0.0)
+        vpa_IC = initial_condition_input(species.ion[is].vpa_IC.initialization_option,
+            species.ion[is].vpa_IC.width, species.ion[is].vpa_IC.wavenumber,
+            species.ion[is].vpa_IC.density_amplitude, species.ion[is].vpa_IC.density_phase,
+            species.ion[is].vpa_IC.upar_amplitude, species.ion[is].vpa_IC.upar_phase,
+            species.ion[is].vpa_IC.temperature_amplitude,
+            species.ion[is].vpa_IC.temperature_phase, species.ion[is].vpa_IC.monomial_degree,
             get(scan_input, "vpa_IC_v0_$is", 0.5*sqrt(vperp.L^2 + (0.5*vpa.L)^2)),
             get(scan_input, "vpa_IC_vth0$is", 0.1*sqrt(vperp.L^2 + (0.5*vpa.L)^2)),
             get(scan_input, "vpa_IC_vpa0$is", 0.25*0.5*abs(vpa.L)),
             get(scan_input, "vpa_IC_vperp0$is", 0.5*abs(vperp.L)))
-        species_charged_immutable[is] = species_parameters(species_type, species.charged[is].initial_temperature,
-            species.charged[is].initial_density, z_IC, r_IC, vpa_IC)
+        species_ion_immutable[is] = species_parameters(species_type, species.ion[is].initial_temperature,
+            species.ion[is].initial_density, z_IC, r_IC, vpa_IC)
     end
     if n_neutral_species > 0
         for is ∈ 1:n_neutral_species
@@ -578,7 +584,7 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
                 species.neutral[is].initial_density, z_IC, r_IC, vpa_IC)
         end
     end 
-    species_immutable = (charged = species_charged_immutable, neutral = species_neutral_immutable)
+    species_immutable = (ion = species_ion_immutable, neutral = species_neutral_immutable)
     
     force_Er_zero = get(scan_input, "force_Er_zero_at_wall", false)
     drive_immutable = drive_input(drive.force_phi, drive.amplitude, drive.frequency, force_Er_zero)
@@ -590,6 +596,15 @@ function mk_input(scan_input=Dict(); save_inputs_to_txt=false, ignore_MPI=true)
     io_settings["binary_format"] = get(io_settings, "binary_format", hdf5)
     io_settings["parallel_io"] = get(io_settings, "parallel_io",
                                      io_has_parallel(Val(io_settings["binary_format"])))
+    run_id = string(uuid4())
+    if !ignore_MPI
+        # Communicate run_id to all blocks
+        # Need to convert run_id to a Vector{Char} for MPI
+        run_id_chars = [run_id...]
+        MPI.Bcast!(run_id_chars, 0, comm_world)
+        run_id = string(run_id_chars...)
+    end
+    io_settings["run_id"] = run_id
     io_immutable = io_input(; output_dir=output_dir, run_name=run_name,
                               Dict(Symbol(k)=>v for (k,v) in io_settings)...)
 
@@ -1013,7 +1028,7 @@ function load_defaults(n_ion_species, n_neutral_species, electron_physics)
         electron_physics, use_test_neutral_wall_pdf, T_e, T_wall, phi_wall, Er_constant,
         mn_over_mi, me_over_mi, recycling_fraction, gyrokinetic_ions, allocate_float(n_species))
     
-    species_charged = Array{species_parameters_mutable,1}(undef,n_ion_species)
+    species_ion = Array{species_parameters_mutable,1}(undef,n_ion_species)
     species_neutral = Array{species_parameters_mutable,1}(undef,n_neutral_species)
     
     # initial temperature for each species defaults to Tₑ
@@ -1084,7 +1099,7 @@ function load_defaults(n_ion_species, n_neutral_species, electron_physics)
 
     # fill in entries in species struct corresponding to ion species
     for is ∈ 1:n_ion_species
-        species_charged[is] = species_parameters_mutable("ion", initial_temperature, initial_density,
+        species_ion[is] = species_parameters_mutable("ion", initial_temperature, initial_density,
             deepcopy(z_initial_conditions), deepcopy(r_initial_conditions),
             deepcopy(vpa_initial_conditions))
     end
@@ -1096,7 +1111,7 @@ function load_defaults(n_ion_species, n_neutral_species, electron_physics)
                 deepcopy(r_initial_conditions), deepcopy(vpa_initial_conditions))
         end
     end
-    species = (charged = species_charged, neutral = species_neutral)
+    species = (ion = species_ion, neutral = species_neutral)
     
     # if drive_phi = true, include external electrostatic potential of form
     # phi(z,t=0)*drive_amplitude*sinpi(time*drive_frequency)
diff --git a/moment_kinetics/src/moment_kinetics_structs.jl b/moment_kinetics/src/moment_kinetics_structs.jl
index 25d23be1f..5ac80b23c 100644
--- a/moment_kinetics/src/moment_kinetics_structs.jl
+++ b/moment_kinetics/src/moment_kinetics_structs.jl
@@ -9,9 +9,9 @@ using ..type_definitions: mk_float
 
 """
 """
-struct scratch_pdf{n_distribution_charged, n_moment, n_distribution_neutral,n_moment_neutral}
-    # charged particles
-    pdf::MPISharedArray{mk_float, n_distribution_charged}
+struct scratch_pdf{n_distribution_ion, n_moment, n_distribution_neutral,n_moment_neutral}
+    # ions
+    pdf::MPISharedArray{mk_float, n_distribution_ion}
     density::MPISharedArray{mk_float, n_moment}
     upar::MPISharedArray{mk_float, n_moment}
     ppar::MPISharedArray{mk_float, n_moment}
@@ -50,6 +50,235 @@ struct em_fields_struct
     force_Er_zero_at_wall::Bool
 end
 
+"""
+"""
+struct moments_ion_substruct
+    # this is the particle density
+    dens::MPISharedArray{mk_float,3}
+    # flag that keeps track of if the density needs updating before use
+    # Note: may not be set for all species on this process, but this process only ever
+    # sets/uses the value for the same subset of species. This means dens_update does
+    # not need to be a shared memory array.
+    dens_updated::Vector{Bool}
+    # this is the parallel flow
+    upar::MPISharedArray{mk_float,3}
+    # flag that keeps track of whether or not upar needs updating before use
+    # Note: may not be set for all species on this process, but this process only ever
+    # sets/uses the value for the same subset of species. This means upar_update does
+    # not need to be a shared memory array.
+    upar_updated::Vector{Bool}
+    # this is the parallel pressure
+    ppar::MPISharedArray{mk_float,3}
+    # flag that keeps track of whether or not ppar needs updating before use
+    # Note: may not be set for all species on this process, but this process only ever
+    # sets/uses the value for the same subset of species. This means ppar_update does
+    # not need to be a shared memory array.
+    ppar_updated::Vector{Bool}
+    # this is the perpendicular pressure
+    pperp::MPISharedArray{mk_float,3}
+    # this is the parallel heat flux
+    qpar::MPISharedArray{mk_float,3}
+    # flag that keeps track of whether or not qpar needs updating before use
+    # Note: may not be set for all species on this process, but this process only ever
+    # sets/uses the value for the same subset of species. This means qpar_update does
+    # not need to be a shared memory array.
+    qpar_updated::Vector{Bool}
+    # this is the thermal speed based on the parallel temperature Tpar = ppar/dens: vth = sqrt(2*Tpar/m)
+    vth::MPISharedArray{mk_float,3}
+    # generalised Chodura integrals for the lower and upper plates
+    chodura_integral_lower::MPISharedArray{mk_float,2}
+    chodura_integral_upper::MPISharedArray{mk_float,2}
+    # if evolve_ppar = true, then the velocity variable is (vpa - upa)/vth, which introduces
+    # a factor of vth for each power of wpa in velocity space integrals.
+    # v_norm_fac accounts for this: it is vth if using the above definition for the parallel velocity,
+    # and it is one otherwise
+    v_norm_fac::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the particle density
+    ddens_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the upwinded z-derivative of the particle density
+    ddens_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the second-z-derivative of the particle density
+    d2dens_dz2::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the parallel flow
+    dupar_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the upwinded z-derivative of the parallel flow
+    dupar_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the second-z-derivative of the parallel flow
+    d2upar_dz2::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the parallel pressure
+    dppar_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the upwinded z-derivative of the parallel pressure
+    dppar_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the second-z-derivative of the parallel pressure
+    d2ppar_dz2::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the parallel heat flux
+    dqpar_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the thermal speed based on the parallel temperature Tpar = ppar/dens: vth = sqrt(2*Tpar/m)
+    dvth_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the entropy production dS/dt = - int (ln f sum_s' C_ss' [f_s,f_s']) d^3 v
+    dSdt::MPISharedArray{mk_float,3}
+    # Spatially varying amplitude of the external source term
+    external_source_amplitude::MPISharedArray{mk_float,2}
+    # Spatially varying amplitude of the density moment of the external source term
+    external_source_density_amplitude::MPISharedArray{mk_float,2}
+    # Spatially varying amplitude of the parallel momentum moment of the external source
+    # term
+    external_source_momentum_amplitude::MPISharedArray{mk_float,2}
+    # Spatially varying amplitude of the parallel pressure moment of the external source
+    # term
+    external_source_pressure_amplitude::MPISharedArray{mk_float,2}
+    # Integral term for the PID controller of the external source term
+    external_source_controller_integral::MPISharedArray{mk_float,2}
+    # Store coefficient 'A' from applying moment constraints so we can write it out as a
+    # diagnostic
+    constraints_A_coefficient::Union{MPISharedArray{mk_float,3},Nothing}
+    # Store coefficient 'B' from applying moment constraints so we can write it out as a
+    # diagnostic
+    constraints_B_coefficient::Union{MPISharedArray{mk_float,3},Nothing}
+    # Store coefficient 'C' from applying moment constraints so we can write it out as a
+    # diagnostic
+    constraints_C_coefficient::Union{MPISharedArray{mk_float,3},Nothing}
+end
+
+"""
+"""
+struct moments_neutral_substruct
+    # this is the particle density
+    dens::MPISharedArray{mk_float,3}
+    # flag that keeps track of if the density needs updating before use
+    # Note: may not be set for all species on this process, but this process only ever
+    # sets/uses the value for the same subset of species. This means dens_update does
+    # not need to be a shared memory array.
+    dens_updated::Vector{Bool}
+    # this is the particle mean velocity in z
+    uz::MPISharedArray{mk_float,3}
+    # flag that keeps track of if uz needs updating before use
+    uz_updated::Vector{Bool}
+    # this is the particle mean velocity in r
+    ur::MPISharedArray{mk_float,3}
+    # flag that keeps track of if ur needs updating before use
+    ur_updated::Vector{Bool}
+    # this is the particle mean velocity in zeta
+    uzeta::MPISharedArray{mk_float,3}
+    # flag that keeps track of if uzeta needs updating before use
+    uzeta_updated::Vector{Bool}
+    # this is the zz particle pressure tensor component
+    pz::MPISharedArray{mk_float,3}
+    # flag that keeps track of if pz needs updating before use
+    pz_updated::Vector{Bool}
+    # this is the rr particle pressure tensor component
+    pr::MPISharedArray{mk_float,3}
+    # flag that keeps track of if pr needs updating before use
+    pr_updated::Vector{Bool}
+    # this is the zetazeta particle pressure tensor component
+    pzeta::MPISharedArray{mk_float,3}
+    # flag that keeps track of if pzeta needs updating before use
+    pzeta_updated::Vector{Bool}
+    # this is the total (isotropic) particle pressure
+    ptot::MPISharedArray{mk_float,3}
+    # this is the heat flux along z
+    qz::MPISharedArray{mk_float,3}
+    # flag that keeps track of if qz needs updating before use
+    qz_updated::Vector{Bool}
+    # this is the thermal speed based on the temperature T = ptot/dens: vth = sqrt(2*T/m)
+    vth::MPISharedArray{mk_float,3}
+    # if evolve_ppar = true, then the velocity variable is (vz - uz)/vth, which introduces
+    # a factor of vth for each power of wz in velocity space integrals.
+    # v_norm_fac accounts for this: it is vth if using the above definition for the parallel velocity,
+    # and it is one otherwise
+    v_norm_fac::MPISharedArray{mk_float,3}
+    # this is the z-derivative of the particle density
+    ddens_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the particle density
+    ddens_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the second-z-derivative of the particle density
+    d2dens_dz2::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the particle mean velocity in z
+    duz_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the upwinded z-derivative of the particle mean velocity in z
+    duz_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the second-z-derivative of the particle mean velocity in z
+    d2uz_dz2::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the zz particle pressure tensor component
+    dpz_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the upwinded z-derivative of the zz particle pressure tensor component
+    dpz_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the second-z-derivative of the zz particle pressure tensor component
+    d2pz_dz2::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the thermal speed based on the temperature T = ptot/dens: vth = sqrt(2*T/m)
+    dvth_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # this is the z-derivative of the heat flux along z
+    dqz_dz::Union{MPISharedArray{mk_float,3},Nothing}
+    # Spatially varying amplitude of the external source term
+    external_source_amplitude::MPISharedArray{mk_float,2}
+    # Spatially varying amplitude of the density moment of the external source term
+    external_source_density_amplitude::MPISharedArray{mk_float,2}
+    # Spatially varying amplitude of the parallel momentum moment of the external source
+    # term
+    external_source_momentum_amplitude::MPISharedArray{mk_float,2}
+    # Spatially varying amplitude of the parallel pressure moment of the external source
+    # term
+    external_source_pressure_amplitude::MPISharedArray{mk_float,2}
+    # Integral term for the PID controller of the external source term
+    external_source_controller_integral::MPISharedArray{mk_float,2}
+    # Store coefficient 'A' from applying moment constraints so we can write it out as a
+    # diagnostic
+    constraints_A_coefficient::Union{MPISharedArray{mk_float,3},Nothing}
+    # Store coefficient 'B' from applying moment constraints so we can write it out as a
+    # diagnostic
+    constraints_B_coefficient::Union{MPISharedArray{mk_float,3},Nothing}
+    # Store coefficient 'C' from applying moment constraints so we can write it out as a
+    # diagnostic
+    constraints_C_coefficient::Union{MPISharedArray{mk_float,3},Nothing}
+end
+
+"""
+"""
+struct pdf_substruct{n_distribution}
+    norm::MPISharedArray{mk_float,n_distribution}
+    buffer::MPISharedArray{mk_float,n_distribution} # for collision operator terms when pdfs must be interpolated onto different velocity space grids, and for gyroaveraging
+end
+
+# struct of structs neatly contains i+n info?
+"""
+"""
+struct pdf_struct
+    #ion particles: s + r + z + vperp + vpa
+    ion::pdf_substruct{5}
+    #neutral particles: s + r + z + vzeta + vr + vz
+    neutral::pdf_substruct{6}
+end
+
+"""
+"""
+struct moments_struct
+    ion::moments_ion_substruct
+    neutral::moments_neutral_substruct
+    # flag that indicates if the density should be evolved via continuity equation
+    evolve_density::Bool
+    # flag that indicates if particle number should be conserved for each species
+    # effects like ionisation or net particle flux from the domain would lead to
+    # non-conservation
+    particle_number_conserved::Bool
+    # flag that indicates if exact particle conservation should be enforced
+    enforce_conservation::Bool
+    # flag that indicates if the parallel flow should be evolved via force balance
+    evolve_upar::Bool
+    # flag that indicates if the parallel pressure should be evolved via the energy equation
+    evolve_ppar::Bool
+end
+
+"""
+"""
+struct boundary_distributions_struct
+    # knudsen cosine distribution for imposing the neutral wall boundary condition
+    knudsen::MPISharedArray{mk_float,3}
+    # ion particle r boundary values (vpa,vperp,z,r,s)
+    pdf_rboundary_ion::MPISharedArray{mk_float,5}
+    # neutral particle r boundary values (vz,vr,vzeta,z,r,s)
+    pdf_rboundary_neutral::MPISharedArray{mk_float,6}
+end
+
 """
 discretization_info for one dimension
 
diff --git a/moment_kinetics/src/neutral_vz_advection.jl b/moment_kinetics/src/neutral_vz_advection.jl
index 36ef2c2c9..96b61cd39 100644
--- a/moment_kinetics/src/neutral_vz_advection.jl
+++ b/moment_kinetics/src/neutral_vz_advection.jl
@@ -127,19 +127,21 @@ function update_speed_n_u_p_evolution_neutral!(advect, fvec, moments, vz, z, r,
         end
     end
     if neutral_source_settings.active
-        source_amplitude = moments.neutral.external_source_amplitude
-        source_T = neutral_source_settings.source_T
+        source_density_amplitude = moments.neutral.external_source_density_amplitude
+        source_momentum_amplitude = moments.neutral.external_source_momentum_amplitude
+        source_pressure_amplitude = moments.neutral.external_source_pressure_amplitude
         density = fvec.density_neutral
         uz = fvec.uz_neutral
         pz = fvec.pz_neutral
         vth = moments.neutral.vth
         vz_grid = vz.grid
         @loop_s_r_z is ir iz begin
-            prefactor = source_amplitude[iz,ir]
-            term1 = prefactor * uz[iz,ir,is]/(density[iz,ir,is]*vth[iz,ir,is])
+            term1 = source_density_amplitude[iz,ir] * uz[iz,ir,is]/(density[iz,ir,is]*vth[iz,ir,is])
             term2_over_vpa =
-                0.5 * prefactor * (-(0.5*source_T + uz[iz,ir,is]^2) / pz[iz,ir,is]
-                                   + 1.0/density[iz,ir,is])
+                -0.5 * (source_pressure_amplitude[iz,ir] +
+                        2.0 * uz[iz,ir,is] * source_momentum_amplitude[iz,ir]) /
+                       pz[iz,ir,is] +
+                0.5 * source_density_amplitude[iz,ir] / density[iz,ir,is]
             @loop_vzeta_vr_vz ivzeta ivr ivz begin
                 advect[is].speed[ivz,ivr,ivzeta,iz,ir] += term1 +
                                                           vz_grid[ivz] * term2_over_vpa
@@ -218,13 +220,12 @@ function update_speed_n_u_evolution_neutral!(advect, fvec, moments, vz, z, r, co
         end
     end
     if neutral_source_settings.active
-        source_amplitude = moments.neutral.external_source_amplitude
-        source_T = neutral_source_settings.source_T
+        source_density_amplitude = moments.neutral.external_source_density_amplitude
         density = fvec.density_neutral
         uz = fvec.uz_neutral
         vth = moments.neutral.vth
         @loop_sn_r_z isn ir iz begin
-            term = source_amplitude[iz,ir] * uz[iz,ir,isn] / density[iz,ir,isn]
+            term = source_density_amplitude[iz,ir] * uz[iz,ir,isn] / density[iz,ir,isn]
             @loop_vzeta_vr_vz ivzeta ivr ivz begin
                 advect[isn].speed[ivz,ivr,ivzeta,iz,ir] += term
             end
diff --git a/moment_kinetics/src/numerical_dissipation.jl b/moment_kinetics/src/numerical_dissipation.jl
index 64eb28138..054357c29 100644
--- a/moment_kinetics/src/numerical_dissipation.jl
+++ b/moment_kinetics/src/numerical_dissipation.jl
@@ -16,11 +16,36 @@ using ..calculus: derivative!, second_derivative!
 using ..derivatives: derivative_r!, derivative_z!
 using ..type_definitions: mk_float
 
-Base.@kwdef struct numerical_dissipation_parameters
+
+#############################################################
+########### Numerical Dissipation Parameter setup ###########
+"""
+Define the dissipation parameters for each species, which means
+there need to be three sections in each input file that specify
+the parameters required of each species, as follows:
+
+```
+[ion_numerical_dissipation]
+vpa_dissipation_coefficient
+...
+
+[electron_numerical_dissipation]
+vpa_dissipation_coefficient
+...
+
+[neutral_numerical_dissipation]
+vz_dissipation_coefficient
+...
+```
+
+There will still be the -1.0 default parameters.
+"""
+
+# define individual structs for each species with their particular parameters
+Base.@kwdef struct ion_num_diss_params
     vpa_boundary_buffer_damping_rate::mk_float = -1.0
     vpa_boundary_buffer_diffusion_coefficient::mk_float = -1.0
     vpa_dissipation_coefficient::mk_float = -1.0
-    vz_dissipation_coefficient::mk_float = -1.0
     vperp_dissipation_coefficient::mk_float = -1.0
     z_dissipation_coefficient::mk_float = -1.0
     r_dissipation_coefficient::mk_float = -1.0
@@ -28,18 +53,52 @@ Base.@kwdef struct numerical_dissipation_parameters
     force_minimum_pdf_value::Union{Nothing,mk_float} = nothing
 end
 
-function setup_numerical_dissipation(input_section::Dict, is_1V)
-    if is_1V && "vpa_dissipation_coefficient" ∈ keys(input_section)
+Base.@kwdef struct electron_num_diss_params
+    vpa_boundary_buffer_damping_rate::mk_float = -1.0
+    vpa_boundary_buffer_diffusion_coefficient::mk_float = -1.0
+    vpa_dissipation_coefficient::mk_float = -1.0
+    vperp_dissipation_coefficient::mk_float = -1.0
+    z_dissipation_coefficient::mk_float = -1.0
+    r_dissipation_coefficient::mk_float = -1.0
+    moment_dissipation_coefficient::mk_float = -1.0
+    force_minimum_pdf_value::Union{Nothing,mk_float} = nothing
+end
+
+Base.@kwdef struct neutral_num_diss_params
+    vz_dissipation_coefficient::mk_float = -1.0
+    z_dissipation_coefficient::mk_float = -1.0
+    r_dissipation_coefficient::mk_float = -1.0
+    moment_dissipation_coefficient::mk_float = -1.0
+    force_minimum_pdf_value::Union{Nothing,mk_float} = nothing
+end
+
+struct numerical_dissipation_parameters
+    ion::ion_num_diss_params
+    electron::electron_num_diss_params
+    neutral::neutral_num_diss_params
+end
+
+######### End Of Numerical Dissipation Parameter setup #########
+################################################################
+
+function setup_numerical_dissipation(ion_input::Dict, electron_input::Dict, 
+                                     neutral_input::Dict, is_1V)
+    if is_1V && "vpa_dissipation_coefficient" ∈ keys(ion_input)
         # Set default for vz_dissipation_coefficient the same as
-        # vpa_dissipation_coefficient for 1V case
-        input_section["vz_dissipation_coefficient"] =
-            get(input_section, "vz_dissipation_coefficient",
-                input_section["vpa_dissipation_coefficient"])
+        # ion_vpa_dissipation_coefficient for 1V case
+        neutral_input["vz_dissipation_coefficient"] =
+            get(neutral_input, "vz_dissipation_coefficient",
+                ion_input["vpa_dissipation_coefficient"])
     end
 
-    input = Dict(Symbol(k)=>v for (k,v) in input_section)
+    ion_input_dict = Dict(Symbol(k)=>v for (k,v) in ion_input)
+    ion_params = ion_num_diss_params(; ion_input_dict...)
+    electron_input_dict = Dict(Symbol(k)=>v for (k,v) in electron_input)
+    electron_params = electron_num_diss_params(; electron_input_dict...)
+    neutral_input_dict = Dict(Symbol(k)=>v for (k,v) in neutral_input)
+    neutral_params = neutral_num_diss_params(; neutral_input_dict...)
 
-    return numerical_dissipation_parameters(; input...)
+    return numerical_dissipation_parameters(ion_params, electron_params, neutral_params)
 end
 
 """
@@ -50,13 +109,11 @@ Disabled by default.
 
 The damping rate is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_boundary_buffer_damping_rate = 0.1
 ```
 """
-function vpa_boundary_buffer_decay!(f_out, fvec_in, moments, vpa, dt,
-                                    num_diss_params::numerical_dissipation_parameters)
-    damping_rate_prefactor = num_diss_params.vpa_boundary_buffer_damping_rate
+function vpa_boundary_buffer_decay!(f_out, fvec_in, moments, vpa, dt, damping_rate_prefactor)
 
     if damping_rate_prefactor <= 0.0
         return nothing
@@ -149,13 +206,11 @@ Disabled by default.
 
 The maximum diffusion rate in the buffer is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_boundary_buffer_diffusion_coefficient = 0.1
 ```
 """
-function vpa_boundary_buffer_diffusion!(f_out, fvec_in, vpa, vpa_spectral, dt,
-                                        num_diss_params::numerical_dissipation_parameters)
-    diffusion_prefactor = num_diss_params.vpa_boundary_buffer_diffusion_coefficient
+function vpa_boundary_buffer_diffusion!(f_out, fvec_in, vpa, vpa_spectral, dt, diffusion_prefactor)
 
     if diffusion_prefactor <= 0.0
         return nothing
@@ -238,14 +293,13 @@ Disabled by default.
 
 The diffusion coefficient is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.1
 ```
 """
 function vpa_dissipation!(f_out, f_in, vpa, spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters) where T_spectral
+                          diffusion_coefficient) where T_spectral
 
-    diffusion_coefficient = num_diss_params.vpa_dissipation_coefficient
     if diffusion_coefficient <= 0.0 || vpa.n == 1
         return nothing
     end
@@ -300,16 +354,15 @@ Disabled by default.
 
 The diffusion coefficient is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vperp_dissipation_coefficient = 0.1
 ```
 """
 function vperp_dissipation!(f_out, f_in, vperp, spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters) where T_spectral
+                            diffusion_coefficient) where T_spectral
     
     begin_s_r_z_vpa_region()
 
-    diffusion_coefficient = num_diss_params.vperp_dissipation_coefficient
     if diffusion_coefficient <= 0.0 || vperp.n == 1
         return nothing
     end
@@ -329,7 +382,7 @@ Disabled by default.
 
 The diffusion coefficient is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[ion_numerical_dissipation]
 z_dissipation_coefficient = 0.1
 ```
 
@@ -339,9 +392,8 @@ on internal or external element boundaries
 
 """
 function z_dissipation!(f_out, f_in, z, z_spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters, scratch_dummy) where T_spectral
+                        diffusion_coefficient, scratch_dummy) where T_spectral
 
-    diffusion_coefficient = num_diss_params.z_dissipation_coefficient
     if diffusion_coefficient <= 0.0 || z.n == 1
         return nothing
     end
@@ -374,7 +426,7 @@ Disabled by default.
 
 The diffusion coefficient is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[ion_numerical_dissipation]
 r_dissipation_coefficient = 0.1
 
 ```
@@ -385,9 +437,8 @@ on internal or external element boundaries
 
 """
 function r_dissipation!(f_out, f_in, r, r_spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters, scratch_dummy) where T_spectral
+                        diffusion_coefficient, scratch_dummy) where T_spectral
 
-    diffusion_coefficient = num_diss_params.r_dissipation_coefficient
     if diffusion_coefficient <= 0.0 || r.n == 1
         return nothing
     end
@@ -420,14 +471,13 @@ Disabled by default.
 
 The diffusion coefficient is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[neutral_numerical_dissipation]
 vz_dissipation_coefficient = 0.1
 ```
 """
 function vz_dissipation_neutral!(f_out, f_in, vz, spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters) where T_spectral
+                                 diffusion_coefficient) where T_spectral
 
-    diffusion_coefficient = num_diss_params.vz_dissipation_coefficient
     if diffusion_coefficient <= 0.0
         return nothing
     end
@@ -449,7 +499,7 @@ Disabled by default.
 
 The diffusion coefficient is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[neutral_numerical_dissipation]
 z_dissipation_coefficient = 0.1
 ```
 
@@ -459,9 +509,8 @@ on internal or external element boundaries
 
 """
 function z_dissipation_neutral!(f_out, f_in, z, z_spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters, scratch_dummy) where T_spectral
+                                diffusion_coefficient, scratch_dummy) where T_spectral
 
-    diffusion_coefficient = num_diss_params.z_dissipation_coefficient
     if diffusion_coefficient <= 0.0
         return nothing
     end
@@ -494,7 +543,7 @@ Disabled by default.
 
 The diffusion coefficient is set in the input TOML file by the parameter
 ```
-[numerical_dissipation]
+[neutral_numerical_dissipation]
 r_dissipation_coefficient = 0.1
 
 ```
@@ -505,9 +554,8 @@ on internal or external element boundaries
 
 """
 function r_dissipation_neutral!(f_out, f_in, r, r_spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters, scratch_dummy) where T_spectral
+                                diffusion_coefficient, scratch_dummy) where T_spectral
 
-    diffusion_coefficient = num_diss_params.r_dissipation_coefficient
     if diffusion_coefficient <= 0.0 || r.n == 1
         return nothing
     end
@@ -534,17 +582,16 @@ function r_dissipation_neutral!(f_out, f_in, r, r_spectral::T_spectral, dt,
 end
 
 """
-    force_minimum_pdf_value!(f, num_diss_paras::numerical_dissipation_parameters)
+    force_minimum_pdf_value!(f, minval)
 
 Set a minimum value for the pdf-sized array `f`. Any points less than the minimum are
 set to the minimum. By default, no minimum is applied. The minimum value can be set by
 ```
-[numerical_dissipation]
+[ion_numerical_dissipation]
 force_minimum_pdf_value = 0.0
 ```
 """
-function force_minimum_pdf_value!(f, num_diss_params::numerical_dissipation_parameters)
-    minval = num_diss_params.force_minimum_pdf_value
+function force_minimum_pdf_value!(f, minval)
 
     if minval === nothing
         return nothing
@@ -560,17 +607,16 @@ function force_minimum_pdf_value!(f, num_diss_params::numerical_dissipation_para
 end
 
 """
-    force_minimum_pdf_value_neutral!(f, num_diss_paras::numerical_dissipation_parameters)
+    force_minimum_pdf_value_neutral!(f, minval)
 
 Set a minimum value for the neutral-pdf-sized array `f`. Any points less than the minimum
 are set to the minimum. By default, no minimum is applied. The minimum value can be set by
 ```
-[numerical_dissipation]
+[neutral_numerical_dissipation]
 force_minimum_pdf_value = 0.0
 ```
 """
-function force_minimum_pdf_value_neutral!(f, num_diss_params::numerical_dissipation_parameters)
-    minval = num_diss_params.force_minimum_pdf_value
+function force_minimum_pdf_value_neutral!(f, minval)
 
     if minval === nothing
         return nothing
diff --git a/moment_kinetics/src/r_advection.jl b/moment_kinetics/src/r_advection.jl
index e3f23aef7..3d7d3a0a4 100644
--- a/moment_kinetics/src/r_advection.jl
+++ b/moment_kinetics/src/r_advection.jl
@@ -21,7 +21,7 @@ function r_advection!(f_out, fvec_in, moments, fields, advect, r, z, vperp, vpa,
     @loop_s is begin
         # get the updated speed along the r direction using the current f
         @views update_speed_r!(advect[is], fvec_in.upar[:,:,is],
-                               moments.charged.vth[:,:,is], fields, moments.evolve_upar,
+                               moments.ion.vth[:,:,is], fields, moments.evolve_upar,
                                moments.evolve_ppar, vpa, vperp, z, r, geometry, is)
         # advance r-advection equation
         @loop_z_vpa iz ivpa begin
@@ -30,14 +30,14 @@ function r_advection!(f_out, fvec_in, moments, fields, advect, r, z, vperp, vpa,
         @loop_z_vperp_vpa iz ivperp ivpa begin
             @views adjust_advection_speed!(advect[is].speed[:,ivpa,ivperp,iz],
                                            fvec_in.density[iz,:,is],
-                                           moments.charged.vth[iz,:,is],
+                                           moments.ion.vth[iz,:,is],
                                            moments.evolve_density, moments.evolve_ppar)
             # take the normalized pdf contained in fvec_in.pdf and remove the normalization,
             # returning the true (un-normalized) particle distribution function in r.scratch
             @views unnormalize_pdf!(
                        scratch_dummy.buffer_vpavperpzrs_2[ivpa,ivperp,iz,:,is],
                        fvec_in.pdf[ivpa,ivperp,iz,:,is], fvec_in.density[iz,:,is],
-                       moments.charged.vth[iz,:,is], moments.evolve_density,
+                       moments.ion.vth[iz,:,is], moments.evolve_density,
                        moments.evolve_ppar)
             advect[is].adv_fac[:,ivpa,ivperp,iz] .= -dt.*advect[is].speed[:,ivpa,ivperp,iz]
         end
diff --git a/moment_kinetics/src/reference_parameters.jl b/moment_kinetics/src/reference_parameters.jl
index 7ccddb581..869451cc4 100644
--- a/moment_kinetics/src/reference_parameters.jl
+++ b/moment_kinetics/src/reference_parameters.jl
@@ -8,7 +8,7 @@ physical units of the simulation, and are needed for a few specific steps during
 module reference_parameters
 
 export setup_reference_parameters
-export get_reference_collision_frequency
+export get_reference_collision_frequency_ii
 
 using ..constants
 using ..input_structs
@@ -29,28 +29,33 @@ function setup_reference_parameters(input_dict)
     reference_parameter_section["timeref"] = reference_parameter_section["Lref"] / reference_parameter_section["cref"]
     reference_parameter_section["Omegaref"] = proton_charge * reference_parameter_section["Bref"] / reference_parameter_section["mref"]
 
+    Nref_per_cm3 = reference_parameter_section["Nref"] * 1.0e-6
+    Tref = reference_parameter_section["Tref"]
+
+    reference_parameter_section["me"] = electron_mass
+
+    # Coulomb logarithm at reference parameters for same-species, singly-charged ion-ion
+    # collisions, using NRL formulary. Formula given for n in units of cm^-3 and T in
+    # units of eV.
+    reference_parameter_section["logLambda_ii"] = 23.0 - log(sqrt(2.0*Nref_per_cm3) / Tref^1.5)
+
     reference_params = Dict_to_NamedTuple(reference_parameter_section)
 
     return reference_params
 end
 
 """
-Calculate normalized collision frequency at reference parameters for Coulomb collisions.
+Calculate normalized ion-ion collision frequency at reference parameters for Coulomb collisions.
 
 Currently valid only for hydrogenic ions (Z=1)
 """
-function get_reference_collision_frequency(reference_params)
+function get_reference_collision_frequency_ii(reference_params)
     Nref = reference_params.Nref
     Tref = reference_params.Tref
     mref = reference_params.mref
     timeref = reference_params.timeref
     cref = reference_params.cref
-
-    Nref_per_cm3 = Nref * 1.0e-6
-
-    # Coulomb logarithm at reference parameters for same-species ion-ion collisions, using
-    # NRL formulary. Formula given for n in units of cm^-3 and T in units of eV.
-    logLambda_ii = 23.0 - log(sqrt(2.0*Nref_per_cm3) / Tref^1.5)
+    logLambda_ii = reference_params.logLambda_ii
 
     # Collision frequency, using \hat{\nu} from Appendix, p. 277 of Helander "Collisional
     # Transport in Magnetized Plasmas" (2002).
diff --git a/moment_kinetics/src/source_terms.jl b/moment_kinetics/src/source_terms.jl
index 53dd88b26..9850d6f23 100644
--- a/moment_kinetics/src/source_terms.jl
+++ b/moment_kinetics/src/source_terms.jl
@@ -22,9 +22,9 @@ function source_terms!(pdf_out, fvec_in, moments, vpa, z, r, dt, spectral, compo
         @loop_s is begin
             @views source_terms_evolve_ppar_no_collisions!(
                 pdf_out[:,:,:,:,is], fvec_in.pdf[:,:,:,:,is], fvec_in.density[:,:,is],
-                fvec_in.upar[:,:,is], fvec_in.ppar[:,:,is], moments.charged.vth[:,:,is],
-                moments.charged.qpar[:,:,is], moments.charged.ddens_dz[:,:,is],
-                moments.charged.dvth_dz[:,:,is], moments.charged.dqpar_dz[:,:,is],
+                fvec_in.upar[:,:,is], fvec_in.ppar[:,:,is], moments.ion.vth[:,:,is],
+                moments.ion.qpar[:,:,is], moments.ion.ddens_dz[:,:,is],
+                moments.ion.dvth_dz[:,:,is], moments.ion.dqpar_dz[:,:,is],
                 moments, z, r, dt, spectral, ion_source_settings)
             if composition.n_neutral_species > 0
                 if abs(collisions.charge_exchange) > 0.0 || abs(collisions.ionization) > 0.0
@@ -41,8 +41,8 @@ function source_terms!(pdf_out, fvec_in, moments, vpa, z, r, dt, spectral, compo
         @loop_s is begin
             @views source_terms_evolve_density!(
                 pdf_out[:,:,:,:,is], fvec_in.pdf[:,:,:,:,is], fvec_in.density[:,:,is],
-                fvec_in.upar[:,:,is], moments.charged.ddens_dz[:,:,is],
-                moments.charged.dupar_dz[:,:,is], moments, z, r, dt, spectral,
+                fvec_in.upar[:,:,is], moments.ion.ddens_dz[:,:,is],
+                moments.ion.dupar_dz[:,:,is], moments, z, r, dt, spectral,
                 ion_source_settings)
         end
     end
@@ -65,9 +65,9 @@ function source_terms_evolve_density!(pdf_out, pdf_in, dens, upar, ddens_dz, dup
     end
 
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_amplitude
+        source_density_amplitude = moments.ion.external_source_density_amplitude
         @loop_r_z ir iz begin
-            term = dt * source_amplitude[iz,ir] / dens[iz,ir]
+            term = dt * source_density_amplitude[iz,ir] / dens[iz,ir]
             @loop_vperp_vpa ivperp ivpa begin
                 pdf_out[ivpa,ivperp,iz,ir] -= term * pdf_in[ivpa,ivperp,iz,ir]
             end
@@ -97,11 +97,13 @@ function source_terms_evolve_ppar_no_collisions!(pdf_out, pdf_in, dens, upar, pp
     end
 
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_amplitude
-        source_T = ion_source_settings.source_T
+        source_density_amplitude = moments.ion.external_source_density_amplitude
+        source_momentum_amplitude = moments.ion.external_source_momentum_amplitude
+        source_pressure_amplitude = moments.ion.external_source_pressure_amplitude
         @loop_r_z ir iz begin
-            term = dt * source_amplitude[iz,ir] *
-                   (1.5/dens[iz,ir] - (0.25 * source_T + 0.5 * upar[iz,ir]^2) / ppar[iz,ir])
+            term = dt * (1.5 * source_density_amplitude[iz,ir] / dens[iz,ir] -
+                         (0.5 * source_pressure_amplitude[iz,ir] +
+                          source_momentum_amplitude[iz,ir]) / ppar[iz,ir])
             @loop_vperp_vpa ivperp ivpa begin
                 pdf_out[ivpa,ivperp,iz,ir] -= term * pdf_in[ivpa,ivperp,iz,ir]
             end
@@ -191,9 +193,9 @@ function source_terms_evolve_density_neutral!(pdf_out, pdf_in, dens, upar, ddens
     end
 
     if neutral_source_settings.active
-        source_amplitude = moments.neutral.external_source_amplitude
+        source_density_amplitude = moments.neutral.external_source_density_amplitude
         @loop_r_z ir iz begin
-            term = dt * source_amplitude[iz,ir] / dens[iz,ir]
+            term = dt * source_density_amplitude[iz,ir] / dens[iz,ir]
             @loop_vzeta_vr_vz ivzeta ivr ivz begin
                 pdf_out[ivz,ivr,ivzeta,iz,ir] -= term * pdf_in[ivz,ivr,ivzeta,iz,ir]
             end
@@ -222,11 +224,13 @@ function source_terms_evolve_ppar_no_collisions_neutral!(pdf_out, pdf_in, dens,
     end
 
     if neutral_source_settings.active
-        source_amplitude = moments.neutral.external_source_amplitude
-        source_T = neutral_source_settings.source_T
+        source_density_amplitude = moments.neutral.external_source_density_amplitude
+        source_momentum_amplitude = moments.neutral.external_source_momentum_amplitude
+        source_pressure_amplitude = moments.neutral.external_source_pressure_amplitude
         @loop_r_z ir iz begin
-            term = dt * source_amplitude[iz,ir] *
-                   (1.5/dens[iz,ir] - (0.25 * source_T + 0.5 * upar[iz,ir]^2) / ppar[iz,ir])
+            term = dt * (1.5 * source_density_amplitude[iz,ir] / dens[iz,ir] -
+                         (0.5 * source_pressure_amplitude[iz,ir] +
+                          source_momentum_amplitude[iz,ir]) / ppar[iz,ir])
             @loop_vzeta_vr_vz ivzeta ivr ivz begin
                 pdf_out[ivz,ivr,ivzeta,iz,ir] -= term * pdf_in[ivz,ivr,ivzeta,iz,ir]
             end
@@ -257,7 +261,7 @@ end
 """
 advance the dfn with an arbitrary source function 
 """
-function source_terms_manufactured!(pdf_charged_out, pdf_neutral_out, vz, vr, vzeta, vpa, vperp, z, r, t, dt, composition, manufactured_source_list)
+function source_terms_manufactured!(pdf_ion_out, pdf_neutral_out, vz, vr, vzeta, vpa, vperp, z, r, t, dt, composition, manufactured_source_list)
     if manufactured_source_list.time_independent_sources
         # the (time-independent) manufactured source arrays
         Source_i = manufactured_source_list.Source_i_array
@@ -267,7 +271,7 @@ function source_terms_manufactured!(pdf_charged_out, pdf_neutral_out, vz, vr, vz
 
         @loop_s is begin
             @loop_r_z_vperp_vpa ir iz ivperp ivpa begin
-                pdf_charged_out[ivpa,ivperp,iz,ir,is] += dt*Source_i[ivpa,ivperp,iz,ir]
+                pdf_ion_out[ivpa,ivperp,iz,ir,is] += dt*Source_i[ivpa,ivperp,iz,ir]
             end
         end
 
@@ -288,7 +292,7 @@ function source_terms_manufactured!(pdf_charged_out, pdf_neutral_out, vz, vr, vz
 
         @loop_s is begin
             @loop_r_z_vperp_vpa ir iz ivperp ivpa begin
-                pdf_charged_out[ivpa,ivperp,iz,ir,is] += dt*Source_i_func(vpa.grid[ivpa],vperp.grid[ivperp],z.grid[iz],r.grid[ir],t)
+                pdf_ion_out[ivpa,ivperp,iz,ir,is] += dt*Source_i_func(vpa.grid[ivpa],vperp.grid[ivperp],z.grid[iz],r.grid[ir],t)
             end
         end
 
diff --git a/moment_kinetics/src/time_advance.jl b/moment_kinetics/src/time_advance.jl
index f8506f656..e5cdc0ef4 100644
--- a/moment_kinetics/src/time_advance.jl
+++ b/moment_kinetics/src/time_advance.jl
@@ -4,6 +4,7 @@ module time_advance
 
 export setup_time_advance!
 export time_advance!
+export allocate_advection_structs
 export setup_dummy_and_buffer_arrays
 
 using MPI
@@ -12,7 +13,7 @@ using ..array_allocation: allocate_float, allocate_shared_float, allocate_shared
 using ..communication
 using ..communication: _block_synchronize
 using ..debugging
-using ..file_io: write_data_to_ascii, write_moments_data_to_binary, write_dfns_data_to_binary, debug_dump
+using ..file_io: write_data_to_ascii, write_all_moments_data_to_binary, write_all_dfns_data_to_binary, debug_dump
 using ..looping
 using ..moment_kinetics_structs: scratch_pdf
 using ..velocity_moments: update_moments!, update_moments_neutral!, reset_moments_status!
@@ -20,12 +21,12 @@ using ..velocity_moments: update_density!, update_upar!, update_ppar!, update_pp
 using ..velocity_moments: update_neutral_density!, update_neutral_qz!
 using ..velocity_moments: update_neutral_uzeta!, update_neutral_uz!, update_neutral_ur!
 using ..velocity_moments: update_neutral_pzeta!, update_neutral_pz!, update_neutral_pr!
-using ..velocity_moments: calculate_moment_derivatives!, calculate_moment_derivatives_neutral!
+using ..velocity_moments: calculate_ion_moment_derivatives!, calculate_neutral_moment_derivatives!
 using ..velocity_moments: update_chodura!
 using ..velocity_grid_transforms: vzvrvzeta_to_vpavperp!, vpavperp_to_vzvrvzeta!
-using ..initial_conditions: enforce_boundary_conditions!
-using ..initial_conditions: enforce_neutral_boundary_conditions!
-using ..input_structs: advance_info, time_info
+using ..boundary_conditions: enforce_boundary_conditions!
+using ..boundary_conditions: enforce_neutral_boundary_conditions!
+using ..input_structs
 using ..moment_constraints: hard_force_moment_constraints!,
                             hard_force_moment_constraints_neutral!
 using ..advection: setup_advection
@@ -178,24 +179,71 @@ struct spectral_object_struct{Tvz,Tvr,Tvzeta,Tvpa,Tvperp,Tz,Tr}
     r_spectral::Tr
 end
 
-"""
-create arrays and do other work needed to setup
-the main time advance loop.
-this includes creating and populating structs
-for Chebyshev transforms, velocity space moments,
-EM fields, and advection terms
-"""
-function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz_spectral,
-                             vr_spectral, vzeta_spectral, vpa_spectral, vperp_spectral,
-                             z_spectral, r_spectral, composition, drive_input, moments,
-                             t_input, code_time, dt_reload, dt_before_last_fail_reload,
-                             collisions, species, geometry, boundary_distributions,
-                             external_source_settings, num_diss_params,
-                             manufactured_solns_input, restarting)
+function allocate_advection_structs(composition, z, r, vpa, vperp, vz, vr, vzeta)
     # define some local variables for convenience/tidiness
-    n_species = composition.n_species
     n_ion_species = composition.n_ion_species
     n_neutral_species = composition.n_neutral_species
+    n_neutral_species_alloc = max(1,composition.n_neutral_species)
+    ##                              ##
+    # ion particle advection structs #
+    ##                              ##
+    # create structure z_advect whose members are the arrays needed to compute
+    # the advection term(s) appearing in the part of the ion kinetic equation dealing
+    # with advection in z
+    begin_serial_region()
+    z_advect = setup_advection(n_ion_species, z, vpa, vperp, r)
+    # create structure r_advect whose members are the arrays needed to compute
+    # the advection term(s) appearing in the split part of the ion kinetic equation dealing
+    # with advection in r
+    begin_serial_region()
+    r_advect = setup_advection(n_ion_species, r, vpa, vperp, z)
+    # create structure vpa_advect whose members are the arrays needed to compute
+    # the advection term(s) appearing in the split part of the ion kinetic equation dealing
+    # with advection in vpa
+    begin_serial_region()
+    vpa_advect = setup_advection(n_ion_species, vpa, vperp, z, r)
+    # create structure vperp_advect whose members are the arrays needed to compute
+    # the advection term(s) appearing in the split part of the ion kinetic equation dealing
+    # with advection in vperp
+    begin_serial_region()
+    vperp_advect = setup_advection(n_ion_species, vperp, vpa, z, r)
+    ##                                  ##
+    # neutral particle advection structs #
+    ##                                  ##
+    # create structure neutral_z_advect for neutral particle advection
+    begin_serial_region()
+    neutral_z_advect = setup_advection(n_neutral_species_alloc, z, vz, vr, vzeta, r)
+    # create structure neutral_r_advect for neutral particle advection
+    begin_serial_region()
+    neutral_r_advect = setup_advection(n_neutral_species_alloc, r, vz, vr, vzeta, z)
+    # create structure neutral_vz_advect for neutral particle advection
+    begin_serial_region()
+    neutral_vz_advect = setup_advection(n_neutral_species_alloc, vz, vr, vzeta, z, r)
+    ##                                                                 ##
+    # construct named list of advection structs to compactify arguments #
+    ##                                                                 ##
+    advection_structs = advect_object_struct(vpa_advect, vperp_advect, z_advect, r_advect, 
+                                             neutral_z_advect, neutral_r_advect, neutral_vz_advect)
+    return advection_structs
+end
+
+"""
+    setup_time_info(t_input; electrons=nothing)
+
+Create a [`input_structs.time_info`](@ref) struct using the settings in `t_input`.
+"""
+function setup_time_info(t_input, code_time, dt_reload, dt_before_last_fail_reload,
+                         manufactured_solns_input, io_input)
+    rk_coefs, n_rk_stages, rk_order, adaptive, low_storage, CFL_prefactor =
+        setup_runge_kutta_coefficients!(t_input.type,
+                                        t_input.CFL_prefactor,
+                                        t_input.split_operators)
+
+    if !adaptive
+        # No adaptive timestep, want to use the value from the input file even when we are
+        # restarting
+        dt_reload = nothing
+    end
 
     dt_shared = allocate_shared_float(1)
     previous_dt_shared = allocate_shared_float(1)
@@ -215,37 +263,67 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
 
     end_time = code_time + t_input.dt * t_input.nstep
     epsilon = 1.e-11
-    moments_output_times = [code_time + i*t_input.dt
-                            for i ∈ t_input.nwrite:t_input.nwrite:t_input.nstep]
+    if t_input.nwrite == 0
+        moments_output_times = [end_time]
+    else
+        moments_output_times = [code_time + i*t_input.dt
+                                for i ∈ t_input.nwrite:t_input.nwrite:t_input.nstep]
+    end
     if moments_output_times[end] < end_time - epsilon
         push!(moments_output_times, end_time)
     end
-    dfns_output_times = [code_time + i*t_input.dt
-                         for i ∈ t_input.nwrite_dfns:t_input.nwrite_dfns:t_input.nstep]
+    if t_input.nwrite_dfns == 0
+        dfns_output_times = [end_time]
+    else
+        dfns_output_times = [code_time + i*t_input.dt
+                             for i ∈ t_input.nwrite_dfns:t_input.nwrite_dfns:t_input.nstep]
+    end
     if dfns_output_times[end] < end_time - epsilon
         push!(dfns_output_times, end_time)
     end
-    rk_coefs, n_rk_stages, rk_order, adaptive, low_storage, CFL_prefactor =
-        setup_runge_kutta_coefficients!(t_input.type,
-                                        t_input.CFL_prefactor,
-                                        t_input.split_operators)
+
     if t_input.high_precision_error_sum
         error_sum_zero = Float128(0.0)
     else
         error_sum_zero = 0.0
     end
-    t_params = time_info(t_input.nstep, end_time, dt_shared, previous_dt_shared, next_output_time,
-                         dt_before_output, dt_before_last_fail, CFL_prefactor,
-                         step_to_output, Ref(0), Ref(0), mk_int[], mk_int[],
-                         moments_output_times, dfns_output_times, t_input.type, rk_coefs,
-                         n_rk_stages, rk_order, adaptive, low_storage, t_input.rtol,
-                         t_input.atol, t_input.atol_upar, t_input.step_update_prefactor,
-                         t_input.max_increase_factor,
-                         t_input.max_increase_factor_near_last_fail,
-                         t_input.last_fail_proximity_factor, t_input.minimum_dt,
-                         t_input.maximum_dt, error_sum_zero, t_input.split_operators,
-                         t_input.steady_state_residual, t_input.converged_residual_value,
-                         manufactured_solns_input.use_for_advance, t_input.stopfile_name)
+    return time_info(t_input.nstep, end_time, dt_shared, previous_dt_shared, next_output_time,
+                     dt_before_output, dt_before_last_fail, CFL_prefactor, step_to_output,
+                     Ref(0), Ref(0), mk_int[], mk_int[], moments_output_times,
+                     dfns_output_times, t_input.type, rk_coefs, n_rk_stages, rk_order,
+                     adaptive, low_storage, t_input.rtol, t_input.atol, t_input.atol_upar,
+                     t_input.step_update_prefactor, t_input.max_increase_factor,
+                     t_input.max_increase_factor_near_last_fail,
+                     t_input.last_fail_proximity_factor, t_input.minimum_dt,
+                     t_input.maximum_dt, error_sum_zero, t_input.split_operators,
+                     t_input.steady_state_residual, t_input.converged_residual_value,
+                     manufactured_solns_input.use_for_advance, t_input.stopfile_name)
+end
+
+"""
+create arrays and do other work needed to setup
+the main time advance loop.
+this includes creating and populating structs
+for Chebyshev transforms, velocity space moments,
+EM fields, and advection terms
+"""
+function setup_time_advance!(pdf, fields, vz, vr, vzeta, vpa, vperp, z, r, gyrophase,
+                             vz_spectral, vr_spectral, vzeta_spectral, vpa_spectral,
+                             vperp_spectral, z_spectral, r_spectral, composition,
+                             moments, t_input, code_time, dt_reload,
+                             dt_before_last_fail_reload, collisions, species, geometry,
+                             boundary_distributions, external_source_settings,
+                             num_diss_params, manufactured_solns_input, advection_structs,
+                             scratch_dummy, restarting)
+    # define some local variables for convenience/tidiness
+    n_ion_species = composition.n_ion_species
+    n_neutral_species = composition.n_neutral_species
+    ion_mom_diss_coeff = num_diss_params.ion.moment_dissipation_coefficient
+    electron_mom_diss_coeff = num_diss_params.electron.moment_dissipation_coefficient
+    neutral_mom_diss_coeff = num_diss_params.neutral.moment_dissipation_coefficient
+
+    t_params = setup_time_info(t_input, code_time, dt_reload, dt_before_last_fail_reload,
+                               manufactured_solns_input, io_input)
 
     # Make Vectors that count which variable caused timestep limits and timestep failures
     # the right length. Do this setup even when not using adaptive timestepping, because
@@ -302,11 +380,9 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
 
     # create an array of structs containing scratch arrays for the pdf and low-order moments
     # that may be evolved separately via fluid equations
-    scratch = setup_scratch_arrays(moments, pdf.charged.norm, pdf.neutral.norm, t_params.n_rk_stages)
+    scratch = setup_scratch_arrays(moments, pdf.ion.norm, pdf.neutral.norm, t_params.n_rk_stages)
     # setup dummy arrays & buffer arrays for z r MPI
     n_neutral_species_alloc = max(1,composition.n_neutral_species)
-    scratch_dummy = setup_dummy_and_buffer_arrays(r.n,z.n,vpa.n,vperp.n,vz.n,vr.n,vzeta.n,
-                                   composition.n_ion_species,n_neutral_species_alloc)
     # create arrays for Fokker-Planck collisions 
     if advance.explicit_weakform_fp_collisions
         fp_arrays = init_fokker_planck_collisions_weak_form(vpa,vperp,vpa_spectral,vperp_spectral; precompute_weights=true)
@@ -316,10 +392,6 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
     # create gyroaverage matrix arrays
     gyroavs = init_gyro_operators(vperp,z,r,gyrophase,geometry,composition)
 
-    # create the "fields" structure that contains arrays
-    # for the electrostatic potential phi and eventually the electromagnetic fields
-    fields = setup_em_fields(vperp.n, z.n, r.n, composition.n_ion_species, drive_input.force_phi,
-      drive_input.amplitude, drive_input.frequency, drive_input.force_Er_zero_at_wall)
     # initialize the electrostatic potential
     begin_serial_region()
     update_phi!(fields, scratch[1], vperp, z, r, composition, z_spectral, r_spectral, scratch_dummy, gyroavs)
@@ -332,62 +404,50 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
     # 'speed' in advect objects, which are needed for boundary conditions on the
     # distribution function which is then used to (possibly) re-calculate the moments
     # after which the initial values of moment derivatives are re-calculated.
-    calculate_moment_derivatives!(moments, scratch[1], scratch_dummy, z, z_spectral, num_diss_params)
-    calculate_moment_derivatives_neutral!(moments, scratch[1], scratch_dummy, z,
-                                          z_spectral, num_diss_params)
-
+    calculate_ion_moment_derivatives!(moments, scratch[1], scratch_dummy, z, z_spectral, 
+                                      ion_mom_diss_coeff)
+    calculate_neutral_moment_derivatives!(moments, scratch[1], scratch_dummy, z, z_spectral, 
+                                          neutral_mom_diss_coeff)
+
+    r_advect = advection_structs.r_advect
+    z_advect = advection_structs.z_advect
+    vperp_advect = advection_structs.vperp_advect
+    vpa_advect = advection_structs.vpa_advect
+    neutral_r_advect = advection_structs.neutral_r_advect
+    neutral_z_advect = advection_structs.neutral_z_advect
+    neutral_vz_advect = advection_structs.neutral_vz_advect
     ##
-    # Charged particle advection only
+    # ion particle advection only
     ##
 
-    # create structure r_advect whose members are the arrays needed to compute
-    # the advection term(s) appearing in the split part of the GK equation dealing
-    # with advection in r
-    begin_serial_region()
-    r_advect = setup_advection(n_ion_species, r, vpa, vperp, z)
     if r.n > 1
         # initialise the r advection speed
         begin_s_z_vperp_vpa_region()
         @loop_s is begin
-            @views update_speed_r!(r_advect[is], moments.charged.upar[:,:,is],
-                                   moments.charged.vth[:,:,is], fields, moments.evolve_upar,
+            @views update_speed_r!(r_advect[is], moments.ion.upar[:,:,is],
+                                   moments.ion.vth[:,:,is], fields, moments.evolve_upar,
                                    moments.evolve_ppar, vpa, vperp, z, r, geometry, is)
         end
         # enforce prescribed boundary condition in r on the distribution function f
     end
 
-    # create structure z_advect whose members are the arrays needed to compute
-    # the advection term(s) appearing in the split part of the GK equation dealing
-    # with advection in z
-    begin_serial_region()
-    z_advect = setup_advection(n_ion_species, z, vpa, vperp, r)
     if z.n > 1
         # initialise the z advection speed
         begin_s_r_vperp_vpa_region()
         @loop_s is begin
-            @views update_speed_z!(z_advect[is], moments.charged.upar[:,:,is],
-                                   moments.charged.vth[:,:,is], moments.evolve_upar,
+            @views update_speed_z!(z_advect[is], moments.ion.upar[:,:,is],
+                                   moments.ion.vth[:,:,is], moments.evolve_upar,
                                    moments.evolve_ppar, fields, vpa, vperp, z, r, 0.0,
                                    geometry, is)
         end
     end
-    begin_serial_region()
 
-    # create structure vpa_advect whose members are the arrays needed to compute
-    # the advection term(s) appearing in the split part of the GK equation dealing
-    # with advection in vpa
-    vpa_advect = setup_advection(n_ion_species, vpa, vperp, z, r)
     # initialise the vpa advection speed
     begin_s_r_z_vperp_region()
     update_speed_vpa!(vpa_advect, fields, scratch[1], moments, vpa, vperp, z, r,
                       composition, collisions, external_source_settings.ion, 0.0,
                       geometry)
 
-    # create structure vperp_advect whose members are the arrays needed to compute
-    # the advection term(s) appearing in the split part of the GK equation dealing
-    # with advection in vperp
-    begin_serial_region()
-    vperp_advect = setup_advection(n_ion_species, vperp, vpa, z, r)
     # initialise the vperp advection speed
     # Note that z_advect and r_advect are arguments of update_speed_vperp!
     # This means that z_advect[is].speed and r_advect[is].speed are used to determine
@@ -406,9 +466,6 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
     # Neutral particle advection
     ##
 
-    # create structure neutral_r_advect for neutral particle advection
-    begin_serial_region()
-    neutral_r_advect = setup_advection(n_neutral_species_alloc, r, vz, vr, vzeta, z)
     if n_neutral_species > 0 && r.n > 1
         # initialise the r advection speed
         begin_sn_z_vzeta_vr_vz_region()
@@ -417,9 +474,6 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
         end
     end
 
-    # create structure neutral_z_advect for neutral particle advection
-    begin_serial_region()
-    neutral_z_advect = setup_advection(n_neutral_species_alloc, z, vz, vr, vzeta, r)
     if n_neutral_species > 0 && z.n > 1
         # initialise the z advection speed
         begin_sn_r_vzeta_vr_vz_region()
@@ -432,9 +486,6 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
         end
     end
 
-    # create structure neutral_vz_advect for neutral particle advection
-    begin_serial_region()
-    neutral_vz_advect = setup_advection(n_neutral_species_alloc, vz, vr, vzeta, z, r)
     if n_neutral_species > 0
         # initialise the z advection speed
         @serial_region begin
@@ -455,7 +506,6 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
     # construct advect & spectral objects to compactify arguments
     ##
 
-    advect_objects = advect_object_struct(vpa_advect, vperp_advect, z_advect, r_advect, neutral_z_advect, neutral_r_advect, neutral_vz_advect)
     spectral_objects = spectral_object_struct(vz_spectral, vr_spectral, vzeta_spectral, vpa_spectral, vperp_spectral, z_spectral, r_spectral)
     if(advance.manufactured_solns_test)
         manufactured_source_list = manufactured_sources(manufactured_solns_input, r, z,
@@ -469,43 +519,55 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
     if !restarting
         begin_serial_region()
         # ensure initial pdf has no negative values
-        force_minimum_pdf_value!(pdf.charged.norm, num_diss_params)
-        force_minimum_pdf_value_neutral!(pdf.neutral.norm, num_diss_params)
+        force_minimum_pdf_value!(pdf.ion.norm, num_diss_params.ion.force_minimum_pdf_value)
+        force_minimum_pdf_value_neutral!(pdf.neutral.norm, num_diss_params.neutral.force_minimum_pdf_value)
         # enforce boundary conditions and moment constraints to ensure a consistent initial
         # condition
         enforce_boundary_conditions!(
-            pdf.charged.norm, boundary_distributions.pdf_rboundary_charged,
-            moments.charged.dens, moments.charged.upar, moments.charged.ppar, moments,
+            pdf.ion.norm, boundary_distributions.pdf_rboundary_ion,
+            moments.ion.dens, moments.ion.upar, moments.ion.ppar, moments,
             vpa.bc, z.bc, r.bc, vpa, vperp, z, r, vpa_spectral, vperp_spectral,
             vpa_advect, vperp_advect, z_advect, r_advect,
             composition, scratch_dummy, advance.r_diffusion,
             advance.vpa_diffusion, advance.vperp_diffusion)
         # Ensure normalised pdf exactly obeys integral constraints if evolving moments
         begin_s_r_z_region()
-        @loop_s_r_z is ir iz begin
-            @views hard_force_moment_constraints!(pdf.charged.norm[:,:,iz,ir,is], moments,
-                                                  vpa)
+        if moments.evolve_density && moments.enforce_conservation
+            A = moments.ion.constraints_A_coefficient
+            B = moments.ion.constraints_B_coefficient
+            C = moments.ion.constraints_C_coefficient
+            @loop_s_r_z is ir iz begin
+                (A[iz,ir,is], B[iz,ir,is], C[iz,ir,is]) =
+                    @views hard_force_moment_constraints!(pdf.ion.norm[:,:,iz,ir,is],
+                                                          moments, vpa)
+            end
         end
         # update moments in case they were affected by applying boundary conditions or
         # constraints to the pdf
         reset_moments_status!(moments)
-        update_moments!(moments, pdf.charged.norm, gyroavs, vpa, vperp, z, r, composition,
+        update_moments!(moments, pdf.ion.norm, gyroavs, vpa, vperp, z, r, composition,
            r_spectral,geometry,scratch_dummy,z_advect)
         # enforce boundary conditions in r and z on the neutral particle distribution function
         if n_neutral_species > 0
             # Note, so far vr and vzeta do not need advect objects, so pass `nothing` for
             # those as a placeholder
             enforce_neutral_boundary_conditions!(
-                pdf.neutral.norm, pdf.charged.norm, boundary_distributions,
+                pdf.neutral.norm, pdf.ion.norm, boundary_distributions,
                 moments.neutral.dens, moments.neutral.uz, moments.neutral.pz, moments,
-                moments.charged.dens, moments.charged.upar, fields.Er, vzeta_spectral,
+                moments.ion.dens, moments.ion.upar, fields.Er, vzeta_spectral,
                 vr_spectral, vz_spectral, neutral_r_advect, neutral_z_advect, nothing,
                 nothing, neutral_vz_advect, r, z, vzeta, vr, vz, composition, geometry,
                 scratch_dummy, advance.r_diffusion, advance.vz_diffusion)
             begin_sn_r_z_region()
-            @loop_sn_r_z isn ir iz begin
-                @views hard_force_moment_constraints_neutral!(
-                    pdf.neutral.norm[:,:,:,iz,ir,isn], moments, vz)
+            if moments.evolve_density && moments.enforce_conservation
+                A = moments.neutral.constraints_A_coefficient
+                B = moments.neutral.constraints_B_coefficient
+                C = moments.neutral.constraints_C_coefficient
+                @loop_sn_r_z isn ir iz begin
+                    (A[iz,ir,isn], B[iz,ir,isn], C[iz,ir,isn]) =
+                        @views hard_force_moment_constraints_neutral!(
+                            pdf.neutral.norm[:,:,:,iz,ir,isn], moments, vz)
+                end
             end
             update_moments_neutral!(moments, pdf.neutral.norm, vz, vr, vzeta, z, r,
                                     composition)
@@ -515,10 +577,10 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
         # or constraints to the pdf
         begin_s_r_z_region()
         @loop_s_r_z is ir iz begin
-            scratch[1].pdf[:,:,iz,ir,is] .= pdf.charged.norm[:,:,iz,ir,is]
-            scratch[1].density[iz,ir,is] = moments.charged.dens[iz,ir,is]
-            scratch[1].upar[iz,ir,is] = moments.charged.upar[iz,ir,is]
-            scratch[1].ppar[iz,ir,is] = moments.charged.ppar[iz,ir,is]
+            scratch[1].pdf[:,:,iz,ir,is] .= pdf.ion.norm[:,:,iz,ir,is]
+            scratch[1].density[iz,ir,is] = moments.ion.dens[iz,ir,is]
+            scratch[1].upar[iz,ir,is] = moments.ion.upar[iz,ir,is]
+            scratch[1].ppar[iz,ir,is] = moments.ion.ppar[iz,ir,is]
         end
 
         begin_sn_r_z_region(no_synchronize=true)
@@ -532,16 +594,16 @@ function setup_time_advance!(pdf, vz, vr, vzeta, vpa, vperp, z, r, gyrophase, vz
 
     update_phi!(fields, scratch[1], vperp, z, r, composition, z_spectral, r_spectral,
                 scratch_dummy, gyroavs)
-    calculate_moment_derivatives!(moments, scratch[1], scratch_dummy, z, z_spectral, num_diss_params)
-    calculate_moment_derivatives_neutral!(moments, scratch[1], scratch_dummy, z,
-                                          z_spectral, num_diss_params)
+    calculate_ion_moment_derivatives!(moments, scratch[1], scratch_dummy, z, z_spectral, 
+                                      ion_mom_diss_coeff)
+    calculate_neutral_moment_derivatives!(moments, scratch[1], scratch_dummy, z, z_spectral, 
+                                      neutral_mom_diss_coeff)
 
     # Ensure all processes are synchronized at the end of the setup
     _block_synchronize()
 
-    return moments, fields, spectral_objects, advect_objects,
-    scratch, advance, t_params, fp_arrays, gyroavs, scratch_dummy,
-    manufactured_source_list
+    return moments, spectral_objects, scratch, advance, t_params, fp_arrays, gyroavs,
+           manufactured_source_list
 end
 
 """
@@ -563,7 +625,7 @@ function setup_advance_flags(moments, composition, t_params, collisions,
     advance_ionization = false
     advance_ionization_1V = false
     advance_ionization_source = false
-    advance_krook_collisions = false
+    advance_krook_collisions_ii = false
     advance_external_source = false
     advance_numerical_dissipation = false
     advance_sources = false
@@ -641,8 +703,8 @@ function setup_advance_flags(moments, composition, t_params, collisions,
         if collisions.ionization > 0.0 && collisions.constant_ionization_rate
             advance_ionization_source = true
         end
-        if collisions.krook.krook_collision_frequency_prefactor > 0.0
-            advance_krook_collisions = true
+        if collisions.krook.nuii0 > 0.0
+            advance_krook_collisions_ii = true
         end
         advance_external_source = external_source_settings.ion.active
         advance_neutral_external_source = external_source_settings.neutral.active
@@ -682,11 +744,11 @@ function setup_advance_flags(moments, composition, t_params, collisions,
         end
 
         # flag to determine if a d^2/dr^2 operator is present
-        r_diffusion = (advance_numerical_dissipation && num_diss_params.r_dissipation_coefficient > 0.0)
+        r_diffusion = (advance_numerical_dissipation && num_diss_params.ion.r_dissipation_coefficient > 0.0)
         # flag to determine if a d^2/dvpa^2 operator is present
-        vpa_diffusion = ((advance_numerical_dissipation && num_diss_params.vpa_dissipation_coefficient > 0.0) || explicit_weakform_fp_collisions)
-        vperp_diffusion = ((advance_numerical_dissipation && num_diss_params.vperp_dissipation_coefficient > 0.0) || explicit_weakform_fp_collisions)
-        vz_diffusion = (advance_numerical_dissipation && num_diss_params.vz_dissipation_coefficient > 0.0)
+        vpa_diffusion = ((advance_numerical_dissipation && num_diss_params.ion.vpa_dissipation_coefficient > 0.0) || explicit_weakform_fp_collisions)
+        vperp_diffusion = ((advance_numerical_dissipation && num_diss_params.ion.vperp_dissipation_coefficient > 0.0) || explicit_weakform_fp_collisions)
+        vz_diffusion = (advance_numerical_dissipation && num_diss_params.neutral.vz_dissipation_coefficient > 0.0)
     end
 
     manufactured_solns_test = manufactured_solns_input.use_for_advance
@@ -695,7 +757,7 @@ function setup_advance_flags(moments, composition, t_params, collisions,
                         advance_neutral_z_advection, advance_neutral_r_advection,
                         advance_neutral_vz_advection, advance_cx, advance_cx_1V,
                         advance_ionization, advance_ionization_1V,
-                        advance_ionization_source, advance_krook_collisions,
+                        advance_ionization_source, advance_krook_collisions_ii,
                         explicit_weakform_fp_collisions,
                         advance_external_source, advance_numerical_dissipation,
                         advance_sources, advance_continuity, advance_force_balance,
@@ -833,12 +895,12 @@ end
 create an array of structs containing scratch arrays for the normalised pdf and low-order moments
 that may be evolved separately via fluid equations
 """
-function setup_scratch_arrays(moments, pdf_charged_in, pdf_neutral_in, n_rk_stages)
+function setup_scratch_arrays(moments, pdf_ion_in, pdf_neutral_in, n_rk_stages)
     # create n_rk_stages+1 structs, each of which will contain one pdf,
     # one density, and one parallel flow array
     scratch = Vector{scratch_pdf{5,3,6,3}}(undef, n_rk_stages+1)
-    pdf_dims = size(pdf_charged_in)
-    moment_dims = size(moments.charged.dens)
+    pdf_dims = size(pdf_ion_in)
+    moment_dims = size(moments.ion.dens)
     pdf_neutral_dims = size(pdf_neutral_in)
     moment_neutral_dims = size(moments.neutral.dens)
     # populate each of the structs
@@ -863,11 +925,11 @@ function setup_scratch_arrays(moments, pdf_charged_in, pdf_neutral_in, n_rk_stag
                                       pdf_neutral_array, density_neutral_array,
                                       uz_neutral_array, pz_neutral_array)
         @serial_region begin
-            scratch[istage].pdf .= pdf_charged_in
-            scratch[istage].density .= moments.charged.dens
-            scratch[istage].upar .= moments.charged.upar
-            scratch[istage].ppar .= moments.charged.ppar
-            scratch[istage].pperp .= moments.charged.pperp
+            scratch[istage].pdf .= pdf_ion_in
+            scratch[istage].density .= moments.ion.dens
+            scratch[istage].upar .= moments.ion.upar
+            scratch[istage].ppar .= moments.ion.ppar
+            scratch[istage].pperp .= moments.ion.pperp
 
             scratch[istage].pdf_neutral .= pdf_neutral_in
             scratch[istage].density_neutral .= moments.neutral.dens
@@ -935,6 +997,11 @@ function time_advance!(pdf, scratch, t, t_params, vz, vr, vzeta, vpa, vperp, gyr
     iwrite_dfns = 2
     finish_now = false
     t_params.step_counter[] = 1
+    if t ≥ t_params.end_time - epsilon
+        # User must have requested zero output steps, i.e. to just write out the initial
+        # profiles
+        return nothing
+    end
     while true
         
         diagnostic_checks = (t + t_params.dt[] ≥ t_params.moments_output_times[moments_output_counter] - epsilon
@@ -1059,12 +1126,13 @@ function time_advance!(pdf, scratch, t, t_params, vz, vr, vzeta, vpa, vperp, gyr
                     print(Dates.format(now(), dateformat"H:MM:SS"))
                 end
             end
-            write_data_to_ascii(moments, fields, vpa, vperp, z, r, t,
+            write_data_to_ascii(pdf, moments, fields, vpa, vperp, z, r, t,
                                 composition.n_ion_species, composition.n_neutral_species,
                                 ascii_io)
-            write_moments_data_to_binary(moments, fields, t, composition.n_ion_species,
-                                         composition.n_neutral_species, io_moments,
-                                         iwrite_moments, time_for_run, t_params, r, z)
+            write_all_moments_data_to_binary(moments, fields, t,
+                                             composition.n_ion_species,
+                                             composition.n_neutral_species, io_moments,
+                                             iwrite_moments, time_for_run, t_params, r, z)
 
             if t_params.steady_state_residual
                 # Calculate some residuals to see how close simulation is to steady state
@@ -1144,11 +1212,11 @@ function time_advance!(pdf, scratch, t, t_params, vz, vr, vzeta, vpa, vperp, gyr
                     flush(stdout)
                 end
             end
-            write_dfns_data_to_binary(pdf.charged.norm, pdf.neutral.norm, moments, fields,
-                                      t, composition.n_ion_species,
-                                      composition.n_neutral_species, io_dfns, iwrite_dfns,
-                                      time_for_run, t_params, r, z, vperp, vpa, vzeta, vr,
-                                      vz)
+            write_all_dfns_data_to_binary(pdf, moments, fields, t,
+                                          composition.n_ion_species,
+                                          composition.n_neutral_species, io_dfns,
+                                          iwrite_dfns, time_for_run, t_params, r, z,
+                                          vperp, vpa, vzeta, vr, vz)
             iwrite_dfns += 1
             begin_s_r_z_vperp_region()
             @debug_detect_redundant_block_synchronize begin
@@ -1190,7 +1258,7 @@ function time_advance_split_operators!(pdf, scratch, t, t_params, vpa, z,
     flipflop = (mod(istep,2)==0)
     if flipflop
         # advance the operator-split 1D advection equation in vpa
-        # vpa-advection only applies for charged species
+        # vpa-advection only applies for ion species
         advance.vpa_advection = true
         time_advance_no_splitting!(pdf, scratch, t, t_params, vpa, z,
             vpa_spectral, z_spectral, moments, fields, vpa_advect, z_advect,
@@ -1198,7 +1266,7 @@ function time_advance_split_operators!(pdf, scratch, t, t_params, vpa, z,
             istep)
         advance.vpa_advection = false
         # z_advection! advances the operator-split 1D advection equation in z
-        # apply z-advection operation to all species (charged and neutral)
+        # apply z-advection operation to all species (ion and neutral)
         advance.z_advection = true
         time_advance_no_splitting!(pdf, scratch, t, t_params, vpa, z,
             vpa_spectral, z_spectral, moments, fields, vpa_advect, z_advect,
@@ -1225,12 +1293,12 @@ function time_advance_split_operators!(pdf, scratch, t, t_params, vpa, z,
             end
         end
         if collisions.krook_collision_frequency_prefactor  > 0.0
-            advance.krook_collisions = true
+            advance.krook_collisions_ii = true
             time_advance_no_splitting!(pdf, scratch, t, t_params, z, vpa,
                 z_spectral, vpa_spectral, moments, fields, z_advect, vpa_advect,
                 z_SL, vpa_SL, composition, collisions, sources, num_diss_params,
                 advance, istep)
-            advance.krook_collisions = false
+            advance.krook_collisions_ii = false
         end
         # and add the source terms associated with redefining g = pdf/density or pdf*vth/density
         # to the kinetic equation
@@ -1327,7 +1395,7 @@ function time_advance_split_operators!(pdf, scratch, t, t_params, vpa, z,
             end
         end
         # z_advection! advances the operator-split 1D advection equation in z
-        # apply z-advection operation to all species (charged and neutral)
+        # apply z-advection operation to all species (ion and neutral)
         advance.z_advection = true
         time_advance_no_splitting!(pdf, scratch, t, t_params, vpa, z,
             vpa_spectral, z_spectral, moments, fields, vpa_advect, z_advect,
@@ -1335,7 +1403,7 @@ function time_advance_split_operators!(pdf, scratch, t, t_params, vpa, z,
             istep)
         advance.z_advection = false
         # advance the operator-split 1D advection equation in vpa
-        # vpa-advection only applies for charged species
+        # vpa-advection only applies for ion species
         advance.vpa_advection = true
         time_advance_no_splitting!(pdf, scratch, t, t_params, vpa, z,
             vpa_spectral, z_spectral, moments, fields, vpa_advect, z_advect,
@@ -1386,7 +1454,7 @@ function rk_update!(scratch, pdf, moments, fields, boundary_distributions, vz, v
     neutral_z_advect, neutral_r_advect, neutral_vz_advect = advect_objects.neutral_z_advect, advect_objects.neutral_r_advect, advect_objects.neutral_vz_advect
 
     ##
-    # update the charged particle distribution and moments
+    # update the ion distribution and moments
     ##
     # here we seem to have duplicate arrays for storing n, u||, p||, etc, but not for vth
     # 'scratch' is for the multiple stages of time advanced quantities, but 'moments' can be updated directly at each stage
@@ -1397,7 +1465,7 @@ function rk_update!(scratch, pdf, moments, fields, boundary_distributions, vz, v
     # Ensure there are no negative values in the pdf before applying boundary
     # conditions, so that negative deviations do not mess up the integral-constraint
     # corrections in the sheath boundary conditions.
-    force_minimum_pdf_value!(new_scratch.pdf, num_diss_params)
+    force_minimum_pdf_value!(new_scratch.pdf, num_diss_params.ion.force_minimum_pdf_value)
 
     # Enforce boundary conditions in z and vpa on the distribution function.
     # Must be done after Runge Kutta update so that the boundary condition applied to
@@ -1407,16 +1475,20 @@ function rk_update!(scratch, pdf, moments, fields, boundary_distributions, vz, v
     # contribution from one or more of the terms.
     # NB: probably need to do the same for the evolved moments
     enforce_boundary_conditions!(new_scratch, moments,
-        boundary_distributions.pdf_rboundary_charged, vpa.bc, z.bc, r.bc, vpa, vperp, z,
+        boundary_distributions.pdf_rboundary_ion, vpa.bc, z.bc, r.bc, vpa, vperp, z,
         r, vpa_spectral, vperp_spectral, 
         vpa_advect, vperp_advect, z_advect, r_advect, composition, scratch_dummy,
         advance.r_diffusion, advance.vpa_diffusion, advance.vperp_diffusion)
 
     if moments.evolve_density && moments.enforce_conservation
         begin_s_r_z_region()
+        A = moments.ion.constraints_A_coefficient
+        B = moments.ion.constraints_B_coefficient
+        C = moments.ion.constraints_C_coefficient
         @loop_s_r_z is ir iz begin
-            @views hard_force_moment_constraints!(new_scratch.pdf[:,:,iz,ir,is], moments,
-                                                  vpa)
+            (A[iz,ir,is], B[iz,ir,is], C[iz,ir,is]) =
+                @views hard_force_moment_constraints!(new_scratch.pdf[:,:,iz,ir,is],
+                                                     moments, vpa)
         end
     end
 
@@ -1428,8 +1500,8 @@ function rk_update!(scratch, pdf, moments, fields, boundary_distributions, vz, v
         update_derived_moments!(new_scratch, moments, vpa, vperp, z, r, composition,
             r_spectral, geometry, gyroavs, scratch_dummy, z_advect, diagnostic_moments)
 
-        calculate_moment_derivatives!(moments, new_scratch, scratch_dummy, z, z_spectral,
-                                      num_diss_params)
+        calculate_ion_moment_derivatives!(moments, new_scratch, scratch_dummy, z, z_spectral,
+                                          num_diss_params.ion.moment_dissipation_coefficient)
     end
     update_derived_ion_moments_and_derivatives()
 
@@ -1444,7 +1516,7 @@ function rk_update!(scratch, pdf, moments, fields, boundary_distributions, vz, v
         # Ensure there are no negative values in the pdf before applying boundary
         # conditions, so that negative deviations do not mess up the integral-constraint
         # corrections in the sheath boundary conditions.
-        force_minimum_pdf_value_neutral!(new_scratch.pdf_neutral, num_diss_params)
+        force_minimum_pdf_value_neutral!(new_scratch.pdf_neutral, num_diss_params.neutral.force_minimum_pdf_value)
 
         # Enforce boundary conditions in z and vpa on the distribution function.
         # Must be done after Runge Kutta update so that the boundary condition applied to
@@ -1465,9 +1537,13 @@ function rk_update!(scratch, pdf, moments, fields, boundary_distributions, vz, v
 
         if moments.evolve_density && moments.enforce_conservation
             begin_sn_r_z_region()
+            A = moments.neutral.constraints_A_coefficient
+            B = moments.neutral.constraints_B_coefficient
+            C = moments.neutral.constraints_C_coefficient
             @loop_sn_r_z isn ir iz begin
-                @views hard_force_moment_constraints_neutral!(
-                    new_scratch.pdf_neutral[:,:,:,iz,ir,isn], moments, vz)
+                (A[iz,ir,isn], B[iz,ir,isn], C[iz,ir,isn]) =
+                    @views hard_force_moment_constraints_neutral!(
+                        new_scratch.pdf_neutral[:,:,:,iz,ir,isn], moments, vz)
             end
         end
 
@@ -1488,8 +1564,9 @@ function rk_update!(scratch, pdf, moments, fields, boundary_distributions, vz, v
                                r, composition, moments.evolve_density, moments.evolve_upar,
                                moments.evolve_ppar)
 
-            calculate_moment_derivatives_neutral!(moments, new_scratch, scratch_dummy, z,
-                                                  z_spectral, num_diss_params)
+            calculate_neutral_moment_derivatives!(moments, new_scratch, scratch_dummy, z,
+                                                  z_spectral,
+                                                  num_diss_params.neutral.moment_dissipation_coefficient)
         end
         update_derived_neutral_moments_and_derivatives()
     end
@@ -1587,9 +1664,8 @@ function adaptive_timestep_update!(scratch, t, t_params, moments, fields, compos
     begin_r_vperp_vpa_region(; no_synchronize=true)
     ion_z_CFL = Inf
     @loop_s is begin
-        update_speed_z!(z_advect[is], moments.charged.upar, moments.charged.vth,
-                        evolve_upar, evolve_ppar, fields, vpa, vperp, z, r, t, geometry,
-                        is)
+        update_speed_z!(z_advect[is], moments.ion.upar, moments.ion.vth, evolve_upar,
+                        evolve_ppar, fields, vpa, vperp, z, r, t, geometry, is)
         this_minimum = get_minimum_CFL_z(z_advect[is].speed, z)
         @serial_region begin
             ion_z_CFL = min(ion_z_CFL, this_minimum)
@@ -1752,7 +1828,7 @@ function adaptive_timestep_update!(scratch, t, t_params, moments, fields, compos
 end
 
 """
-update velocity moments that are calculable from the evolved charged pdf
+update velocity moments that are calculable from the evolved ion pdf
 """
 function update_derived_moments!(new_scratch, moments, vpa, vperp, z, r, composition,
     r_spectral, geometry, gyroavs, scratch_dummy, z_advect, diagnostic_moments)
@@ -1766,20 +1842,20 @@ function update_derived_moments!(new_scratch, moments, vpa, vperp, z, r, composi
     end
     
     if !moments.evolve_density
-        update_density!(new_scratch.density, moments.charged.dens_updated,
+        update_density!(new_scratch.density, moments.ion.dens_updated,
                         ff, vpa, vperp, z, r, composition)
     end
     if !moments.evolve_upar
-        update_upar!(new_scratch.upar, moments.charged.upar_updated, new_scratch.density,
+        update_upar!(new_scratch.upar, moments.ion.upar_updated, new_scratch.density,
                      new_scratch.ppar, ff, vpa, vperp, z, r, composition,
                      moments.evolve_density, moments.evolve_ppar)
     end
     if !moments.evolve_ppar
         # update_ppar! calculates (p_parallel/m_s N_e c_s^2) + (n_s/N_e)*(upar_s/c_s)^2 = (1/√π)∫d(vpa/c_s) (vpa/c_s)^2 * (√π f_s c_s / N_e)
-        update_ppar!(new_scratch.ppar, moments.charged.ppar_updated, new_scratch.density,
+        update_ppar!(new_scratch.ppar, moments.ion.ppar_updated, new_scratch.density,
                      new_scratch.upar, ff, vpa, vperp, z, r, composition,
                      moments.evolve_density, moments.evolve_upar)
-    end 
+    end
     update_pperp!(new_scratch.pperp, ff, vpa, vperp, z, r, composition)
     
     # if diagnostic time step/RK stage
@@ -1790,7 +1866,7 @@ function update_derived_moments!(new_scratch, moments, vpa, vperp, z, r, composi
     # update the thermal speed
     begin_s_r_z_region()
     try #below block causes DomainError if ppar < 0 or density, so exit cleanly if possible
-        update_vth!(moments.charged.vth, new_scratch.ppar, new_scratch.pperp, new_scratch.density, vperp, z, r, composition)
+        update_vth!(moments.ion.vth, new_scratch.ppar, new_scratch.pperp, new_scratch.density, vperp, z, r, composition)
     catch e
         if global_size[] > 1
             println("ERROR: error calculating vth in time_advance.jl")
@@ -1803,8 +1879,8 @@ function update_derived_moments!(new_scratch, moments, vpa, vperp, z, r, composi
         rethrow(e)
     end
     # update the parallel heat flux
-    update_qpar!(moments.charged.qpar, moments.charged.qpar_updated, new_scratch.density,
-                 new_scratch.upar, moments.charged.vth, ff, vpa, vperp, z, r,
+    update_qpar!(moments.ion.qpar, moments.ion.qpar_updated, new_scratch.density,
+                 new_scratch.upar, moments.ion.vth, ff, vpa, vperp, z, r,
                  composition, moments.evolve_density, moments.evolve_upar,
                  moments.evolve_ppar)
     # add further moments to be computed here
@@ -1847,13 +1923,13 @@ function ssp_rk!(pdf, scratch, t, t_params, vz, vr, vzeta, vpa, vperp, gyrophase
 
     first_scratch = scratch[1]
     @loop_s_r_z_vperp_vpa is ir iz ivperp ivpa begin
-        first_scratch.pdf[ivpa,ivperp,iz,ir,is] = pdf.charged.norm[ivpa,ivperp,iz,ir,is]
+        first_scratch.pdf[ivpa,ivperp,iz,ir,is] = pdf.ion.norm[ivpa,ivperp,iz,ir,is]
     end
     @loop_s_r_z is ir iz begin
-        first_scratch.density[iz,ir,is] = moments.charged.dens[iz,ir,is]
-        first_scratch.upar[iz,ir,is] = moments.charged.upar[iz,ir,is]
-        first_scratch.ppar[iz,ir,is] = moments.charged.ppar[iz,ir,is]
-        first_scratch.pperp[iz,ir,is] = moments.charged.pperp[iz,ir,is]
+        first_scratch.density[iz,ir,is] = moments.ion.dens[iz,ir,is]
+        first_scratch.upar[iz,ir,is] = moments.ion.upar[iz,ir,is]
+        first_scratch.ppar[iz,ir,is] = moments.ion.ppar[iz,ir,is]
+        first_scratch.pperp[iz,ir,is] = moments.ion.pperp[iz,ir,is]
     end
 
     if composition.n_neutral_species > 0
@@ -1899,13 +1975,13 @@ function ssp_rk!(pdf, scratch, t, t_params, vz, vr, vzeta, vpa, vperp, gyrophase
     begin_s_r_z_region()
     final_scratch = scratch[istage]
     @loop_s_r_z_vperp_vpa is ir iz ivperp ivpa begin
-        pdf.charged.norm[ivpa,ivperp,iz,ir,is] = final_scratch.pdf[ivpa,ivperp,iz,ir,is]
+        pdf.ion.norm[ivpa,ivperp,iz,ir,is] = final_scratch.pdf[ivpa,ivperp,iz,ir,is]
     end
     @loop_s_r_z is ir iz begin
-        moments.charged.dens[iz,ir,is] = final_scratch.density[iz,ir,is]
-        moments.charged.upar[iz,ir,is] = final_scratch.upar[iz,ir,is]
-        moments.charged.ppar[iz,ir,is] = final_scratch.ppar[iz,ir,is]
-        moments.charged.pperp[iz,ir,is] = final_scratch.pperp[iz,ir,is]
+        moments.ion.dens[iz,ir,is] = final_scratch.density[iz,ir,is]
+        moments.ion.upar[iz,ir,is] = final_scratch.upar[iz,ir,is]
+        moments.ion.ppar[iz,ir,is] = final_scratch.ppar[iz,ir,is]
+        moments.ion.pperp[iz,ir,is] = final_scratch.pperp[iz,ir,is]
     end
     if composition.n_neutral_species > 0
         # No need to synchronize here as we only change neutral quantities and previous
@@ -1978,7 +2054,7 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
     n_ion_species = composition.n_ion_species
     n_neutral_species = composition.n_neutral_species
     # vpa_advection! advances the 1D advection equation in vpa.
-    # only charged species have a force accelerating them in vpa;
+    # only ion species have a force accelerating them in vpa;
     # however, neutral species do have non-zero d(wpa)/dt, so there is advection in wpa
 
     vpa_spectral, vperp_spectral, r_spectral, z_spectral = spectral_objects.vpa_spectral, spectral_objects.vperp_spectral, spectral_objects.r_spectral, spectral_objects.z_spectral
@@ -2001,7 +2077,7 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
     end
 
     # z_advection! advances 1D advection equation in z
-    # apply z-advection operation to charged species
+    # apply z-advection operation to ion species
 
     if advance.z_advection
         z_advection!(fvec_out.pdf, fvec_in, moments, fields, z_advect, z, vpa, vperp, r,
@@ -2051,9 +2127,9 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
     end
 
     if advance.cx_collisions || advance.ionization_collisions
-        # gyroaverage neutral dfn and place it in the charged.buffer array for use in the collisions step
-        vzvrvzeta_to_vpavperp!(pdf.charged.buffer, fvec_in.pdf_neutral, vz, vr, vzeta, vpa, vperp, gyrophase, z, r, geometry, composition)
-        # interpolate charged particle dfn and place it in the neutral.buffer array for use in the collisions step
+        # gyroaverage neutral dfn and place it in the ion.buffer array for use in the collisions step
+        vzvrvzeta_to_vpavperp!(pdf.ion.buffer, fvec_in.pdf_neutral, vz, vr, vzeta, vpa, vperp, gyrophase, z, r, geometry, composition)
+        # interpolate ion particle dfn and place it in the neutral.buffer array for use in the collisions step
         vpavperp_to_vzvrvzeta!(pdf.neutral.buffer, fvec_in.pdf, vz, vr, vzeta, vpa, vperp, z, r, geometry, composition)
     end
 
@@ -2064,7 +2140,7 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
                                        collisions.charge_exchange, vpa_spectral,
                                        vz_spectral, dt)
     elseif advance.cx_collisions
-        charge_exchange_collisions_3V!(fvec_out.pdf, fvec_out.pdf_neutral, pdf.charged.buffer, pdf.neutral.buffer, fvec_in, composition,
+        charge_exchange_collisions_3V!(fvec_out.pdf, fvec_out.pdf_neutral, pdf.ion.buffer, pdf.neutral.buffer, fvec_in, composition,
                                         vz, vr, vzeta, vpa, vperp, z, r, collisions.charge_exchange, dt)
     end
     # account for ionization collisions between ions and neutrals
@@ -2073,7 +2149,7 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
                                   vperp, z, r, vz_spectral, moments, composition,
                                   collisions, dt)
     elseif advance.ionization_collisions
-        ionization_collisions_3V!(fvec_out.pdf, fvec_out.pdf_neutral, pdf.charged.buffer, fvec_in, composition,
+        ionization_collisions_3V!(fvec_out.pdf, fvec_out.pdf_neutral, pdf.ion.buffer, fvec_in, composition,
                                         vz, vr, vzeta, vpa, vperp, z, r, collisions, dt)
     end
     if advance.ionization_source
@@ -2082,7 +2158,7 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
     end
 
     # Add Krook collision operator for ions
-    if advance.krook_collisions
+    if advance.krook_collisions_ii
         krook_collisions!(fvec_out.pdf, fvec_in, moments, composition, collisions,
                           vperp, vpa, dt)
     end
@@ -2099,32 +2175,32 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
     # add numerical dissipation
     if advance.numerical_dissipation
         vpa_dissipation!(fvec_out.pdf, fvec_in.pdf, vpa, vpa_spectral, dt,
-                         num_diss_params)
+                         num_diss_params.ion.vpa_dissipation_coefficient)
         vperp_dissipation!(fvec_out.pdf, fvec_in.pdf, vperp, vperp_spectral, dt,
-                         num_diss_params)
+                         num_diss_params.ion.vperp_dissipation_coefficient)
         z_dissipation!(fvec_out.pdf, fvec_in.pdf, z, z_spectral, dt,
-                       num_diss_params, scratch_dummy)
+                       num_diss_params.ion.z_dissipation_coefficient, scratch_dummy)
         r_dissipation!(fvec_out.pdf, fvec_in.pdf, r, r_spectral, dt,
-                       num_diss_params, scratch_dummy)
+                       num_diss_params.ion.r_dissipation_coefficient, scratch_dummy)
         vz_dissipation_neutral!(fvec_out.pdf_neutral, fvec_in.pdf_neutral, vz,
-                                vz_spectral, dt, num_diss_params)
+                                vz_spectral, dt, num_diss_params.neutral.vz_dissipation_coefficient)
         z_dissipation_neutral!(fvec_out.pdf_neutral, fvec_in.pdf_neutral, z, z_spectral,
-                               dt, num_diss_params, scratch_dummy)
+                               dt, num_diss_params.neutral.z_dissipation_coefficient, scratch_dummy)
         r_dissipation_neutral!(fvec_out.pdf_neutral, fvec_in.pdf_neutral, r, r_spectral,
-                               dt, num_diss_params, scratch_dummy)
+                               dt, num_diss_params.neutral.r_dissipation_coefficient, scratch_dummy)
     end
     # advance with the Fokker-Planck self-collision operator
     if advance.explicit_weakform_fp_collisions
         update_entropy_diagnostic = (istage == 1)
         if collisions.fkpl.self_collisions
             # self collisions for each species
-            explicit_fokker_planck_collisions_weak_form!(fvec_out.pdf,fvec_in.pdf,moments.charged.dSdt,composition,
+            explicit_fokker_planck_collisions_weak_form!(fvec_out.pdf,fvec_in.pdf,moments.ion.dSdt,composition,
                                  collisions,dt,fp_arrays,r,z,vperp,vpa,vperp_spectral,vpa_spectral,scratch_dummy,
                                                      diagnose_entropy_production = update_entropy_diagnostic)
         end
         if collisions.fkpl.slowing_down_test
         # include cross-collsions with fixed Maxwellian backgrounds
-            explicit_fp_collisions_weak_form_Maxwellian_cross_species!(fvec_out.pdf,fvec_in.pdf,moments.charged.dSdt,
+            explicit_fp_collisions_weak_form_Maxwellian_cross_species!(fvec_out.pdf,fvec_in.pdf,moments.ion.dSdt,
                              composition,collisions,dt,fp_arrays,r,z,vperp,vpa,vperp_spectral,vpa_spectral,
                                              diagnose_entropy_production = update_entropy_diagnostic)
         end
diff --git a/moment_kinetics/src/utils.jl b/moment_kinetics/src/utils.jl
index 6ac8c2754..b2a434435 100644
--- a/moment_kinetics/src/utils.jl
+++ b/moment_kinetics/src/utils.jl
@@ -8,11 +8,13 @@ export get_unnormalized_parameters, print_unnormalized_parameters, to_seconds, t
 
 using ..communication
 using ..constants
+using ..input_structs
 using ..looping
 using ..moment_kinetics_input: mk_input
 using ..reference_parameters
 
 using Dates
+using Glob
 using MPI
 using OrderedCollections
 using TOML
@@ -125,6 +127,173 @@ Convert a time period `x` to seconds
 """
 to_hours(x::T) where {T<:TimePeriod} = x/convert(T, Hour(1))
 
+# Utility functions used for restarting
+
+"""
+Append a number to the filename, to get a new, non-existing filename to backup the file
+to.
+"""
+function get_backup_filename(filename)
+    if !isfile(filename)
+        error("Requested to restart from $filename, but this file does not exist")
+    end
+    counter = 1
+    temp, extension = splitext(filename)
+    extension = extension[2:end]
+    temp, iblock_or_type = splitext(temp)
+    iblock_or_type = iblock_or_type[2:end]
+    iblock = nothing
+    basename = nothing
+    type = nothing
+    if iblock_or_type ∈ ("dfns", "initial_electron")
+        iblock = nothing
+        type = iblock_or_type
+        basename = temp
+        parallel_io = true
+    else
+        # Filename had an iblock, so we are not using parallel I/O, but actually want to
+        # use the iblock for this block, not necessarily for the exact file that was
+        # passed.
+        iblock = iblock_index[]
+        basename, type = splitext(temp)
+        type = type[2:end]
+        parallel_io = false
+    end
+    if type ∉ ("dfns", "initial_electron")
+        error("Must pass the '.dfns.h5' output file for restarting. Got $filename.")
+    end
+    backup_dfns_filename = ""
+    if parallel_io
+        # Using parallel I/O
+        while true
+            backup_dfns_filename = "$(basename)_$(counter).$(type).$(extension)"
+            if !isfile(backup_dfns_filename)
+                break
+            end
+            counter += 1
+        end
+        # Create dfns_filename here even though it is the filename passed in, as
+        # parallel_io=false branch needs to get the right `iblock` for this block.
+        dfns_filename = "$(basename).$(type).$(extension)"
+        if type == "dfns"
+            moments_filename = "$(basename).moments.$(extension)"
+        else
+            moments_filename = nothing
+        end
+        backup_moments_filename = "$(basename)_$(counter).moments.$(extension)"
+    else
+        while true
+            backup_dfns_filename = "$(basename)_$(counter).$(type).$(iblock).$(extension)"
+            if !isfile(backup_dfns_filename)
+                break
+            end
+            counter += 1
+        end
+        # Create dfns_filename here even though it is almost the filename passed in, in
+        # order to get the right `iblock` for this block.
+        dfns_filename = "$(basename).$(type).$(iblock).$(extension)"
+        if type == "dfns"
+            moments_filename = "$(basename).moments.$(iblock).$(extension)"
+        else
+            moments_filename = nothing
+        end
+        backup_moments_filename = "$(basename)_$(counter).moments.$(iblock).$(extension)"
+    end
+    backup_dfns_filename == "" && error("Failed to find a name for backup file.")
+    backup_prefix_iblock = ("$(basename)_$(counter)", iblock)
+    original_prefix_iblock = (basename, iblock)
+    return dfns_filename, backup_dfns_filename, parallel_io, moments_filename,
+           backup_moments_filename, backup_prefix_iblock, original_prefix_iblock
+end
+
+"""
+    get_default_restart_filename(io_input, prefix; error_if_no_file_found=true)
+
+Get the default name for the file to restart from, using the input from `io_input`.
+
+`prefix` gives the type of file to open, e.g. "moments", "dfns", or "initial_electron".
+
+If no matching file is found, raise an error unless `error_if_no_file_found=false` is
+passed, in which case no error is raised and instead the function returns `nothing`.
+"""
+function get_default_restart_filename(io_input, prefix; error_if_no_file_found=true)
+    binary_format = io_input.binary_format
+    if binary_format === hdf5
+        ext = "h5"
+    elseif binary_format === netcdf
+        ext = "cdf"
+    else
+        error("Unrecognized binary_format '$binary_format'")
+    end
+    restart_filename_pattern = joinpath(io_input.output_dir, io_input.run_name * ".$prefix*." * ext)
+    restart_filename_glob = glob(restart_filename_pattern)
+    if length(restart_filename_glob) == 0
+        if error_if_no_file_found
+            error("No '$prefix' output file to restart from found matching the pattern "
+                  * "$restart_filename_pattern")
+        end
+        restart_filename = nothing
+    else
+        restart_filename = restart_filename_glob[1]
+    end
+    return restart_filename
+end
+
+"""
+    get_prefix_iblock_and_move_existing_file(restart_filename, output_dir)
+
+Move `restart_filename` to a backup location (if it is in `output_dir`), returning a
+prefix and block-index (which might be `nothing`) which can be used to open the file for
+reloading variables.
+"""
+function get_prefix_iblock_and_move_existing_file(restart_filename, output_dir)
+    # Move the output file being restarted from to make sure it doesn't get
+    # overwritten.
+    dfns_filename, backup_dfns_filename, parallel_io, moments_filename,
+    backup_moments_filename, backup_prefix_iblock, original_prefix_iblock =
+        get_backup_filename(restart_filename)
+
+    # Ensure every process got the filenames and checked files exist before moving
+    # files
+    MPI.Barrier(comm_world)
+
+    if abspath(output_dir) == abspath(dirname(dfns_filename))
+        # Only move the file if it is in our current run directory. Otherwise we are
+        # restarting from another run, and will not be overwriting the file.
+        if (parallel_io && global_rank[] == 0) || (!parallel_io && block_rank[] == 0)
+            mv(dfns_filename, backup_dfns_filename)
+            if moments_filename !== nothing
+                mv(moments_filename, backup_moments_filename)
+            end
+        end
+    else
+        # Reload from dfns_filename without moving the file
+        backup_prefix_iblock = original_prefix_iblock
+    end
+
+    # Ensure files have been moved before any process tries to read from them
+    MPI.Barrier(comm_world)
+
+    return backup_prefix_iblock
+end
+
+"""
+    enum_from_string(enum_type, name)
+
+Get an the value of `enum_type`, whose name is given by the String (or Symbol) `name`.
+
+Returns `nothing` if the name is not found.
+"""
+function enum_from_string(enum_type, name)
+    name = Symbol(name)
+    for e ∈ instances(enum_type)
+        if name == Symbol(e)
+            return e
+        end
+    end
+    return nothing
+end
+
 # Utility functions for timestepping
 
 """
diff --git a/moment_kinetics/src/velocity_moments.jl b/moment_kinetics/src/velocity_moments.jl
index 3da3e251f..a0c7388b3 100644
--- a/moment_kinetics/src/velocity_moments.jl
+++ b/moment_kinetics/src/velocity_moments.jl
@@ -5,7 +5,7 @@ module velocity_moments
 export integrate_over_vspace
 export integrate_over_positive_vpa, integrate_over_negative_vpa
 export integrate_over_positive_vz, integrate_over_negative_vz
-export create_moments_chrg, create_moments_ntrl
+export create_moments_ion, create_moments_neutral
 export update_moments!
 export update_density!
 export update_upar!
@@ -14,7 +14,6 @@ export update_pperp!
 export update_qpar!
 export update_vth!
 export reset_moments_status!
-export moments_chrg_substruct, moments_ntrl_substruct
 export update_neutral_density!
 export update_neutral_uz!
 export update_neutral_ur!
@@ -42,6 +41,9 @@ using ..derivatives: derivative_z!
 using ..derivatives: derivative_r!
 using ..looping
 using ..gyroaverages: gyro_operators, gyroaverage_pdf!
+using ..moment_kinetics_structs: moments_ion_substruct,
+                                 moments_neutral_substruct
+
 #global tmpsum1 = 0.0
 #global tmpsum2 = 0.0
 #global dens_hist = zeros(17,1)
@@ -49,172 +51,8 @@ using ..gyroaverages: gyro_operators, gyroaverage_pdf!
 
 """
 """
-struct moments_charged_substruct
-    # this is the particle density
-    dens::MPISharedArray{mk_float,3}
-    # flag that keeps track of if the density needs updating before use
-    # Note: may not be set for all species on this process, but this process only ever
-    # sets/uses the value for the same subset of species. This means dens_update does
-    # not need to be a shared memory array.
-    dens_updated::Vector{Bool}
-    # this is the parallel flow
-    upar::MPISharedArray{mk_float,3}
-    # flag that keeps track of whether or not upar needs updating before use
-    # Note: may not be set for all species on this process, but this process only ever
-    # sets/uses the value for the same subset of species. This means upar_update does
-    # not need to be a shared memory array.
-    upar_updated::Vector{Bool}
-    # this is the parallel pressure
-    ppar::MPISharedArray{mk_float,3}
-    # flag that keeps track of whether or not ppar needs updating before use
-    # Note: may not be set for all species on this process, but this process only ever
-    # sets/uses the value for the same subset of species. This means ppar_update does
-    # not need to be a shared memory array.
-    ppar_updated::Vector{Bool}
-    # this is the perpendicular pressure
-    pperp::MPISharedArray{mk_float,3}
-    # this is the parallel heat flux
-    qpar::MPISharedArray{mk_float,3}
-    # flag that keeps track of whether or not qpar needs updating before use
-    # Note: may not be set for all species on this process, but this process only ever
-    # sets/uses the value for the same subset of species. This means qpar_update does
-    # not need to be a shared memory array.
-    qpar_updated::Vector{Bool}
-    # this is the thermal speed based on the parallel temperature Tpar = ppar/dens: vth = sqrt(2*Tpar/m)
-    vth::MPISharedArray{mk_float,3}
-    # generalised Chodura integrals for the lower and upper plates
-    chodura_integral_lower::MPISharedArray{mk_float,2}
-    chodura_integral_upper::MPISharedArray{mk_float,2}
-    # if evolve_ppar = true, then the velocity variable is (vpa - upa)/vth, which introduces
-    # a factor of vth for each power of wpa in velocity space integrals.
-    # v_norm_fac accounts for this: it is vth if using the above definition for the parallel velocity,
-    # and it is one otherwise
-    v_norm_fac::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the particle density
-    ddens_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the upwinded z-derivative of the particle density
-    ddens_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the second-z-derivative of the particle density
-    d2dens_dz2::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the parallel flow
-    dupar_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the upwinded z-derivative of the parallel flow
-    dupar_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the second-z-derivative of the parallel flow
-    d2upar_dz2::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the parallel pressure
-    dppar_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the upwinded z-derivative of the parallel pressure
-    dppar_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the second-z-derivative of the parallel pressure
-    d2ppar_dz2::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the parallel heat flux
-    dqpar_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the thermal speed based on the parallel temperature Tpar = ppar/dens: vth = sqrt(2*Tpar/m)
-    dvth_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the entropy production dS/dt = - int (ln f sum_s' C_ss' [f_s,f_s']) d^3 v
-    dSdt::MPISharedArray{mk_float,3}
-    # Spatially varying amplitude of the external source term
-    external_source_amplitude::MPISharedArray{mk_float,2}
-    # Spatially varying amplitude of the density moment of the external source term
-    external_source_density_amplitude::MPISharedArray{mk_float,2}
-    # Spatially varying amplitude of the parallel momentum moment of the external source
-    # term
-    external_source_momentum_amplitude::MPISharedArray{mk_float,2}
-    # Spatially varying amplitude of the parallel pressure moment of the external source
-    # term
-    external_source_pressure_amplitude::MPISharedArray{mk_float,2}
-    # Integral term for the PID controller of the external source term
-    external_source_controller_integral::MPISharedArray{mk_float,2}
-end
-
-"""
-"""
-struct moments_neutral_substruct
-    # this is the particle density
-    dens::MPISharedArray{mk_float,3}
-    # flag that keeps track of if the density needs updating before use
-    # Note: may not be set for all species on this process, but this process only ever
-    # sets/uses the value for the same subset of species. This means dens_update does
-    # not need to be a shared memory array.
-    dens_updated::Vector{Bool}
-    # this is the particle mean velocity in z
-    uz::MPISharedArray{mk_float,3}
-    # flag that keeps track of if uz needs updating before use
-    uz_updated::Vector{Bool}
-    # this is the particle mean velocity in r
-    ur::MPISharedArray{mk_float,3}
-    # flag that keeps track of if ur needs updating before use
-    ur_updated::Vector{Bool}
-    # this is the particle mean velocity in zeta
-    uzeta::MPISharedArray{mk_float,3}
-    # flag that keeps track of if uzeta needs updating before use
-    uzeta_updated::Vector{Bool}
-    # this is the zz particle pressure tensor component
-    pz::MPISharedArray{mk_float,3}
-    # flag that keeps track of if pz needs updating before use
-    pz_updated::Vector{Bool}
-    # this is the rr particle pressure tensor component
-    pr::MPISharedArray{mk_float,3}
-    # flag that keeps track of if pr needs updating before use
-    pr_updated::Vector{Bool}
-    # this is the zetazeta particle pressure tensor component
-    pzeta::MPISharedArray{mk_float,3}
-    # flag that keeps track of if pzeta needs updating before use
-    pzeta_updated::Vector{Bool}
-    # this is the total (isotropic) particle pressure
-    ptot::MPISharedArray{mk_float,3}
-    # this is the heat flux along z
-    qz::MPISharedArray{mk_float,3}
-    # flag that keeps track of if qz needs updating before use
-    qz_updated::Vector{Bool}
-    # this is the thermal speed based on the temperature T = ptot/dens: vth = sqrt(2*T/m)
-    vth::MPISharedArray{mk_float,3}
-    # if evolve_ppar = true, then the velocity variable is (vz - uz)/vth, which introduces
-    # a factor of vth for each power of wz in velocity space integrals.
-    # v_norm_fac accounts for this: it is vth if using the above definition for the parallel velocity,
-    # and it is one otherwise
-    v_norm_fac::MPISharedArray{mk_float,3}
-    # this is the z-derivative of the particle density
-    ddens_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the particle density
-    ddens_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the second-z-derivative of the particle density
-    d2dens_dz2::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the particle mean velocity in z
-    duz_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the upwinded z-derivative of the particle mean velocity in z
-    duz_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the second-z-derivative of the particle mean velocity in z
-    d2uz_dz2::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the zz particle pressure tensor component
-    dpz_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the upwinded z-derivative of the zz particle pressure tensor component
-    dpz_dz_upwind::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the second-z-derivative of the zz particle pressure tensor component
-    d2pz_dz2::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the thermal speed based on the temperature T = ptot/dens: vth = sqrt(2*T/m)
-    dvth_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # this is the z-derivative of the heat flux along z
-    dqz_dz::Union{MPISharedArray{mk_float,3},Nothing}
-    # Spatially varying amplitude of the external source term
-    external_source_amplitude::MPISharedArray{mk_float,2}
-    # Spatially varying amplitude of the density moment of the external source term
-    external_source_density_amplitude::MPISharedArray{mk_float,2}
-    # Spatially varying amplitude of the parallel momentum moment of the external source
-    # term
-    external_source_momentum_amplitude::MPISharedArray{mk_float,2}
-    # Spatially varying amplitude of the parallel pressure moment of the external source
-    # term
-    external_source_pressure_amplitude::MPISharedArray{mk_float,2}
-    # Integral term for the PID controller of the external source term
-    external_source_controller_integral::MPISharedArray{mk_float,2}
-end
-
-"""
-"""
-function create_moments_charged(nz, nr, n_species, evolve_density, evolve_upar,
-                                evolve_ppar, ion_source_settings, numerical_dissipation)
+function create_moments_ion(nz, nr, n_species, evolve_density, evolve_upar,
+                            evolve_ppar, ion_source_settings, num_diss_params)
     # allocate array used for the particle density
     density = allocate_shared_float(nz, nr, n_species)
     # allocate array of Bools that indicate if the density is updated for each species
@@ -258,8 +96,7 @@ function create_moments_charged(nz, nr, n_species, evolve_density, evolve_upar,
         ddens_dz = nothing
         ddens_dz_upwind = nothing
     end
-    if evolve_density &&
-            numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if evolve_density && num_diss_params.ion.moment_dissipation_coefficient > 0.0
 
         d2dens_dz2 = allocate_shared_float(nz, nr, n_species)
     else
@@ -275,8 +112,7 @@ function create_moments_charged(nz, nr, n_species, evolve_density, evolve_upar,
     else
         dupar_dz_upwind = nothing
     end
-    if evolve_upar &&
-            numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if evolve_upar && num_diss_params.ion.moment_dissipation_coefficient > 0.0
 
         d2upar_dz2 = allocate_shared_float(nz, nr, n_species)
     else
@@ -336,8 +172,18 @@ function create_moments_charged(nz, nr, n_species, evolve_density, evolve_upar,
         external_source_controller_integral = allocate_shared_float(1, 1)
     end
 
+    if evolve_density || evolve_upar || evolve_ppar
+        constraints_A_coefficient = allocate_shared_float(nz, nr, n_species)
+        constraints_B_coefficient = allocate_shared_float(nz, nr, n_species)
+        constraints_C_coefficient = allocate_shared_float(nz, nr, n_species)
+    else
+        constraints_A_coefficient = nothing
+        constraints_B_coefficient = nothing
+        constraints_C_coefficient = nothing
+    end
+
     # return struct containing arrays needed to update moments
-    return moments_charged_substruct(density, density_updated, parallel_flow,
+    return moments_ion_substruct(density, density_updated, parallel_flow,
         parallel_flow_updated, parallel_pressure, parallel_pressure_updated,perpendicular_pressure,
         parallel_heat_flux, parallel_heat_flux_updated, thermal_speed, 
         chodura_integral_lower, chodura_integral_upper, v_norm_fac,
@@ -345,7 +191,8 @@ function create_moments_charged(nz, nr, n_species, evolve_density, evolve_upar,
         dppar_dz, dppar_dz_upwind, d2ppar_dz2, dqpar_dz, dvth_dz, entropy_production,
         external_source_amplitude, external_source_density_amplitude,
         external_source_momentum_amplitude, external_source_pressure_amplitude,
-        external_source_controller_integral)
+        external_source_controller_integral, constraints_A_coefficient,
+        constraints_B_coefficient, constraints_C_coefficient)
 end
 
 # neutral particles have natural mean velocities 
@@ -355,7 +202,7 @@ end
     
 function create_moments_neutral(nz, nr, n_species, evolve_density, evolve_upar,
                                 evolve_ppar, neutral_source_settings,
-                                numerical_dissipation)
+                                num_diss_params)
     density = allocate_shared_float(nz, nr, n_species)
     density_updated = allocate_bool(n_species)
     density_updated .= false
@@ -398,8 +245,7 @@ function create_moments_neutral(nz, nr, n_species, evolve_density, evolve_upar,
         ddens_dz = nothing
         ddens_dz_upwind = nothing
     end
-    if evolve_density &&
-            numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if evolve_density && num_diss_params.neutral.moment_dissipation_coefficient > 0.0
 
         d2dens_dz2 = allocate_shared_float(nz, nr, n_species)
     else
@@ -415,8 +261,7 @@ function create_moments_neutral(nz, nr, n_species, evolve_density, evolve_upar,
     else
         duz_dz_upwind = nothing
     end
-    if evolve_upar &&
-            numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if evolve_upar && num_diss_params.neutral.moment_dissipation_coefficient > 0.0
 
         d2uz_dz2 = allocate_shared_float(nz, nr, n_species)
     else
@@ -474,6 +319,16 @@ function create_moments_neutral(nz, nr, n_species, evolve_density, evolve_upar,
         external_source_controller_integral = allocate_shared_float(1, 1)
     end
 
+    if evolve_density || evolve_upar || evolve_ppar
+        constraints_A_coefficient = allocate_shared_float(nz, nr, n_species)
+        constraints_B_coefficient = allocate_shared_float(nz, nr, n_species)
+        constraints_C_coefficient = allocate_shared_float(nz, nr, n_species)
+    else
+        constraints_A_coefficient = nothing
+        constraints_B_coefficient = nothing
+        constraints_C_coefficient = nothing
+    end
+
     # return struct containing arrays needed to update moments
     return moments_neutral_substruct(density, density_updated, uz, uz_updated, ur,
         ur_updated, uzeta, uzeta_updated, pz, pz_updated, pr, pr_updated, pzeta,
@@ -481,7 +336,8 @@ function create_moments_neutral(nz, nr, n_species, evolve_density, evolve_upar,
         d2dens_dz2, duz_dz, duz_dz_upwind, d2uz_dz2, dpz_dz, dpz_dz_upwind, d2pz_dz2,
         dqz_dz, dvth_dz, external_source_amplitude, external_source_density_amplitude,
         external_source_momentum_amplitude, external_source_pressure_amplitude,
-        external_source_controller_integral)
+        external_source_controller_integral, constraints_A_coefficient,
+        constraints_B_coefficient, constraints_C_coefficient)
 end
 
 """
@@ -492,7 +348,7 @@ the function used to update moments at run time is update_derived_moments! in ti
 function update_moments!(moments, ff_in, gyroavs::gyro_operators, vpa, vperp, z, r, composition,
         r_spectral, geometry, scratch_dummy, z_advect)
     if composition.gyrokinetic_ions
-        ff = scratch_dummy.buffer_vpavperpzrs_1 # the buffer array for the charged pdf -> make sure not to reuse this array below
+        ff = scratch_dummy.buffer_vpavperpzrs_1 # the buffer array for the ion pdf -> make sure not to reuse this array below
         # fill buffer with ring-averaged F (gyroaverage at fixed position)
         gyroaverage_pdf!(ff,ff_in,gyroavs,vpa,vperp,z,r,composition)
     else
@@ -500,46 +356,46 @@ function update_moments!(moments, ff_in, gyroavs::gyro_operators, vpa, vperp, z,
     end
     begin_s_r_z_region()
     n_species = size(ff,5)
-    @boundscheck n_species == size(moments.charged.dens,3) || throw(BoundsError(moments))
+    @boundscheck n_species == size(moments.ion.dens,3) || throw(BoundsError(moments))
     @loop_s is begin
-        if moments.charged.dens_updated[is] == false
-            @views update_density_species!(moments.charged.dens[:,:,is], ff[:,:,:,:,is],
+        if moments.ion.dens_updated[is] == false
+            @views update_density_species!(moments.ion.dens[:,:,is], ff[:,:,:,:,is],
                                            vpa, vperp, z, r)
-            moments.charged.dens_updated[is] = true
+            moments.ion.dens_updated[is] = true
         end
-        if moments.charged.upar_updated[is] == false
+        if moments.ion.upar_updated[is] == false
             # Can pass moments.ppar here even though it has not been updated yet,
             # because moments.ppar is only needed if evolve_ppar=true, in which case it
             # will not be updated because it is not calculated from the distribution
             # function
-            @views update_upar_species!(moments.charged.upar[:,:,is],
-                                        moments.charged.dens[:,:,is],
-                                        moments.charged.ppar[:,:,is], ff[:,:,:,:,is], vpa,
+            @views update_upar_species!(moments.ion.upar[:,:,is],
+                                        moments.ion.dens[:,:,is],
+                                        moments.ion.ppar[:,:,is], ff[:,:,:,:,is], vpa,
                                         vperp, z, r, moments.evolve_density,
                                         moments.evolve_ppar)
-            moments.charged.upar_updated[is] = true
+            moments.ion.upar_updated[is] = true
         end
-        if moments.charged.ppar_updated[is] == false
-            @views update_ppar_species!(moments.charged.ppar[:,:,is],
-                                        moments.charged.dens[:,:,is],
-                                        moments.charged.upar[:,:,is], ff[:,:,:,:,is], vpa,
+        if moments.ion.ppar_updated[is] == false
+            @views update_ppar_species!(moments.ion.ppar[:,:,is],
+                                        moments.ion.dens[:,:,is],
+                                        moments.ion.upar[:,:,is], ff[:,:,:,:,is], vpa,
                                         vperp, z, r, moments.evolve_density,
                                         moments.evolve_upar)
-            moments.charged.ppar_updated[is] = true
-        end
-        @views update_pperp_species!(moments.charged.pperp[:,:,is], ff[:,:,:,:,is], vpa, vperp, z, r)
-        if moments.charged.qpar_updated[is] == false
-            @views update_qpar_species!(moments.charged.qpar[:,:,is],
-                                        moments.charged.dens[:,:,is],
-                                        moments.charged.upar[:,:,is],
-                                        moments.charged.vth[:,:,is], ff[:,:,:,:,is], vpa,
+            moments.ion.ppar_updated[is] = true
+        end
+        @views update_pperp_species!(moments.ion.pperp[:,:,is], ff[:,:,:,:,is], vpa, vperp, z, r)
+        if moments.ion.qpar_updated[is] == false
+            @views update_qpar_species!(moments.ion.qpar[:,:,is],
+                                        moments.ion.dens[:,:,is],
+                                        moments.ion.upar[:,:,is],
+                                        moments.ion.vth[:,:,is], ff[:,:,:,:,is], vpa,
                                         vperp, z, r, moments.evolve_density,
                                         moments.evolve_upar, moments.evolve_ppar)
-            moments.charged.qpar_updated[is] = true
+            moments.ion.qpar_updated[is] = true
         end
     end
 
-    update_vth!(moments.charged.vth, moments.charged.ppar, moments.charged.pperp, moments.charged.dens, vperp, z, r, composition)
+    update_vth!(moments.ion.vth, moments.ion.ppar, moments.ion.pperp, moments.ion.dens, vperp, z, r, composition)
     # update the Chodura diagnostic -- note that the pdf should be the unnormalised one
     # so this will break for the split moments cases
     update_chodura!(moments,ff,vpa,vperp,z,r,r_spectral,composition,geometry,scratch_dummy,z_advect)
@@ -884,22 +740,22 @@ function update_chodura!(moments,ff,vpa,vperp,z,r,r_spectral,composition,geometr
     begin_s_r_region()
     if z.irank == 0
         @loop_s_r is ir begin
-            @views moments.charged.chodura_integral_lower[ir,is] = update_chodura_integral_species!(ff[:,:,1,ir,is],dffdr[:,:,1,ir,is],
-            ff_dummy[:,:],vpa,vperp,z,r,composition,geometry,z_advect[is].speed[1,:,:,ir],moments.charged.dens[1,ir,is],del_vpa,1,ir)
+            @views moments.ion.chodura_integral_lower[ir,is] = update_chodura_integral_species!(ff[:,:,1,ir,is],dffdr[:,:,1,ir,is],
+            ff_dummy[:,:],vpa,vperp,z,r,composition,geometry,z_advect[is].speed[1,:,:,ir],moments.ion.dens[1,ir,is],del_vpa,1,ir)
         end
     else # we do not save this Chodura integral to the output file
         @loop_s_r is ir begin
-            moments.charged.chodura_integral_lower[ir,is] = 0.0
+            moments.ion.chodura_integral_lower[ir,is] = 0.0
         end
     end
     if z.irank == z.nrank - 1
         @loop_s_r is ir begin
-            @views moments.charged.chodura_integral_upper[ir,is] = update_chodura_integral_species!(ff[:,:,end,ir,is],dffdr[:,:,end,ir,is],
-            ff_dummy[:,:],vpa,vperp,z,r,composition,geometry,z_advect[is].speed[end,:,:,ir],moments.charged.dens[end,ir,is],del_vpa,z.n,ir)
+            @views moments.ion.chodura_integral_upper[ir,is] = update_chodura_integral_species!(ff[:,:,end,ir,is],dffdr[:,:,end,ir,is],
+            ff_dummy[:,:],vpa,vperp,z,r,composition,geometry,z_advect[is].speed[end,:,:,ir],moments.ion.dens[end,ir,is],del_vpa,z.n,ir)
         end
     else # we do not save this Chodura integral to the output file
         @loop_s_r is ir begin
-            moments.charged.chodura_integral_upper[ir,is] =  0.0
+            moments.ion.chodura_integral_upper[ir,is] =  0.0
         end
     end
 end
@@ -947,15 +803,15 @@ end
 """
 Pre-calculate spatial derivatives of the moments that will be needed for the time advance
 """
-function calculate_moment_derivatives!(moments, scratch, scratch_dummy, z, z_spectral,
-                                       numerical_dissipation)
+function calculate_ion_moment_derivatives!(moments, scratch, scratch_dummy, z, z_spectral,
+                                           ion_mom_diss_coeff)
     begin_s_r_region()
 
     density = scratch.density
     upar = scratch.upar
     ppar = scratch.ppar
-    qpar = moments.charged.qpar
-    vth = moments.charged.vth
+    qpar = moments.ion.qpar
+    vth = moments.ion.vth
     dummy_zrs = scratch_dummy.dummy_zrs
     buffer_r_1 = scratch_dummy.buffer_rs_1
     buffer_r_2 = scratch_dummy.buffer_rs_2
@@ -964,27 +820,26 @@ function calculate_moment_derivatives!(moments, scratch, scratch_dummy, z, z_spe
     buffer_r_5 = scratch_dummy.buffer_rs_5
     buffer_r_6 = scratch_dummy.buffer_rs_6
     if moments.evolve_density
-        @views derivative_z!(moments.charged.ddens_dz, density, buffer_r_1,
+        @views derivative_z!(moments.ion.ddens_dz, density, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
         # Upwinded using upar as advection velocity, to be used in continuity equation
         @loop_s_r_z is ir iz begin
             dummy_zrs[iz,ir,is] = -upar[iz,ir,is]
         end
-        @views derivative_z!(moments.charged.ddens_dz_upwind, density,
+        @views derivative_z!(moments.ion.ddens_dz_upwind, density,
                              dummy_zrs, buffer_r_1, buffer_r_2, buffer_r_3, buffer_r_4,
                              buffer_r_5, buffer_r_6, z_spectral, z)
     end
-    if moments.evolve_density &&
-        numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if moments.evolve_density && ion_mom_diss_coeff > 0.0
 
         # centred second derivative for dissipation
         @views derivative_z!(dummy_zrs, density, buffer_r_1, buffer_r_2, buffer_r_3,
                              buffer_r_4, z_spectral, z)
-        @views derivative_z!(moments.charged.d2dens_dz2, dummy_zrs, buffer_r_1,
+        @views derivative_z!(moments.ion.d2dens_dz2, dummy_zrs, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
     end
     if moments.evolve_density || moments.evolve_upar || moments.evolve_ppar
-        @views derivative_z!(moments.charged.dupar_dz, upar, buffer_r_1,
+        @views derivative_z!(moments.ion.dupar_dz, upar, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
     end
     if moments.evolve_upar
@@ -993,21 +848,20 @@ function calculate_moment_derivatives!(moments, scratch, scratch_dummy, z, z_spe
         @loop_s_r_z is ir iz begin
             dummy_zrs[iz,ir,is] = -upar[iz,ir,is]
         end
-        @views derivative_z!(moments.charged.dupar_dz_upwind, upar, dummy_zrs,
+        @views derivative_z!(moments.ion.dupar_dz_upwind, upar, dummy_zrs,
                              buffer_r_1, buffer_r_2, buffer_r_3, buffer_r_4,
                              buffer_r_5, buffer_r_6, z_spectral, z)
     end
-    if moments.evolve_upar &&
-        numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if moments.evolve_upar && ion_mom_diss_coeff > 0.0
 
         # centred second derivative for dissipation
         @views derivative_z!(dummy_zrs, upar, buffer_r_1, buffer_r_2, buffer_r_3,
                              buffer_r_4, z_spectral, z)
-        @views derivative_z!(moments.charged.d2upar_dz2, dummy_zrs, buffer_r_1,
+        @views derivative_z!(moments.ion.d2upar_dz2, dummy_zrs, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
     end
     if moments.evolve_upar
-        @views derivative_z!(moments.charged.dppar_dz, ppar, buffer_r_1,
+        @views derivative_z!(moments.ion.dppar_dz, ppar, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
     end
     if moments.evolve_ppar
@@ -1015,19 +869,19 @@ function calculate_moment_derivatives!(moments, scratch, scratch_dummy, z, z_spe
         @loop_s_r_z is ir iz begin
             dummy_zrs[iz,ir,is] = -upar[iz,ir,is]
         end
-        @views derivative_z!(moments.charged.dppar_dz_upwind, ppar, dummy_zrs,
+        @views derivative_z!(moments.ion.dppar_dz_upwind, ppar, dummy_zrs,
                              buffer_r_1, buffer_r_2, buffer_r_3, buffer_r_4,
                              buffer_r_5, buffer_r_6, z_spectral, z)
 
         # centred second derivative for dissipation
         @views derivative_z!(dummy_zrs, ppar, buffer_r_1, buffer_r_2, buffer_r_3,
                              buffer_r_4, z_spectral, z)
-        @views derivative_z!(moments.charged.d2ppar_dz2, dummy_zrs, buffer_r_1,
+        @views derivative_z!(moments.ion.d2ppar_dz2, dummy_zrs, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
 
-        @views derivative_z!(moments.charged.dqpar_dz, qpar, buffer_r_1,
+        @views derivative_z!(moments.ion.dqpar_dz, qpar, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
-        @views derivative_z!(moments.charged.dvth_dz, vth, buffer_r_1,
+        @views derivative_z!(moments.ion.dvth_dz, vth, buffer_r_1,
                              buffer_r_2, buffer_r_3, buffer_r_4, z_spectral, z)
     end
 end
@@ -1506,8 +1360,8 @@ end
 Pre-calculate spatial derivatives of the neutral moments that will be needed for the time
 advance
 """
-function calculate_moment_derivatives_neutral!(moments, scratch, scratch_dummy, z,
-                                               z_spectral, numerical_dissipation)
+function calculate_neutral_moment_derivatives!(moments, scratch, scratch_dummy, z,
+                                               z_spectral, neutral_mom_diss_coeff)
     begin_sn_r_region()
 
     density = scratch.density_neutral
@@ -1534,8 +1388,7 @@ function calculate_moment_derivatives_neutral!(moments, scratch, scratch_dummy,
                              dummy_zrsn, buffer_r_1, buffer_r_2, buffer_r_3, buffer_r_4,
                              buffer_r_5, buffer_r_6, z_spectral, z; neutrals=true)
     end
-    if moments.evolve_density &&
-        numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if moments.evolve_density && neutral_mom_diss_coeff > 0.0
 
         # centred second derivative for dissipation
         @views derivative_z!(dummy_zrsn, density, buffer_r_1, buffer_r_2, buffer_r_3,
@@ -1559,8 +1412,7 @@ function calculate_moment_derivatives_neutral!(moments, scratch, scratch_dummy,
                              buffer_r_1, buffer_r_2, buffer_r_3, buffer_r_4,
                              buffer_r_5, buffer_r_6, z_spectral, z; neutrals=true)
     end
-    if moments.evolve_upar &&
-        numerical_dissipation.moment_dissipation_coefficient > 0.0
+    if moments.evolve_upar && neutral_mom_diss_coeff > 0.0
 
         # centred second derivative for dissipation
         @views derivative_z!(dummy_zrsn, uz, buffer_r_1, buffer_r_2, buffer_r_3,
@@ -1800,18 +1652,18 @@ end
 """
 function reset_moments_status!(moments)
     if moments.evolve_density == false
-        moments.charged.dens_updated .= false
+        moments.ion.dens_updated .= false
         moments.neutral.dens_updated .= false
     end
     if moments.evolve_upar == false
-        moments.charged.upar_updated .= false
+        moments.ion.upar_updated .= false
         moments.neutral.uz_updated .= false
     end
     if moments.evolve_ppar == false
-        moments.charged.ppar_updated .= false
+        moments.ion.ppar_updated .= false
         moments.neutral.pz_updated .= false
     end
-    moments.charged.qpar_updated .= false
+    moments.ion.qpar_updated .= false
     moments.neutral.uzeta_updated .= false
     moments.neutral.ur_updated .= false
     moments.neutral.pzeta_updated .= false
diff --git a/moment_kinetics/src/vpa_advection.jl b/moment_kinetics/src/vpa_advection.jl
index ed8afd2fa..9d4881b0b 100644
--- a/moment_kinetics/src/vpa_advection.jl
+++ b/moment_kinetics/src/vpa_advection.jl
@@ -113,9 +113,9 @@ function update_speed_n_u_p_evolution!(advect, fvec, moments, vpa, z, r, composi
             # • -wpar^2 * d(vth)/dz term
             @loop_z_vperp iz ivperp begin
                 @views @. advect[is].speed[:,ivperp,iz,ir] =
-                    moments.charged.dppar_dz[iz,ir,is]/(fvec.density[iz,ir,is]*moments.charged.vth[iz,ir,is]) +
-                    0.5*vpa.grid*moments.charged.dqpar_dz[iz,ir,is]/fvec.ppar[iz,ir,is] -
-                    vpa.grid^2*moments.charged.dvth_dz[iz,ir,is]
+                    moments.ion.dppar_dz[iz,ir,is]/(fvec.density[iz,ir,is]*moments.ion.vth[iz,ir,is]) +
+                    0.5*vpa.grid*moments.ion.dqpar_dz[iz,ir,is]/fvec.ppar[iz,ir,is] -
+                    vpa.grid^2*moments.ion.dvth_dz[iz,ir,is]
             end
         end
     end
@@ -134,7 +134,7 @@ function update_speed_n_u_p_evolution!(advect, fvec, moments, vpa, z, r, composi
                           * (fvec.upar[iz,ir,is]-fvec.uz_neutral[iz,ir,is])^2)
                      - fvec.density_neutral[iz,ir,is]
                        * (fvec.uz_neutral[iz,ir,is]-fvec.upar[iz,ir,is])
-                       / moments.charged.vth[iz,ir,is]) +
+                       / moments.ion.vth[iz,ir,is]) +
                     collisions.ionization *
                     (0.5*vpa.grid
                        * (fvec.density_neutral[iz,ir,is]
@@ -145,24 +145,26 @@ function update_speed_n_u_p_evolution!(advect, fvec, moments, vpa, z, r, composi
                             / fvec.ppar[iz,ir,is])
                      - fvec.density_neutral[iz,ir,is]
                        * (fvec.uz_neutral[iz,ir,is] - fvec.upar[iz,ir,is])
-                       / moments.charged.vth[iz,ir,is])
+                       / moments.ion.vth[iz,ir,is])
             end
         end
     end
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_amplitude
-        source_T = ion_source_settings.source_T
+        source_density_amplitude = moments.ion.external_source_density_amplitude
+        source_momentum_amplitude = moments.ion.external_source_momentum_amplitude
+        source_pressure_amplitude = moments.ion.external_source_pressure_amplitude
         density = fvec.density
         upar = fvec.upar
         ppar = fvec.ppar
-        vth = moments.charged.vth
+        vth = moments.ion.vth
         vpa_grid = vpa.grid
         @loop_s_r_z is ir iz begin
-            prefactor = source_amplitude[iz,ir]
-            term1 = prefactor * upar[iz,ir,is]/(density[iz,ir,is]*vth[iz,ir,is])
+            term1 = source_density_amplitude[iz,ir] * upar[iz,ir,is]/(density[iz,ir,is]*vth[iz,ir,is])
             term2_over_vpa =
-                0.5 * prefactor * (-(0.5*source_T + upar[iz,ir,is]^2) / ppar[iz,ir,is]
-                                   + 1.0/density[iz,ir,is])
+                -0.5 * (source_pressure_amplitude[iz,ir] +
+                        2.0 * upar[iz,ir,is] * source_momentum_amplitude[iz,ir]) /
+                       ppar[iz,ir,is] +
+                0.5 * source_density_amplitude[iz,ir] / density[iz,ir,is]
             @loop_vperp_vpa ivperp ivpa begin
                 advect[is].speed[ivpa,ivperp,iz,ir] += term1 + vpa_grid[ivpa] * term2_over_vpa
             end
@@ -187,9 +189,9 @@ function update_speed_n_p_evolution!(advect, fields, fvec, moments, vpa, z, r,
             # • vpahat*d(upar)/dz
             # • -(1/2)*(dphi/dz)/vthi
             @loop_z_vperp iz ivperp begin
-                @views @. advect[is].speed[:,ivperp,iz,ir] = 0.5*vpa.grid*moments.charged.dqpar_dz[iz,ir,is]/fvec.ppar[iz,ir,is] +
-                                                             vpa.grid*moments.charged.dvth_dz[iz] * (fvec.upar[iz,ir,is]/moments.vth[iz,ir,is] - vpa.grid) +
-                                                             vpa.grid*moments.charged.dupar_dz[iz,ir,is] +
+                @views @. advect[is].speed[:,ivperp,iz,ir] = 0.5*vpa.grid*moments.ion.dqpar_dz[iz,ir,is]/fvec.ppar[iz,ir,is] +
+                                                             vpa.grid*moments.ion.dvth_dz[iz] * (fvec.upar[iz,ir,is]/moments.vth[iz,ir,is] - vpa.grid) +
+                                                             vpa.grid*moments.ion.dupar_dz[iz,ir,is] +
                                                              0.5*fields.Ez[iz,ir]/moments.vth[iz,ir,is]
             end
         end
@@ -228,8 +230,8 @@ function update_speed_n_u_evolution!(advect, fvec, moments, vpa, z, r, compositi
             # • -wpar*dupar/dz
             @loop_z_vperp iz ivperp begin
                 @views @. advect[is].speed[:,ivperp,iz,ir] =
-                    moments.charged.dppar_dz[iz,ir,is]/fvec.density[iz,ir,is] -
-                    vpa.grid*moments.charged.dupar_dz[iz,ir,is]
+                    moments.ion.dppar_dz[iz,ir,is]/fvec.density[iz,ir,is] -
+                    vpa.grid*moments.ion.dupar_dz[iz,ir,is]
             end
         end
     end
@@ -253,16 +255,15 @@ function update_speed_n_u_evolution!(advect, fvec, moments, vpa, z, r, compositi
         end
     end
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_amplitude
+        source_density_amplitude = moments.ion.external_source_density_amplitude
         source_strength = ion_source_settings.source_strength
-        source_T = ion_source_settings.source_T
         r_amplitude = ion_source_settings.r_amplitude
         z_amplitude = ion_source_settings.z_amplitude
         density = fvec.density
         upar = fvec.upar
-        vth = moments.charged.vth
+        vth = moments.ion.vth
         @loop_s_r_z is ir iz begin
-            term = source_amplitude[iz,ir] * upar[iz,ir,is] / density[iz,ir,is]
+            term = source_density_amplitude[iz,ir] * upar[iz,ir,is] / density[iz,ir,is]
             @loop_vperp_vpa ivperp ivpa begin
                 advect[is].speed[ivpa,ivperp,iz,ir] += term
             end
diff --git a/moment_kinetics/src/z_advection.jl b/moment_kinetics/src/z_advection.jl
index b88808a3e..9013dd19e 100644
--- a/moment_kinetics/src/z_advection.jl
+++ b/moment_kinetics/src/z_advection.jl
@@ -21,13 +21,13 @@ function z_advection!(f_out, fvec_in, moments, fields, advect, z, vpa, vperp, r,
     @loop_s is begin
         # get the updated speed along the z direction using the current f
         @views update_speed_z!(advect[is], fvec_in.upar[:,:,is],
-                               moments.charged.vth[:,:,is], moments.evolve_upar,
+                               moments.ion.vth[:,:,is], moments.evolve_upar,
                                moments.evolve_ppar, fields, vpa, vperp, z, r, t, geometry, is)
         # update adv_fac
         @loop_r_vperp_vpa ir ivperp ivpa begin
             @views adjust_advection_speed!(advect[is].speed[:,ivpa,ivperp,ir],
                                            fvec_in.density[:,ir,is],
-                                           moments.charged.vth[:,ir,is],
+                                           moments.ion.vth[:,ir,is],
                                            moments.evolve_density, moments.evolve_ppar)
             @views @. advect[is].adv_fac[:,ivpa,ivperp,ir] = -dt*advect[is].speed[:,ivpa,ivperp,ir]
             # take the normalized pdf contained in fvec_in.pdf and remove the normalization,
@@ -35,7 +35,7 @@ function z_advection!(f_out, fvec_in, moments, fields, advect, z, vpa, vperp, r,
             @views unnormalize_pdf!(
                 scratch_dummy.buffer_vpavperpzrs_2[ivpa,ivperp,:,ir,is],
                 fvec_in.pdf[ivpa,ivperp,:,ir,is], fvec_in.density[:,ir,is],
-                moments.charged.vth[:,ir,is], moments.evolve_density, moments.evolve_ppar)
+                moments.ion.vth[:,ir,is], moments.evolve_density, moments.evolve_ppar)
         end
     end
     #calculate the upwind derivative
diff --git a/moment_kinetics/test/Krook_collisions_tests.jl b/moment_kinetics/test/Krook_collisions_tests.jl
index 4f273049d..91e6bb7de 100644
--- a/moment_kinetics/test/Krook_collisions_tests.jl
+++ b/moment_kinetics/test/Krook_collisions_tests.jl
@@ -10,7 +10,7 @@ using moment_kinetics.coordinates: define_coordinate
 using moment_kinetics.input_structs: grid_input, advection_input
 using moment_kinetics.load_data: open_readonly_output_file, load_coordinate_data,
                                  load_species_data, load_fields_data,
-                                 load_charged_particle_moments_data, load_pdf_data,
+                                 load_ion_moments_data, load_pdf_data,
                                  load_neutral_particle_moments_data,
                                  load_neutral_pdf_data, load_time_data, load_species_data
 using moment_kinetics.interpolation: interpolate_to_grid_z, interpolate_to_grid_vpa
@@ -35,48 +35,48 @@ const expected =
           -0.353459763648872 -0.3755795658392631; -0.5494724768120175 -0.5904511161957432;
           -0.8609860698164502 -0.8726509017405427; -1.2115129555832849 -1.1306145497660032;
           -1.3862820803244258 -1.2382381134436695],
-     n_charged=[0.2500030702177186 0.28989452952580286; 0.2977473631375158 0.32283464906590775;
-                0.42274585818529853 0.41784232850006636; 0.5772542465450629 0.5540775204094593;
-                0.7022542481909738 0.6868914177534788; 0.7499999999999394 0.7468272160708606;
-                0.7022542481909738 0.6868914177534787; 0.577254246545063 0.554077520409459;
-                0.42274585818529864 0.4178423285000665; 0.2977473631375159 0.3228346490659078;
-                0.2500030702177185 0.2898945295258028],
+     n_ion=[0.2500030702177186 0.28989452952580286; 0.2977473631375158 0.32283464906590775;
+            0.42274585818529853 0.41784232850006636; 0.5772542465450629 0.5540775204094593;
+            0.7022542481909738 0.6868914177534788; 0.7499999999999394 0.7468272160708606;
+            0.7022542481909738 0.6868914177534787; 0.577254246545063 0.554077520409459;
+            0.42274585818529864 0.4178423285000665; 0.2977473631375159 0.3228346490659078;
+            0.2500030702177185 0.2898945295258028],
      n_neutral=[0.7499999999999382 0.7736770941648626; 0.7022542481909748 0.7056867075427516;
                 0.5772542465450632 0.5582975660019874; 0.4227458581852985 0.4096913953484598;
                 0.29774736313751604 0.3053964124252619; 0.2500030702177186 0.2681998023548167;
                 0.29774736313751604 0.3053964124252619; 0.42274585818529836 0.4096913953484599;
                 0.5772542465450631 0.5582975660019875; 0.7022542481909745 0.7056867075427524;
                 0.7499999999999383 0.7736770941648626],
-     upar_charged=[-2.7135787559953277e-17 -1.6845791254993525e-16; -9.321028970172899e-18 -0.18245939812953485;
-                   -2.8374879811351724e-18 -0.19666454846377826; 1.2124327390522635e-17 -0.11128043369942339;
-                   3.6525788403693063e-17 -0.03317985705380149; -2.0930856430671915e-17 4.720175801869314e-17;
-                   8.753545920086251e-18 0.033179857053801595; 1.1293771270243255e-17 0.11128043369942343;
-                   1.3739171132886587e-17 0.19666454846377784; -6.840453743089351e-18 0.18245939812953468;
-                   -2.7135787559953277e-17 -1.9129596434811267e-16],
+     upar_ion=[-2.7135787559953277e-17 -1.6845791254993525e-16; -9.321028970172899e-18 -0.18245939812953485;
+               -2.8374879811351724e-18 -0.19666454846377826; 1.2124327390522635e-17 -0.11128043369942339;
+               3.6525788403693063e-17 -0.03317985705380149; -2.0930856430671915e-17 4.720175801869314e-17;
+               8.753545920086251e-18 0.033179857053801595; 1.1293771270243255e-17 0.11128043369942343;
+               1.3739171132886587e-17 0.19666454846377784; -6.840453743089351e-18 0.18245939812953468;
+               -2.7135787559953277e-17 -1.9129596434811267e-16],
      upar_neutral=[6.5569385065066925e-18 8.08747058038406e-18; 1.1054500872839027e-17 -0.03620988455458174;
                    -3.241833393685864e-17 -0.009156078199383568; -3.617637280460899e-17 0.05452623197292568;
                    4.417578961284041e-17 0.07607875911384775; 4.9354467746194965e-17 1.635044638743921e-16;
                    6.573091229872379e-18 -0.0760787591138477; 2.989662686945165e-17 -0.05452623197292564;
                    -3.1951996361666834e-17 0.009156078199383685; -4.395464518158184e-18 0.03620988455458165;
                    6.5569385065066925e-18 1.8232586069007834e-18],
-     ppar_charged=[0.18749999999999992 0.23302732230115558; 0.20909325514551116 0.21936799130257528;
-                   0.24403180771238264 0.20856296024163393; 0.24403180771238278 0.2154266357557397;
-                   0.2090932551455113 0.2206183912107678; 0.1875 0.21979739387340663;
-                   0.20909325514551128 0.22061839121076784; 0.2440318077123828 0.21542663575573945;
-                   0.24403180771238256 0.20856296024163395; 0.20909325514551116 0.2193679913025754;
-                   0.18749999999999992 0.23302732230115553],
+     ppar_ion=[0.18749999999999992 0.23302732230115558; 0.20909325514551116 0.21936799130257528;
+               0.24403180771238264 0.20856296024163393; 0.24403180771238278 0.2154266357557397;
+               0.2090932551455113 0.2206183912107678; 0.1875 0.21979739387340663;
+               0.20909325514551128 0.22061839121076784; 0.2440318077123828 0.21542663575573945;
+               0.24403180771238256 0.20856296024163395; 0.20909325514551116 0.2193679913025754;
+               0.18749999999999992 0.23302732230115553],
      ppar_neutral=[0.18750000000000003 0.2480292382671593; 0.20909325514551122 0.24401255100297964;
                    0.24403180771238286 0.22861763406831279; 0.24403180771238278 0.2058922545451891;
                    0.20909325514551144 0.1926313699453636; 0.18749999999999992 0.19090651730415983;
                    0.20909325514551141 0.19263136994536365; 0.2440318077123828 0.20589225454518903;
                    0.24403180771238286 0.2286176340683127; 0.20909325514551114 0.24401255100297964;
                    0.18750000000000006 0.24802923826715936],
-     f_charged=[0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;
-                0.20411991941198782 0.25123395823993105 0.3934413727192304 0.6277900619432855 0.9100364506661008 1.0606601717796504 0.910036450666101 0.6277900619432859 0.39344137271923046 0.25123395823993094 0.20411991941198776;
-                0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;;;
-                0.0538996852594264 0.06066864433237418 0.03746866696438989 0.014783440166032301 0.010917691665145668 0.018422971878502774 0.027170953411068444 0.027269146560166702 0.026567569739750264 0.035612674100528624 0.05389968525942639;
-                0.2118369019176154 0.24917436308523389 0.37345448114678914 0.5972219245577428 0.8859681860177208 1.0485988935814787 0.8859681860177204 0.5972219245577435 0.37345448114678825 0.24917436308523389 0.2118369019176155;
-                0.05389968525942635 0.03561267410052869 0.02656756973975021 0.02726914656016675 0.027170953411068514 0.018422971878502753 0.01091769166514568 0.014783440166032254 0.037468666964389795 0.060668644332374164 0.05389968525942635],
+     f_ion=[0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;
+            0.20411991941198782 0.25123395823993105 0.3934413727192304 0.6277900619432855 0.9100364506661008 1.0606601717796504 0.910036450666101 0.6277900619432859 0.39344137271923046 0.25123395823993094 0.20411991941198776;
+            0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;;;
+            0.0538996852594264 0.06066864433237418 0.03746866696438989 0.014783440166032301 0.010917691665145668 0.018422971878502774 0.027170953411068444 0.027269146560166702 0.026567569739750264 0.035612674100528624 0.05389968525942639;
+            0.2118369019176154 0.24917436308523389 0.37345448114678914 0.5972219245577428 0.8859681860177208 1.0485988935814787 0.8859681860177204 0.5972219245577435 0.37345448114678825 0.24917436308523389 0.2118369019176155;
+            0.05389968525942635 0.03561267410052869 0.02656756973975021 0.02726914656016675 0.027170953411068514 0.018422971878502753 0.01091769166514568 0.014783440166032254 0.037468666964389795 0.060668644332374164 0.05389968525942635],
      f_neutral=[0.0063385294703834595 0.012360459026988546 0.030398267195914108 0.04284314198717859 0.040599270638920985 0.03704623609948259 0.040599270638920965 0.0428431419871786 0.030398267195914094 0.012360459026988546 0.006338529470383456;
                 1.0606601717796493 0.9100364506661016 0.6277900619432857 0.3934413727192303 0.2512339582399308 0.20411991941198754 0.2512339582399307 0.3934413727192301 0.6277900619432853 0.9100364506661016 1.0606601717796487;
                 0.0063385294703834595 0.012360459026988546 0.030398267195914108 0.04284314198717859 0.040599270638920985 0.03704623609948259 0.040599270638920965 0.0428431419871786 0.030398267195914094 0.012360459026988546 0.006338529470383456;;;
@@ -164,6 +164,10 @@ function run_test(test_input, rtol, atol; args...)
     # by passing keyword arguments to run_test, args becomes a Dict which can be used to
     # update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     # Convert keyword arguments to a unique name
     name = test_input["run_name"]
     if length(args) > 0
@@ -191,10 +195,10 @@ function run_test(test_input, rtol, atol; args...)
     end
 
     phi = nothing
-    n_charged = nothing
-    upar_charged = nothing
-    ppar_charged = nothing
-    f_charged = nothing
+    n_ion = nothing
+    upar_ion = nothing
+    ppar_ion = nothing
+    f_ion = nothing
     n_neutral = nothing
     upar_neutral = nothing
     ppar_neutral = nothing
@@ -222,7 +226,7 @@ function run_test(test_input, rtol, atol; args...)
             phi_zrt, Er_zrt, Ez_zrt = load_fields_data(fid)
 
             # load velocity moments data
-            n_charged_zrst, upar_charged_zrst, ppar_charged_zrst, qpar_charged_zrst, v_t_charged_zrst = load_charged_particle_moments_data(fid)
+            n_ion_zrst, upar_ion_zrst, ppar_ion_zrst, qpar_ion_zrst, v_t_ion_zrst = load_ion_moments_data(fid)
             n_neutral_zrst, upar_neutral_zrst, ppar_neutral_zrst, qpar_neutral_zrst, v_t_neutral_zrst = load_neutral_particle_moments_data(fid)
             z, z_spectral = load_coordinate_data(fid, "z")
 
@@ -232,19 +236,19 @@ function run_test(test_input, rtol, atol; args...)
             fid = open_readonly_output_file(path, "dfns")
             
             # load particle distribution function (pdf) data
-            f_charged_vpavperpzrst = load_pdf_data(fid)
+            f_ion_vpavperpzrst = load_pdf_data(fid)
             f_neutral_vzvrvzetazrst = load_neutral_pdf_data(fid)
             vpa, vpa_spectral = load_coordinate_data(fid, "vpa")
 
             close(fid)
             
             phi = phi_zrt[:,1,:]
-            n_charged = n_charged_zrst[:,1,:,:]
-            upar_charged = upar_charged_zrst[:,1,:,:]
-            ppar_charged = ppar_charged_zrst[:,1,:,:]
-            qpar_charged = qpar_charged_zrst[:,1,:,:]
-            v_t_charged = v_t_charged_zrst[:,1,:,:]
-            f_charged = f_charged_vpavperpzrst[:,1,:,1,:,:]
+            n_ion = n_ion_zrst[:,1,:,:]
+            upar_ion = upar_ion_zrst[:,1,:,:]
+            ppar_ion = ppar_ion_zrst[:,1,:,:]
+            qpar_ion = qpar_ion_zrst[:,1,:,:]
+            v_t_ion = v_t_ion_zrst[:,1,:,:]
+            f_ion = f_ion_vpavperpzrst[:,1,:,1,:,:]
             n_neutral = n_neutral_zrst[:,1,:,:]
             upar_neutral = upar_neutral_zrst[:,1,:,:]
             ppar_neutral = ppar_neutral_zrst[:,1,:,:]
@@ -255,7 +259,7 @@ function run_test(test_input, rtol, atol; args...)
             # Unnormalize f
             if input["evolve_moments_density"]
                 for it ∈ 1:length(time), is ∈ 1:n_ion_species, iz ∈ 1:z.n
-                    f_charged[:,iz,is,it] .*= n_charged[iz,is,it]
+                    f_ion[:,iz,is,it] .*= n_ion[iz,is,it]
                 end
                 for it ∈ 1:length(time), isn ∈ 1:n_neutral_species, iz ∈ 1:z.n
                     f_neutral[:,iz,isn,it] .*= n_neutral[iz,isn,it]
@@ -263,7 +267,7 @@ function run_test(test_input, rtol, atol; args...)
             end
             if input["evolve_moments_parallel_pressure"]
                 for it ∈ 1:length(time), is ∈ 1:n_ion_species, iz ∈ 1:z.n
-                    f_charged[:,iz,is,it] ./= v_t_charged[iz,is,it]
+                    f_ion[:,iz,is,it] ./= v_t_ion[iz,is,it]
                 end
                 for it ∈ 1:length(time), isn ∈ 1:n_neutral_species, iz ∈ 1:z.n
                     f_neutral[:,iz,isn,it] ./= v_t_neutral[iz,isn,it]
@@ -281,11 +285,11 @@ function run_test(test_input, rtol, atol; args...)
         #println("phi ", size(newgrid_phi))
         #println(newgrid_phi)
         #println()
-        #newgrid_n_charged = cat(interpolate_to_grid_z(expected.z, n_charged[:, :, 1], z, z_spectral)[:,1],
-        #                        interpolate_to_grid_z(expected.z, n_charged[:, :, 2], z, z_spectral)[:,1];
+        #newgrid_n_ion = cat(interpolate_to_grid_z(expected.z, n_ion[:, :, 1], z, z_spectral)[:,1],
+        #                        interpolate_to_grid_z(expected.z, n_ion[:, :, 2], z, z_spectral)[:,1];
         #                        dims=2)
-        #println("n_charged ", size(newgrid_n_charged))
-        #println(newgrid_n_charged)
+        #println("n_ion ", size(newgrid_n_ion))
+        #println(newgrid_n_ion)
         #println()
         #newgrid_n_neutral = cat(interpolate_to_grid_z(expected.z, n_neutral[:, :, 1], z, z_spectral)[:,1],
         #                        interpolate_to_grid_z(expected.z, n_neutral[:, :, 2], z, z_spectral)[:,1];
@@ -293,11 +297,11 @@ function run_test(test_input, rtol, atol; args...)
         #println("n_neutral ", size(newgrid_n_neutral))
         #println(newgrid_n_neutral)
         #println()
-        #newgrid_upar_charged = cat(interpolate_to_grid_z(expected.z, upar_charged[:, :, 1], z, z_spectral)[:,1],
-        #                           interpolate_to_grid_z(expected.z, upar_charged[:, :, 2], z, z_spectral)[:,1];
+        #newgrid_upar_ion = cat(interpolate_to_grid_z(expected.z, upar_ion[:, :, 1], z, z_spectral)[:,1],
+        #                           interpolate_to_grid_z(expected.z, upar_ion[:, :, 2], z, z_spectral)[:,1];
         #                           dims=2)
-        #println("upar_charged ", size(newgrid_upar_charged))
-        #println(newgrid_upar_charged)
+        #println("upar_ion ", size(newgrid_upar_ion))
+        #println(newgrid_upar_ion)
         #println()
         #newgrid_upar_neutral = cat(interpolate_to_grid_z(expected.z, upar_neutral[:, :, 1], z, z_spectral)[:,1],
         #                           interpolate_to_grid_z(expected.z, upar_neutral[:, :, 2], z, z_spectral)[:,1];
@@ -305,11 +309,11 @@ function run_test(test_input, rtol, atol; args...)
         #println("upar_neutral ", size(newgrid_upar_neutral))
         #println(newgrid_upar_neutral)
         #println()
-        #newgrid_ppar_charged = cat(interpolate_to_grid_z(expected.z, ppar_charged[:, :, 1], z, z_spectral)[:,1],
-        #                           interpolate_to_grid_z(expected.z, ppar_charged[:, :, 2], z, z_spectral)[:,1];
+        #newgrid_ppar_ion = cat(interpolate_to_grid_z(expected.z, ppar_ion[:, :, 1], z, z_spectral)[:,1],
+        #                           interpolate_to_grid_z(expected.z, ppar_ion[:, :, 2], z, z_spectral)[:,1];
         #                           dims=2)
-        #println("ppar_charged ", size(newgrid_ppar_charged))
-        #println(newgrid_ppar_charged)
+        #println("ppar_ion ", size(newgrid_ppar_ion))
+        #println(newgrid_ppar_ion)
         #println()
         #newgrid_ppar_neutral = cat(interpolate_to_grid_z(expected.z, ppar_neutral[:, :, 1], z, z_spectral)[:,1],
         #                           interpolate_to_grid_z(expected.z, ppar_neutral[:, :, 2], z, z_spectral)[:,1];
@@ -317,11 +321,11 @@ function run_test(test_input, rtol, atol; args...)
         #println("ppar_neutral ", size(newgrid_ppar_neutral))
         #println(newgrid_ppar_neutral)
         #println()
-        #newgrid_f_charged = cat(interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_charged[:, :, :, 1], z, z_spectral), vpa, vpa_spectral)[:,:,1],
-        #                        interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_charged[:, :, :, 2], z, z_spectral), vpa, vpa_spectral)[:,:,1];
+        #newgrid_f_ion = cat(interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_ion[:, :, :, 1], z, z_spectral), vpa, vpa_spectral)[:,:,1],
+        #                        interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_ion[:, :, :, 2], z, z_spectral), vpa, vpa_spectral)[:,:,1];
         #                        dims=4)
-        #println("f_charged ", size(newgrid_f_charged))
-        #println(newgrid_f_charged)
+        #println("f_ion ", size(newgrid_f_ion))
+        #println(newgrid_f_ion)
         #println()
         #newgrid_f_neutral = cat(interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_neutral[:, :, :, 1], z, z_spectral), vpa, vpa_spectral)[:,:,1],
         #                        interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_neutral[:, :, :, 2], z, z_spectral), vpa, vpa_spectral)[:,:,1];
@@ -334,36 +338,36 @@ function run_test(test_input, rtol, atol; args...)
                 newgrid_phi = interpolate_to_grid_z(expected.z, phi[:, tind], z, z_spectral)
                 @test isapprox(expected.phi[:, tind], newgrid_phi, rtol=rtol)
 
-                # Check charged particle moments and f
+                # Check ion particle moments and f
                 ######################################
 
-                newgrid_n_charged = interpolate_to_grid_z(expected.z, n_charged[:, :, tind], z, z_spectral)
-                @test isapprox(expected.n_charged[:, tind], newgrid_n_charged[:,1], rtol=rtol)
+                newgrid_n_ion = interpolate_to_grid_z(expected.z, n_ion[:, :, tind], z, z_spectral)
+                @test isapprox(expected.n_ion[:, tind], newgrid_n_ion[:,1], rtol=rtol)
 
-                newgrid_upar_charged = interpolate_to_grid_z(expected.z, upar_charged[:, :, tind], z, z_spectral)
-                @test isapprox(expected.upar_charged[:, tind], newgrid_upar_charged[:,1], rtol=rtol, atol=atol)
+                newgrid_upar_ion = interpolate_to_grid_z(expected.z, upar_ion[:, :, tind], z, z_spectral)
+                @test isapprox(expected.upar_ion[:, tind], newgrid_upar_ion[:,1], rtol=rtol, atol=atol)
 
-                newgrid_ppar_charged = interpolate_to_grid_z(expected.z, ppar_charged[:, :, tind], z, z_spectral)
-                @test isapprox(expected.ppar_charged[:, tind], newgrid_ppar_charged[:,1], rtol=rtol)
+                newgrid_ppar_ion = interpolate_to_grid_z(expected.z, ppar_ion[:, :, tind], z, z_spectral)
+                @test isapprox(expected.ppar_ion[:, tind], newgrid_ppar_ion[:,1], rtol=rtol)
 
-                newgrid_vth_charged = @. sqrt(2.0*newgrid_ppar_charged/newgrid_n_charged)
-                newgrid_f_charged = interpolate_to_grid_z(expected.z, f_charged[:, :, :, tind], z, z_spectral)
-                temp = newgrid_f_charged
-                newgrid_f_charged = fill(NaN, length(expected.vpa),
-                                         size(newgrid_f_charged, 2),
-                                         size(newgrid_f_charged, 3),
-                                         size(newgrid_f_charged, 4))
+                newgrid_vth_ion = @. sqrt(2.0*newgrid_ppar_ion/newgrid_n_ion)
+                newgrid_f_ion = interpolate_to_grid_z(expected.z, f_ion[:, :, :, tind], z, z_spectral)
+                temp = newgrid_f_ion
+                newgrid_f_ion = fill(NaN, length(expected.vpa),
+                                         size(newgrid_f_ion, 2),
+                                         size(newgrid_f_ion, 3),
+                                         size(newgrid_f_ion, 4))
                 for iz ∈ 1:length(expected.z)
                     wpa = copy(expected.vpa)
                     if input["evolve_moments_parallel_flow"]
-                        wpa .-= newgrid_upar_charged[iz,1]
+                        wpa .-= newgrid_upar_ion[iz,1]
                     end
                     if input["evolve_moments_parallel_pressure"]
-                        wpa ./= newgrid_vth_charged[iz,1]
+                        wpa ./= newgrid_vth_ion[iz,1]
                     end
-                    newgrid_f_charged[:,iz,1] = interpolate_to_grid_vpa(wpa, temp[:,iz,1], vpa, vpa_spectral)
+                    newgrid_f_ion[:,iz,1] = interpolate_to_grid_vpa(wpa, temp[:,iz,1], vpa, vpa_spectral)
                 end
-                @test isapprox(expected.f_charged[:, :, tind], newgrid_f_charged[:,:,1], rtol=rtol)
+                @test isapprox(expected.f_ion[:, :, tind], newgrid_f_ion[:,:,1], rtol=rtol)
 
                 # Check neutral particle moments and f
                 ######################################
diff --git a/moment_kinetics/test/calculus_tests.jl b/moment_kinetics/test/calculus_tests.jl
index da09fa0bc..52c0aee90 100644
--- a/moment_kinetics/test/calculus_tests.jl
+++ b/moment_kinetics/test/calculus_tests.jl
@@ -43,6 +43,8 @@ function runtests()
                     discretization, fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x'
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
                 # create array for the function f(x) to be differentiated/integrated
                 f = Array{Float64,1}(undef, x.n)
@@ -93,6 +95,8 @@ function runtests()
                     "finite_difference", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x'
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
 
                 # create array for the derivative df/dx and the expected result
@@ -143,6 +147,8 @@ function runtests()
                     "finite_difference", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x'
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
 
                 # create array for the derivative df/dx and the expected result
@@ -189,6 +195,8 @@ function runtests()
                     "finite_difference", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x'
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
 
                 # create array for the derivative df/dx and the expected result
@@ -243,6 +251,8 @@ function runtests()
                     "finite_difference", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                # create the coordinate struct 'x'
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
 
                 # create array for the derivative df/dx and the expected result
@@ -459,6 +469,8 @@ function runtests()
                     "chebyshev_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
 
                 offset = randn(rng)
@@ -655,6 +667,8 @@ function runtests()
                     "chebyshev_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
 
                 offset = randn(rng)
@@ -698,6 +712,8 @@ function runtests()
                     "chebyshev_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
                 # test polynomials up to order ngrid-1
                 for n ∈ 0:ngrid-1
@@ -748,6 +764,8 @@ function runtests()
                     "chebyshev_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
                 # test polynomials up to order ngrid-1
                 for n ∈ 0:ngrid-1
@@ -884,6 +902,8 @@ function runtests()
                     "gausslegendre_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true, init_YY=false)
 
                 offset = randn(rng)
@@ -1001,6 +1021,8 @@ function runtests()
                     "gausslegendre_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true, init_YY=false)
 
                 offset = randn(rng)
@@ -1045,6 +1067,8 @@ function runtests()
                     "gausslegendre_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true, init_YY=false)
                 # test polynomials up to order ngrid-1
                 for n ∈ 0:ngrid-1
@@ -1096,6 +1120,8 @@ function runtests()
                     "gausslegendre_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true, init_YY=false)
                 # test polynomials up to order ngrid-1
                 for n ∈ 0:ngrid-1
@@ -1310,6 +1336,8 @@ function runtests()
                     "chebyshev_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true)
 
                 offset = randn(rng)
@@ -1418,6 +1446,8 @@ function runtests()
                     "gausslegendre_pseudospectral", fd_option, cheb_option, bc, adv_input, comm,
                     element_spacing_option)
                 # create the coordinate struct 'x' and info for derivatives, etc.
+                # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+                # errors due to communicators not being fully set up.
                 x, spectral = define_coordinate(input; ignore_MPI=true, init_YY=false)
 
                 offset = randn(rng)
diff --git a/moment_kinetics/test/fokker_planck_time_evolution_tests.jl b/moment_kinetics/test/fokker_planck_time_evolution_tests.jl
index 2d251082b..3039b934d 100644
--- a/moment_kinetics/test/fokker_planck_time_evolution_tests.jl
+++ b/moment_kinetics/test/fokker_planck_time_evolution_tests.jl
@@ -8,7 +8,7 @@ using moment_kinetics.coordinates: define_coordinate
 using moment_kinetics.input_structs: grid_input, advection_input
 using moment_kinetics.load_data: open_readonly_output_file, load_coordinate_data,
                                  load_species_data, load_fields_data,
-                                 load_charged_particle_moments_data, load_pdf_data,
+                                 load_ion_moments_data, load_pdf_data,
                                  load_time_data, load_species_data
 using moment_kinetics.type_definitions: mk_float
 
@@ -24,14 +24,14 @@ struct expected_data
     vpa::Array{mk_float, 1}
     vperp::Array{mk_float, 1}
     phi::Array{mk_float, 1} #time
-    n_charged::Array{mk_float, 1} #time
-    upar_charged::Array{mk_float, 1} # time
-    ppar_charged::Array{mk_float, 1} # time
-    pperp_charged::Array{mk_float, 1} # time
-    qpar_charged::Array{mk_float, 1} # time
-    v_t_charged::Array{mk_float, 1} # time
+    n_ion::Array{mk_float, 1} #time
+    upar_ion::Array{mk_float, 1} # time
+    ppar_ion::Array{mk_float, 1} # time
+    pperp_ion::Array{mk_float, 1} # time
+    qpar_ion::Array{mk_float, 1} # time
+    v_t_ion::Array{mk_float, 1} # time
     dSdt::Array{mk_float, 1} # time
-    f_charged::Array{mk_float, 3} # vpa, vperp, time
+    f_ion::Array{mk_float, 3} # vpa, vperp, time
 end
 
 const expected =
@@ -40,21 +40,21 @@ const expected =
    [0.155051025721682, 0.644948974278318, 1.000000000000000, 1.500000000000000, 2.000000000000000, 2.500000000000000, 3.000000000000000],
    # Expected phi:
    [-1.267505494648937, -1.275683298550937],
-   # Expected n_charged:
+   # Expected n_ion:
    [0.2815330322340072, 0.2792400986636072],
-   # Expected upar_charged:
+   # Expected upar_ion:
    [0.0, 0.0],
-   # Expected ppar_charged:
+   # Expected ppar_ion:
    [0.17982280248048935, 0.14891126175332367],
-   # Expected pperp_charged
+   # Expected pperp_ion
    [0.14340146667506784, 0.1581377822859991],
-   # Expected qpar_charged
+   # Expected qpar_ion
    [0.0, 0.0],
-   # Expected v_t_charged
+   # Expected v_t_ion
    [1.0511726083010418, 1.0538509291794658],
    # Expected dSdt
    [0.0, 1.1853081348031516e-5],
-   # Expected f_charged:
+   # Expected f_ion:
    [0.0 0.0 0.0 0.0 0.0 0.0 0.0;
     0.0006199600161806666 0.00047805300997075977 0.0002665817112117718 7.637693901737056e-5 1.3272321881722645e-5 1.3988924344690309e-6 0.0;
     0.005882016862626724 0.0045356406743786385 0.002529256854781707 0.0007246442213864763 0.00012592428394890537 1.3272321881722645e-5 0.0;
@@ -87,25 +87,25 @@ const expected =
 ########################################################################################## 
 """
 fid = open_readonly_output_file(path, "dfns")
-f_charged_vpavperpzrst = load_pdf_data(fid)
-f_charged = f_charged_vpavperpzrst[:,:,1,1,1,:]
+f_ion_vpavperpzrst = load_pdf_data(fid)
+f_ion = f_ion_vpavperpzrst[:,:,1,1,1,:]
 ntind = 2
 nvpa = 13  #subject to grid choices
 nvperp = 7 #subject to grid choices
 for k in 1:ntind
   for j in 1:nvperp-1
       for i in 1:nvpa-1
-         @printf("%.15f ", f_charged[i,j,k])
+         @printf("%.15f ", f_ion[i,j,k])
          print("; ")
       end
-      @printf("%.15f ", f_charged[nvpa,j,k])
+      @printf("%.15f ", f_ion[nvpa,j,k])
       print(";;\n")
   end
   for i in 1:nvpa-1
-    @printf("%.15f ", f_charged[i,nvperp,k])
+    @printf("%.15f ", f_ion[i,nvperp,k])
     print("; ")
   end
-  @printf("%.15f ", f_charged[nvpa,nvperp,k])
+  @printf("%.15f ", f_ion[nvpa,nvperp,k])
   if k < ntind
       print(";;;\n")
   end  
@@ -179,6 +179,10 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
     # by passing keyword arguments to run_test, args becomes a Dict which can be used to
     # update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     if upar_rtol === nothing
         upar_rtol = rtol
     end
@@ -211,14 +215,14 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
     end
 
     phi = nothing
-    n_charged = nothing
-    upar_charged = nothing
-    ppar_charged = nothing
-    pperp_charged = nothing
-    qpar_charged = nothing
-    v_t_charged = nothing
+    n_ion = nothing
+    upar_ion = nothing
+    ppar_ion = nothing
+    pperp_ion = nothing
+    qpar_ion = nothing
+    v_t_ion = nothing
     dSdt = nothing
-    f_charged = nothing
+    f_ion = nothing
     f_err = nothing
     vpa, vpa_spectral = nothing, nothing
     vperp, vperp_spectral = nothing, nothing
@@ -243,8 +247,8 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
             phi_zrt, Er_zrt, Ez_zrt = load_fields_data(fid)
 
             # load velocity moments data
-            n_charged_zrst, upar_charged_zrst, ppar_charged_zrst, 
-            pperp_charged_zrst, qpar_charged_zrst, v_t_charged_zrst, dSdt_zrst = load_charged_particle_moments_data(fid,extended_moments=true)
+            n_ion_zrst, upar_ion_zrst, ppar_ion_zrst, 
+            pperp_ion_zrst, qpar_ion_zrst, v_t_ion_zrst, dSdt_zrst = load_ion_moments_data(fid,extended_moments=true)
             
             close(fid)
             
@@ -255,21 +259,21 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
             vperp, vperp_spectral = load_coordinate_data(fid, "vperp")
 
             # load particle distribution function (pdf) data
-            f_charged_vpavperpzrst = load_pdf_data(fid)
+            f_ion_vpavperpzrst = load_pdf_data(fid)
             
             close(fid)
             # select the single z, r, s point
             # keep the two time points in the arrays
             phi = phi_zrt[1,1,:]
-            n_charged = n_charged_zrst[1,1,1,:]
-            upar_charged = upar_charged_zrst[1,1,1,:]
-            ppar_charged = ppar_charged_zrst[1,1,1,:]
-            pperp_charged = pperp_charged_zrst[1,1,1,:]
-            qpar_charged = qpar_charged_zrst[1,1,1,:]
-            v_t_charged = v_t_charged_zrst[1,1,1,:]
+            n_ion = n_ion_zrst[1,1,1,:]
+            upar_ion = upar_ion_zrst[1,1,1,:]
+            ppar_ion = ppar_ion_zrst[1,1,1,:]
+            pperp_ion = pperp_ion_zrst[1,1,1,:]
+            qpar_ion = qpar_ion_zrst[1,1,1,:]
+            v_t_ion = v_t_ion_zrst[1,1,1,:]
             dSdt = dSdt_zrst[1,1,1,:]
-            f_charged = f_charged_vpavperpzrst[:,:,1,1,1,:]
-            f_err = copy(f_charged)
+            f_ion = f_ion_vpavperpzrst[:,:,1,1,1,:]
+            f_err = copy(f_ion)
             # Unnormalize f
             # NEED TO UPGRADE TO 2V MOMENT KINETICS HERE
             
@@ -288,20 +292,20 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
                 
                 @test isapprox(expected.phi[tind], phi[tind], rtol=rtol)
 
-                # Check charged particle moments and f
+                # Check ion particle moments and f
                 ######################################
 
-                @test isapprox(expected.n_charged[tind], n_charged[tind], atol=atol)
-                @test isapprox(expected.upar_charged[tind], upar_charged[tind], atol=atol)
-                @test isapprox(expected.ppar_charged[tind], ppar_charged[tind], atol=atol)
-                @test isapprox(expected.pperp_charged[tind], pperp_charged[tind], atol=atol)
-                @test isapprox(expected.qpar_charged[tind], qpar_charged[tind], atol=atol)
-                @test isapprox(expected.v_t_charged[tind], v_t_charged[tind], atol=atol)
+                @test isapprox(expected.n_ion[tind], n_ion[tind], atol=atol)
+                @test isapprox(expected.upar_ion[tind], upar_ion[tind], atol=atol)
+                @test isapprox(expected.ppar_ion[tind], ppar_ion[tind], atol=atol)
+                @test isapprox(expected.pperp_ion[tind], pperp_ion[tind], atol=atol)
+                @test isapprox(expected.qpar_ion[tind], qpar_ion[tind], atol=atol)
+                @test isapprox(expected.v_t_ion[tind], v_t_ion[tind], atol=atol)
                 @test isapprox(expected.dSdt[tind], dSdt[tind], atol=atol)
-                @. f_err = abs(expected.f_charged - f_charged)
+                @. f_err = abs(expected.f_ion - f_ion)
                 max_f_err = maximum(f_err)
                 @test isapprox(max_f_err, 0.0, atol=atol)
-                @test isapprox(expected.f_charged[:,:,tind], f_charged[:,:,tind], atol=atol)
+                @test isapprox(expected.f_ion[:,:,tind], f_ion[:,:,tind], atol=atol)
             end
         end
 
diff --git a/moment_kinetics/test/harrisonthompson.jl b/moment_kinetics/test/harrisonthompson.jl
index 8ad05dd24..553515a19 100644
--- a/moment_kinetics/test/harrisonthompson.jl
+++ b/moment_kinetics/test/harrisonthompson.jl
@@ -139,7 +139,7 @@ test_input_chebyshev_split1 = merge(test_input_chebyshev,
 test_input_chebyshev_split2 = merge(test_input_chebyshev_split1,
                                     Dict("run_name" => "chebyshev_pseudospectral_split2",
                                          "evolve_moments_parallel_flow" => true,
-                                         "numerical_dissipation" => Dict("force_minimum_pdf_value" => 0.0)))
+                                         "ion_numerical_dissipation" => Dict("force_minimum_pdf_value" => 0.0)))
 
 test_input_chebyshev_split3 = merge(test_input_chebyshev_split2,
                                     Dict("run_name" => "chebyshev_pseudospectral_split3",
@@ -154,6 +154,10 @@ function run_test(test_input, analytic_rtol, analytic_atol, expected_phi,
     # by passing keyword arguments to run_test, args becomes a Dict which can be used to
     # update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     # Convert keyword arguments to a unique name
     name = test_input["run_name"]
     if length(args) > 0
diff --git a/moment_kinetics/test/interpolation_tests.jl b/moment_kinetics/test/interpolation_tests.jl
index b2fd892a5..9b88deda7 100644
--- a/moment_kinetics/test/interpolation_tests.jl
+++ b/moment_kinetics/test/interpolation_tests.jl
@@ -44,6 +44,8 @@ function runtests()
                                 discretization, fd_option, cheb_option, bc, adv_input, comm,
                                 element_spacing_option)
             # create the coordinate struct 'z'
+            # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+            # errors due to communicators not being fully set up.
             z, spectral = define_coordinate(input; ignore_MPI=true)
 
             test_grid = [z for z in range(-zlim, zlim, length=ntest)]
diff --git a/moment_kinetics/test/nonlinear_sound_wave_inputs_and_expected_data.jl b/moment_kinetics/test/nonlinear_sound_wave_inputs_and_expected_data.jl
index e9d46b1fc..cdee05ac9 100644
--- a/moment_kinetics/test/nonlinear_sound_wave_inputs_and_expected_data.jl
+++ b/moment_kinetics/test/nonlinear_sound_wave_inputs_and_expected_data.jl
@@ -7,13 +7,13 @@ struct expected_data
     z::Array{mk_float, 1}
     vpa::Array{mk_float, 1}
     phi::Array{mk_float, 2}
-    n_charged::Array{mk_float, 2}
+    n_ion::Array{mk_float, 2}
     n_neutral::Array{mk_float, 2}
-    upar_charged::Array{mk_float, 2}
+    upar_ion::Array{mk_float, 2}
     upar_neutral::Array{mk_float, 2}
-    ppar_charged::Array{mk_float, 2}
+    ppar_ion::Array{mk_float, 2}
     ppar_neutral::Array{mk_float, 2}
-    f_charged::Array{mk_float, 3}
+    f_ion::Array{mk_float, 3}
     f_neutral::Array{mk_float, 3}
 end
 
@@ -32,48 +32,48 @@ const expected =
         -0.353459763648872 -0.3755265897483555; -0.5494724768120175 -0.5903597644911376;
         -0.8609860698164502 -0.8726370464896476; -1.2115129555832849 -1.1306355658313922;
         -1.3862820803244258 -1.2382641646968997],
-   n_charged=[0.2500030702177186 0.2898869775083742; 0.2977473631375158 0.3228278662412625;
-              0.42274585818529853 0.417848119539277; 0.5772542465450629 0.5541281150892785;
-              0.7022542481909738 0.6869277664245242; 0.7499999999999394 0.7466605958319346;
-              0.7022542481909738 0.6869277664245237; 0.577254246545063 0.5541281150892783;
-              0.42274585818529864 0.41784811953927686; 0.2977473631375159 0.32282786624126253;
-              0.2500030702177185 0.2898869775083743],
+   n_ion=[0.2500030702177186 0.2898869775083742; 0.2977473631375158 0.3228278662412625;
+          0.42274585818529853 0.417848119539277; 0.5772542465450629 0.5541281150892785;
+          0.7022542481909738 0.6869277664245242; 0.7499999999999394 0.7466605958319346;
+          0.7022542481909738 0.6869277664245237; 0.577254246545063 0.5541281150892783;
+          0.42274585818529864 0.41784811953927686; 0.2977473631375159 0.32282786624126253;
+          0.2500030702177185 0.2898869775083743],
    n_neutral=[0.7499999999999382 0.7736769553678673; 0.7022542481909748 0.7056866352169496;
               0.5772542465450632 0.5582977481633454; 0.4227458581852985 0.40969188756651037;
               0.29774736313751604 0.30539644783353687; 0.2500030702177186 0.268198658560817;
               0.29774736313751604 0.305396447833537; 0.42274585818529836 0.4096918875665103;
               0.5772542465450631 0.5582977481633457; 0.7022542481909745 0.7056866352169494;
               0.7499999999999383 0.7736769553678673],
-   upar_charged=[-2.7135787559953277e-17 -6.299214622140781e-17; -9.321028970172899e-18 -0.1823721921091055;
-                 -2.8374879811351724e-18 -0.19657035490893093; 1.2124327390522635e-17 -0.11139486685283827;
-                 3.6525788403693063e-17 -0.033691837771623996; -2.0930856430671915e-17 4.84147091991613e-17;
-                 8.753545920086251e-18 0.033691837771624024; 1.1293771270243255e-17 0.11139486685283813;
-                 1.3739171132886587e-17 0.19657035490893102; -6.840453743089351e-18 0.18237219210910513;
-                 -2.7135787559953277e-17 -4.656897959900552e-17],
+   upar_ion=[-2.7135787559953277e-17 -6.299214622140781e-17; -9.321028970172899e-18 -0.1823721921091055;
+             -2.8374879811351724e-18 -0.19657035490893093; 1.2124327390522635e-17 -0.11139486685283827;
+             3.6525788403693063e-17 -0.033691837771623996; -2.0930856430671915e-17 4.84147091991613e-17;
+             8.753545920086251e-18 0.033691837771624024; 1.1293771270243255e-17 0.11139486685283813;
+             1.3739171132886587e-17 0.19657035490893102; -6.840453743089351e-18 0.18237219210910513;
+             -2.7135787559953277e-17 -4.656897959900552e-17],
    upar_neutral=[6.5569385065066925e-18 7.469475342067322e-17; 1.1054500872839027e-17 -0.036209130454625794;
                  -3.241833393685864e-17 -0.00915544640981337; -3.617637280460899e-17 0.05452268209340691;
                  4.417578961284041e-17 0.07606644718003618; 4.9354467746194965e-17 4.452343983947504e-17;
                  6.573091229872379e-18 -0.07606644718003616; 2.989662686945165e-17 -0.05452268209340687;
                  -3.1951996361666834e-17 0.009155446409813412; -4.395464518158184e-18 0.03620913045462582;
                  6.5569385065066925e-18 7.150569974151354e-17],
-   ppar_charged=[0.18749999999999992 0.2328164829490338; 0.20909325514551116 0.21912575009260987;
-                 0.24403180771238264 0.20822611102296495; 0.24403180771238278 0.21506741942934832;
-                 0.2090932551455113 0.22097085045011763; 0.1875 0.22119050467096843;
-                 0.20909325514551128 0.2209708504501176; 0.2440318077123828 0.2150674194293483;
-                 0.24403180771238256 0.20822611102296476; 0.20909325514551116 0.21912575009260982;
-                 0.18749999999999992 0.2328164829490338],
+   ppar_ion=[0.18749999999999992 0.2328164829490338; 0.20909325514551116 0.21912575009260987;
+             0.24403180771238264 0.20822611102296495; 0.24403180771238278 0.21506741942934832;
+             0.2090932551455113 0.22097085045011763; 0.1875 0.22119050467096843;
+             0.20909325514551128 0.2209708504501176; 0.2440318077123828 0.2150674194293483;
+             0.24403180771238256 0.20822611102296476; 0.20909325514551116 0.21912575009260982;
+             0.18749999999999992 0.2328164829490338],
    ppar_neutral=[0.18750000000000003 0.2480244331470989; 0.20909325514551122 0.2440075646485762;
                  0.24403180771238286 0.22861256884534023; 0.24403180771238278 0.20588932618946498;
                  0.20909325514551144 0.19263633346696638; 0.18749999999999992 0.19091848744561835;
                  0.20909325514551141 0.19263633346696654; 0.2440318077123828 0.20588932618946482;
                  0.24403180771238286 0.22861256884534029; 0.20909325514551114 0.24400756464857642;
                  0.18750000000000006 0.24802443314709893],
-   f_charged=[0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;
-              0.20411991941198782 0.25123395823993105 0.3934413727192304 0.6277900619432855 0.9100364506661008 1.0606601717796504 0.910036450666101 0.6277900619432859 0.39344137271923046 0.25123395823993094 0.20411991941198776;
-              0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;;;
-              0.05392403019146985 0.06057819609646438 0.03676744157455075 0.013740507879552622 0.010777319583092297 0.019330359159894384 0.027982173790396116 0.027603104735767332 0.02667986700464528 0.035654512254837005 0.05392403019146984;
-              0.21177720235387912 0.24902901234066305 0.3729377138332225 0.596281539172339 0.8870867512643452 1.0533860567375264 0.887086751264345 0.5962815391723388 0.3729377138332225 0.24902901234066285 0.21177720235387912;
-              0.053924030191469796 0.035654512254837074 0.02667986700464531 0.02760310473576733 0.02798217379039615 0.019330359159894287 0.010777319583092311 0.013740507879552624 0.03676744157455069 0.060578196096464365 0.05392403019146979],
+   f_ion=[0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;
+          0.20411991941198782 0.25123395823993105 0.3934413727192304 0.6277900619432855 0.9100364506661008 1.0606601717796504 0.910036450666101 0.6277900619432859 0.39344137271923046 0.25123395823993094 0.20411991941198776;
+          0.0370462360994826 0.04059927063892091 0.0428431419871786 0.030398267195914062 0.01236045902698859 0.006338529470383425 0.012360459026988587 0.030398267195914028 0.04284314198717859 0.0405992706389209 0.0370462360994826;;;
+          0.05392403019146985 0.06057819609646438 0.03676744157455075 0.013740507879552622 0.010777319583092297 0.019330359159894384 0.027982173790396116 0.027603104735767332 0.02667986700464528 0.035654512254837005 0.05392403019146984;
+          0.21177720235387912 0.24902901234066305 0.3729377138332225 0.596281539172339 0.8870867512643452 1.0533860567375264 0.887086751264345 0.5962815391723388 0.3729377138332225 0.24902901234066285 0.21177720235387912;
+          0.053924030191469796 0.035654512254837074 0.02667986700464531 0.02760310473576733 0.02798217379039615 0.019330359159894287 0.010777319583092311 0.013740507879552624 0.03676744157455069 0.060578196096464365 0.05392403019146979],
    f_neutral=[0.0063385294703834595 0.012360459026988546 0.030398267195914108 0.04284314198717859 0.040599270638920985 0.03704623609948259 0.040599270638920965 0.0428431419871786 0.030398267195914094 0.012360459026988546 0.006338529470383456;
               1.0606601717796493 0.9100364506661016 0.6277900619432857 0.3934413727192303 0.2512339582399308 0.20411991941198754 0.2512339582399307 0.3934413727192301 0.6277900619432853 0.9100364506661016 1.0606601717796487;
               0.0063385294703834595 0.012360459026988546 0.030398267195914108 0.04284314198717859 0.040599270638920985 0.03704623609948259 0.040599270638920965 0.0428431419871786 0.030398267195914094 0.012360459026988546 0.006338529470383456;;;
diff --git a/moment_kinetics/test/nonlinear_sound_wave_tests.jl b/moment_kinetics/test/nonlinear_sound_wave_tests.jl
index 7a1e5dde5..0bb965494 100644
--- a/moment_kinetics/test/nonlinear_sound_wave_tests.jl
+++ b/moment_kinetics/test/nonlinear_sound_wave_tests.jl
@@ -8,7 +8,7 @@ using moment_kinetics.coordinates: define_coordinate
 using moment_kinetics.input_structs: grid_input, advection_input
 using moment_kinetics.load_data: open_readonly_output_file, load_coordinate_data,
                                  load_species_data, load_fields_data,
-                                 load_charged_particle_moments_data, load_pdf_data,
+                                 load_ion_moments_data, load_pdf_data,
                                  load_neutral_particle_moments_data,
                                  load_neutral_pdf_data, load_time_data, load_species_data
 using moment_kinetics.interpolation: interpolate_to_grid_z, interpolate_to_grid_vpa
@@ -27,6 +27,10 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
     # by passing keyword arguments to run_test, args becomes a Dict which can be used to
     # update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     if upar_rtol === nothing
         upar_rtol = rtol
     end
@@ -58,10 +62,10 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
     end
 
     phi = nothing
-    n_charged = nothing
-    upar_charged = nothing
-    ppar_charged = nothing
-    f_charged = nothing
+    n_ion = nothing
+    upar_ion = nothing
+    ppar_ion = nothing
+    f_ion = nothing
     n_neutral = nothing
     upar_neutral = nothing
     ppar_neutral = nothing
@@ -89,7 +93,7 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
             phi_zrt, Er_zrt, Ez_zrt = load_fields_data(fid)
 
             # load velocity moments data
-            n_charged_zrst, upar_charged_zrst, ppar_charged_zrst, qpar_charged_zrst, v_t_charged_zrst = load_charged_particle_moments_data(fid)
+            n_ion_zrst, upar_ion_zrst, ppar_ion_zrst, qpar_ion_zrst, v_t_ion_zrst = load_ion_moments_data(fid)
             n_neutral_zrst, upar_neutral_zrst, ppar_neutral_zrst, qpar_neutral_zrst, v_t_neutral_zrst = load_neutral_particle_moments_data(fid)
             z, z_spectral = load_coordinate_data(fid, "z")
 
@@ -99,19 +103,19 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
             fid = open_readonly_output_file(path, "dfns")
             
             # load particle distribution function (pdf) data
-            f_charged_vpavperpzrst = load_pdf_data(fid)
+            f_ion_vpavperpzrst = load_pdf_data(fid)
             f_neutral_vzvrvzetazrst = load_neutral_pdf_data(fid)
             vpa, vpa_spectral = load_coordinate_data(fid, "vpa")
 
             close(fid)
             
             phi = phi_zrt[:,1,:]
-            n_charged = n_charged_zrst[:,1,:,:]
-            upar_charged = upar_charged_zrst[:,1,:,:]
-            ppar_charged = ppar_charged_zrst[:,1,:,:]
-            qpar_charged = qpar_charged_zrst[:,1,:,:]
-            v_t_charged = v_t_charged_zrst[:,1,:,:]
-            f_charged = f_charged_vpavperpzrst[:,1,:,1,:,:]
+            n_ion = n_ion_zrst[:,1,:,:]
+            upar_ion = upar_ion_zrst[:,1,:,:]
+            ppar_ion = ppar_ion_zrst[:,1,:,:]
+            qpar_ion = qpar_ion_zrst[:,1,:,:]
+            v_t_ion = v_t_ion_zrst[:,1,:,:]
+            f_ion = f_ion_vpavperpzrst[:,1,:,1,:,:]
             n_neutral = n_neutral_zrst[:,1,:,:]
             upar_neutral = upar_neutral_zrst[:,1,:,:]
             ppar_neutral = ppar_neutral_zrst[:,1,:,:]
@@ -122,7 +126,7 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
             # Unnormalize f
             if input["evolve_moments_density"]
                 for it ∈ 1:length(time), is ∈ 1:n_ion_species, iz ∈ 1:z.n
-                    f_charged[:,iz,is,it] .*= n_charged[iz,is,it]
+                    f_ion[:,iz,is,it] .*= n_ion[iz,is,it]
                 end
                 for it ∈ 1:length(time), isn ∈ 1:n_neutral_species, iz ∈ 1:z.n
                     f_neutral[:,iz,isn,it] .*= n_neutral[iz,isn,it]
@@ -130,7 +134,7 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
             end
             if input["evolve_moments_parallel_pressure"]
                 for it ∈ 1:length(time), is ∈ 1:n_ion_species, iz ∈ 1:z.n
-                    f_charged[:,iz,is,it] ./= v_t_charged[iz,is,it]
+                    f_ion[:,iz,is,it] ./= v_t_ion[iz,is,it]
                 end
                 for it ∈ 1:length(time), isn ∈ 1:n_neutral_species, iz ∈ 1:z.n
                     f_neutral[:,iz,isn,it] ./= v_t_neutral[iz,isn,it]
@@ -148,11 +152,11 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
         #println("phi ", size(newgrid_phi))
         #println(newgrid_phi)
         #println()
-        #newgrid_n_charged = cat(interpolate_to_grid_z(expected.z, n_charged[:, :, 1], z, z_spectral)[:,1],
-        #                        interpolate_to_grid_z(expected.z, n_charged[:, :, 2], z, z_spectral)[:,1];
+        #newgrid_n_ion = cat(interpolate_to_grid_z(expected.z, n_ion[:, :, 1], z, z_spectral)[:,1],
+        #                        interpolate_to_grid_z(expected.z, n_ion[:, :, 2], z, z_spectral)[:,1];
         #                        dims=2)
-        #println("n_charged ", size(newgrid_n_charged))
-        #println(newgrid_n_charged)
+        #println("n_ion ", size(newgrid_n_ion))
+        #println(newgrid_n_ion)
         #println()
         #newgrid_n_neutral = cat(interpolate_to_grid_z(expected.z, n_neutral[:, :, 1], z, z_spectral)[:,1],
         #                        interpolate_to_grid_z(expected.z, n_neutral[:, :, 2], z, z_spectral)[:,1];
@@ -160,11 +164,11 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
         #println("n_neutral ", size(newgrid_n_neutral))
         #println(newgrid_n_neutral)
         #println()
-        #newgrid_upar_charged = cat(interpolate_to_grid_z(expected.z, upar_charged[:, :, 1], z, z_spectral)[:,1],
-        #                           interpolate_to_grid_z(expected.z, upar_charged[:, :, 2], z, z_spectral)[:,1];
+        #newgrid_upar_ion = cat(interpolate_to_grid_z(expected.z, upar_ion[:, :, 1], z, z_spectral)[:,1],
+        #                           interpolate_to_grid_z(expected.z, upar_ion[:, :, 2], z, z_spectral)[:,1];
         #                           dims=2)
-        #println("upar_charged ", size(newgrid_upar_charged))
-        #println(newgrid_upar_charged)
+        #println("upar_ion ", size(newgrid_upar_ion))
+        #println(newgrid_upar_ion)
         #println()
         #newgrid_upar_neutral = cat(interpolate_to_grid_z(expected.z, upar_neutral[:, :, 1], z, z_spectral)[:,1],
         #                           interpolate_to_grid_z(expected.z, upar_neutral[:, :, 2], z, z_spectral)[:,1];
@@ -172,11 +176,11 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
         #println("upar_neutral ", size(newgrid_upar_neutral))
         #println(newgrid_upar_neutral)
         #println()
-        #newgrid_ppar_charged = cat(interpolate_to_grid_z(expected.z, ppar_charged[:, :, 1], z, z_spectral)[:,1],
-        #                           interpolate_to_grid_z(expected.z, ppar_charged[:, :, 2], z, z_spectral)[:,1];
+        #newgrid_ppar_ion = cat(interpolate_to_grid_z(expected.z, ppar_ion[:, :, 1], z, z_spectral)[:,1],
+        #                           interpolate_to_grid_z(expected.z, ppar_ion[:, :, 2], z, z_spectral)[:,1];
         #                           dims=2)
-        #println("ppar_charged ", size(newgrid_ppar_charged))
-        #println(newgrid_ppar_charged)
+        #println("ppar_ion ", size(newgrid_ppar_ion))
+        #println(newgrid_ppar_ion)
         #println()
         #newgrid_ppar_neutral = cat(interpolate_to_grid_z(expected.z, ppar_neutral[:, :, 1], z, z_spectral)[:,1],
         #                           interpolate_to_grid_z(expected.z, ppar_neutral[:, :, 2], z, z_spectral)[:,1];
@@ -184,11 +188,11 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
         #println("ppar_neutral ", size(newgrid_ppar_neutral))
         #println(newgrid_ppar_neutral)
         #println()
-        #newgrid_f_charged = cat(interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_charged[:, :, :, 1], z, z_spectral), vpa, vpa_spectral)[:,:,1],
-        #                        interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_charged[:, :, :, 2], z, z_spectral), vpa, vpa_spectral)[:,:,1];
+        #newgrid_f_ion = cat(interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_ion[:, :, :, 1], z, z_spectral), vpa, vpa_spectral)[:,:,1],
+        #                        interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_ion[:, :, :, 2], z, z_spectral), vpa, vpa_spectral)[:,:,1];
         #                        dims=4)
-        #println("f_charged ", size(newgrid_f_charged))
-        #println(newgrid_f_charged)
+        #println("f_ion ", size(newgrid_f_ion))
+        #println(newgrid_f_ion)
         #println()
         #newgrid_f_neutral = cat(interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_neutral[:, :, :, 1], z, z_spectral), vpa, vpa_spectral)[:,:,1],
         #                        interpolate_to_grid_vpa(expected.vpa, interpolate_to_grid_z(expected.z, f_neutral[:, :, :, 2], z, z_spectral), vpa, vpa_spectral)[:,:,1];
@@ -201,36 +205,36 @@ function run_test(test_input, rtol, atol, upar_rtol=nothing; args...)
                 newgrid_phi = interpolate_to_grid_z(expected.z, phi[:, tind], z, z_spectral)
                 @test isapprox(expected.phi[:, tind], newgrid_phi, rtol=rtol)
 
-                # Check charged particle moments and f
+                # Check ion particle moments and f
                 ######################################
 
-                newgrid_n_charged = interpolate_to_grid_z(expected.z, n_charged[:, :, tind], z, z_spectral)
-                @test isapprox(expected.n_charged[:, tind], newgrid_n_charged[:,1], rtol=rtol)
+                newgrid_n_ion = interpolate_to_grid_z(expected.z, n_ion[:, :, tind], z, z_spectral)
+                @test isapprox(expected.n_ion[:, tind], newgrid_n_ion[:,1], rtol=rtol)
 
-                newgrid_upar_charged = interpolate_to_grid_z(expected.z, upar_charged[:, :, tind], z, z_spectral)
-                @test isapprox(expected.upar_charged[:, tind], newgrid_upar_charged[:,1], rtol=upar_rtol, atol=atol)
+                newgrid_upar_ion = interpolate_to_grid_z(expected.z, upar_ion[:, :, tind], z, z_spectral)
+                @test isapprox(expected.upar_ion[:, tind], newgrid_upar_ion[:,1], rtol=upar_rtol, atol=atol)
 
-                newgrid_ppar_charged = interpolate_to_grid_z(expected.z, ppar_charged[:, :, tind], z, z_spectral)
-                @test isapprox(expected.ppar_charged[:, tind], newgrid_ppar_charged[:,1], rtol=rtol)
+                newgrid_ppar_ion = interpolate_to_grid_z(expected.z, ppar_ion[:, :, tind], z, z_spectral)
+                @test isapprox(expected.ppar_ion[:, tind], newgrid_ppar_ion[:,1], rtol=rtol)
 
-                newgrid_vth_charged = @. sqrt(2.0*newgrid_ppar_charged/newgrid_n_charged)
-                newgrid_f_charged = interpolate_to_grid_z(expected.z, f_charged[:, :, :, tind], z, z_spectral)
-                temp = newgrid_f_charged
-                newgrid_f_charged = fill(NaN, length(expected.vpa),
-                                         size(newgrid_f_charged, 2),
-                                         size(newgrid_f_charged, 3),
-                                         size(newgrid_f_charged, 4))
+                newgrid_vth_ion = @. sqrt(2.0*newgrid_ppar_ion/newgrid_n_ion)
+                newgrid_f_ion = interpolate_to_grid_z(expected.z, f_ion[:, :, :, tind], z, z_spectral)
+                temp = newgrid_f_ion
+                newgrid_f_ion = fill(NaN, length(expected.vpa),
+                                     size(newgrid_f_ion, 2),
+                                     size(newgrid_f_ion, 3),
+                                     size(newgrid_f_ion, 4))
                 for iz ∈ 1:length(expected.z)
                     wpa = copy(expected.vpa)
                     if input["evolve_moments_parallel_flow"]
-                        wpa .-= newgrid_upar_charged[iz,1]
+                        wpa .-= newgrid_upar_ion[iz,1]
                     end
                     if input["evolve_moments_parallel_pressure"]
-                        wpa ./= newgrid_vth_charged[iz,1]
+                        wpa ./= newgrid_vth_ion[iz,1]
                     end
-                    newgrid_f_charged[:,iz,1] = interpolate_to_grid_vpa(wpa, temp[:,iz,1], vpa, vpa_spectral)
+                    newgrid_f_ion[:,iz,1] = interpolate_to_grid_vpa(wpa, temp[:,iz,1], vpa, vpa_spectral)
                 end
-                @test isapprox(expected.f_charged[:, :, tind], newgrid_f_charged[:,:,1], rtol=rtol)
+                @test isapprox(expected.f_ion[:, :, tind], newgrid_f_ion[:,:,1], rtol=rtol)
 
                 # Check neutral particle moments and f
                 ######################################
diff --git a/moment_kinetics/test/recycling_fraction_tests.jl b/moment_kinetics/test/recycling_fraction_tests.jl
index d4b833817..9e3c1697d 100644
--- a/moment_kinetics/test/recycling_fraction_tests.jl
+++ b/moment_kinetics/test/recycling_fraction_tests.jl
@@ -105,7 +105,8 @@ test_input_split3 = merge(test_input_split2,
                                "vpa_nelement" => 31,
                                "vz_nelement" => 31,
                                "evolve_moments_parallel_pressure" => true,
-                               "numerical_dissipation" => Dict{String,Any}("force_minimum_pdf_value" => 0.0, "vpa_dissipation_coefficient" => 1e-2)))
+                               "ion_numerical_dissipation" => Dict{String,Any}("force_minimum_pdf_value" => 0.0, "vpa_dissipation_coefficient" => 1e-2),
+                               "neutral_numerical_dissipation" => Dict{String,Any}("force_minimum_pdf_value" => 0.0, "vz_dissipation_coefficient" => 1e-2)))
 test_input_split3["timestepping"] = merge(test_input_split3["timestepping"],
                                            Dict("dt" => 1.0e-5))
 
@@ -166,6 +167,10 @@ function run_test(test_input, expected_phi; rtol=4.e-14, atol=1.e-15, args...)
     # by passing keyword arguments to run_test, args becomes a Tuple of Pairs which can be
     # used to update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     # Convert keyword arguments to a unique name
     name = test_input["run_name"]
     if length(args) > 0
diff --git a/moment_kinetics/test/restart_interpolation_tests.jl b/moment_kinetics/test/restart_interpolation_tests.jl
index b8c8899c3..9c0a1c99b 100644
--- a/moment_kinetics/test/restart_interpolation_tests.jl
+++ b/moment_kinetics/test/restart_interpolation_tests.jl
@@ -12,7 +12,7 @@ using moment_kinetics.file_io: io_has_parallel
 using moment_kinetics.input_structs: grid_input, advection_input, hdf5
 using moment_kinetics.load_data: open_readonly_output_file, load_coordinate_data,
                                  load_species_data, load_fields_data,
-                                 load_charged_particle_moments_data, load_pdf_data,
+                                 load_ion_moments_data, load_pdf_data,
                                  load_neutral_particle_moments_data,
                                  load_neutral_pdf_data, load_time_data, load_species_data
 using moment_kinetics.interpolation: interpolate_to_grid_z, interpolate_to_grid_vpa
@@ -70,6 +70,10 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
     # by passing keyword arguments to run_test, kwargs becomes a Tuple of Pairs which can be used to
     # update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     if tol_3V === nothing
         atol_3V = atol
         rtol_3V = rtol
@@ -92,10 +96,15 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
     println("    - testing ", message)
 
     # Convert from Tuple of Pairs with symbol keys to Dict with String keys
-    modified_inputs = Dict(String(k) => v for (k, v) in kwargs)
+    modified_inputs = Dict(String(k) => v for (k, v) in kwargs
+                           if String(k) ∉ keys(test_input["timestepping"]))
+    modified_timestepping_inputs = Dict(String(k) => v for (k, v) in kwargs
+                                        if String(k) ∈ keys(test_input["timestepping"]))
 
     # Update default inputs with values to be changed
     input = merge(test_input, modified_inputs)
+    input["timestepping"] = merge(test_input["timestepping"],
+                                  modified_timestepping_inputs)
 
     input["run_name"] = name
 
@@ -115,10 +124,10 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
     end
 
     phi = nothing
-    n_charged = nothing
-    upar_charged = nothing
-    ppar_charged = nothing
-    f_charged = nothing
+    n_ion = nothing
+    upar_ion = nothing
+    ppar_ion = nothing
+    f_ion = nothing
     n_neutral = nothing
     upar_neutral = nothing
     ppar_neutral = nothing
@@ -150,12 +159,12 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
             time = run_info.time
             n_ion_species = run_info.n_ion_species
             n_neutral_species = run_info.n_neutral_species
-            n_charged_zrst = postproc_load_variable(run_info, "density")
-            upar_charged_zrst = postproc_load_variable(run_info, "parallel_flow")
-            ppar_charged_zrst = postproc_load_variable(run_info, "parallel_pressure")
-            qpar_charged_zrst = postproc_load_variable(run_info, "parallel_heat_flux")
-            v_t_charged_zrst = postproc_load_variable(run_info, "thermal_speed")
-            f_charged_vpavperpzrst  = postproc_load_variable(run_info, "f")
+            n_ion_zrst = postproc_load_variable(run_info, "density")
+            upar_ion_zrst = postproc_load_variable(run_info, "parallel_flow")
+            ppar_ion_zrst = postproc_load_variable(run_info, "parallel_pressure")
+            qpar_ion_zrst = postproc_load_variable(run_info, "parallel_heat_flux")
+            v_t_ion_zrst = postproc_load_variable(run_info, "thermal_speed")
+            f_ion_vpavperpzrst  = postproc_load_variable(run_info, "f")
             n_neutral_zrst = postproc_load_variable(run_info, "density_neutral")
             upar_neutral_zrst = postproc_load_variable(run_info, "uz_neutral")
             ppar_neutral_zrst = postproc_load_variable(run_info, "pz_neutral")
@@ -176,12 +185,12 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
             rm(joinpath(realpath(input["base_directory"]), name); recursive=true)
 
             phi = phi_zrt[:,1,:]
-            n_charged = n_charged_zrst[:,1,:,:]
-            upar_charged = upar_charged_zrst[:,1,:,:]
-            ppar_charged = ppar_charged_zrst[:,1,:,:]
-            qpar_charged = qpar_charged_zrst[:,1,:,:]
-            v_t_charged = v_t_charged_zrst[:,1,:,:]
-            f_charged = f_charged_vpavperpzrst[:,1,:,1,:,:]
+            n_ion = n_ion_zrst[:,1,:,:]
+            upar_ion = upar_ion_zrst[:,1,:,:]
+            ppar_ion = ppar_ion_zrst[:,1,:,:]
+            qpar_ion = qpar_ion_zrst[:,1,:,:]
+            v_t_ion = v_t_ion_zrst[:,1,:,:]
+            f_ion = f_ion_vpavperpzrst[:,1,:,1,:,:]
             n_neutral = n_neutral_zrst[:,1,:,:]
             upar_neutral = upar_neutral_zrst[:,1,:,:]
             ppar_neutral = ppar_neutral_zrst[:,1,:,:]
@@ -192,7 +201,7 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
             # Unnormalize f
             if input["evolve_moments_density"]
                 for it ∈ 1:length(time), is ∈ 1:n_ion_species, iz ∈ 1:z.n
-                    f_charged[:,iz,is,it] .*= n_charged[iz,is,it]
+                    f_ion[:,iz,is,it] .*= n_ion[iz,is,it]
                 end
                 for it ∈ 1:length(time), isn ∈ 1:n_neutral_species, iz ∈ 1:z.n
                     f_neutral[:,iz,isn,it] .*= n_neutral[iz,isn,it]
@@ -200,7 +209,7 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
             end
             if input["evolve_moments_parallel_pressure"]
                 for it ∈ 1:length(time), is ∈ 1:n_ion_species, iz ∈ 1:z.n
-                    f_charged[:,iz,is,it] ./= v_t_charged[iz,is,it]
+                    f_ion[:,iz,is,it] ./= v_t_ion[iz,is,it]
                 end
                 for it ∈ 1:length(time), isn ∈ 1:n_neutral_species, iz ∈ 1:z.n
                     f_neutral[:,iz,isn,it] ./= v_t_neutral[iz,isn,it]
@@ -211,36 +220,36 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, kwargs...)
         newgrid_phi = interpolate_to_grid_z(expected.z, phi[:, end], z, z_spectral)
         @test isapprox(expected.phi[:, end], newgrid_phi, rtol=rtol)
 
-        # Check charged particle moments and f
+        # Check ion particle moments and f
         ######################################
 
-        newgrid_n_charged = interpolate_to_grid_z(expected.z, n_charged[:, :, end], z, z_spectral)
-        @test isapprox(expected.n_charged[:, end], newgrid_n_charged[:,1], rtol=rtol)
+        newgrid_n_ion = interpolate_to_grid_z(expected.z, n_ion[:, :, end], z, z_spectral)
+        @test isapprox(expected.n_ion[:, end], newgrid_n_ion[:,1], rtol=rtol)
 
-        newgrid_upar_charged = interpolate_to_grid_z(expected.z, upar_charged[:, :, end], z, z_spectral)
-        @test isapprox(expected.upar_charged[:, end], newgrid_upar_charged[:,1], rtol=rtol, atol=atol_3V)
+        newgrid_upar_ion = interpolate_to_grid_z(expected.z, upar_ion[:, :, end], z, z_spectral)
+        @test isapprox(expected.upar_ion[:, end], newgrid_upar_ion[:,1], rtol=rtol, atol=atol_3V)
 
-        newgrid_ppar_charged = interpolate_to_grid_z(expected.z, ppar_charged[:, :, end], z, z_spectral)
-        @test isapprox(expected.ppar_charged[:, end], newgrid_ppar_charged[:,1], rtol=rtol)
+        newgrid_ppar_ion = interpolate_to_grid_z(expected.z, ppar_ion[:, :, end], z, z_spectral)
+        @test isapprox(expected.ppar_ion[:, end], newgrid_ppar_ion[:,1], rtol=rtol)
 
-        newgrid_vth_charged = @. sqrt(2.0*newgrid_ppar_charged/newgrid_n_charged)
-        newgrid_f_charged = interpolate_to_grid_z(expected.z, f_charged[:, :, :, end], z, z_spectral)
-        temp = newgrid_f_charged
-        newgrid_f_charged = fill(NaN, length(expected.vpa),
-                                 size(newgrid_f_charged, 2),
-                                 size(newgrid_f_charged, 3),
-                                 size(newgrid_f_charged, 4))
+        newgrid_vth_ion = @. sqrt(2.0*newgrid_ppar_ion/newgrid_n_ion)
+        newgrid_f_ion = interpolate_to_grid_z(expected.z, f_ion[:, :, :, end], z, z_spectral)
+        temp = newgrid_f_ion
+        newgrid_f_ion = fill(NaN, length(expected.vpa),
+                                 size(newgrid_f_ion, 2),
+                                 size(newgrid_f_ion, 3),
+                                 size(newgrid_f_ion, 4))
         for iz ∈ 1:length(expected.z)
             wpa = copy(expected.vpa)
             if input["evolve_moments_parallel_flow"]
-                wpa .-= newgrid_upar_charged[iz,1]
+                wpa .-= newgrid_upar_ion[iz,1]
             end
             if input["evolve_moments_parallel_pressure"]
-                wpa ./= newgrid_vth_charged[iz,1]
+                wpa ./= newgrid_vth_ion[iz,1]
             end
-            newgrid_f_charged[:,iz,1] = interpolate_to_grid_vpa(wpa, temp[:,iz,1], vpa, vpa_spectral)
+            newgrid_f_ion[:,iz,1] = interpolate_to_grid_vpa(wpa, temp[:,iz,1], vpa, vpa_spectral)
         end
-        @test isapprox(expected.f_charged[:, :, end], newgrid_f_charged[:,:,1], rtol=rtol_3V)
+        @test isapprox(expected.f_ion[:, :, end], newgrid_f_ion[:,:,1], rtol=rtol_3V)
 
         # Check neutral particle moments and f
         ######################################
@@ -299,7 +308,7 @@ function runtests()
                                        Dict("evolve_moments_parallel_pressure" => true,
                                             "vpa_L" => 1.5*vpa_L, "vz_L" => 1.5*vpa_L))
 
-        for (base, base_label) ∈ ((base_input, "full-f"),
+        for (base, base_label) ∈ ((base_input_full_f, "full-f"),
                                   (base_input_evolve_density, "split 1"),
                                   (base_input_evolve_upar, "split 2"),
                                   (base_input_evolve_ppar, "split 3"))
diff --git a/moment_kinetics/test/sound_wave_tests.jl b/moment_kinetics/test/sound_wave_tests.jl
index ddfc4d078..813ed5a99 100644
--- a/moment_kinetics/test/sound_wave_tests.jl
+++ b/moment_kinetics/test/sound_wave_tests.jl
@@ -136,6 +136,10 @@ function run_test(test_input, analytic_frequency, analytic_growth_rate,
     # by passing keyword arguments to run_test, args becomes a Dict which can be used to
     # update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     # Convert keyword arguments to a unique name
     name = test_input["run_name"]
     shortname = name
diff --git a/moment_kinetics/test/velocity_integral_tests.jl b/moment_kinetics/test/velocity_integral_tests.jl
index ae210954c..365f92905 100644
--- a/moment_kinetics/test/velocity_integral_tests.jl
+++ b/moment_kinetics/test/velocity_integral_tests.jl
@@ -45,6 +45,8 @@ function runtests()
                                  irank, Lvperp, discretization, fd_option, cheb_option, bc, adv_input,
                                  comm, "uniform")
         # create the coordinate struct 'x'
+        # This test runs effectively in serial, so use `ignore_MPI=true` to avoid
+        # errors due to communicators not being fully set up.
         vpa, vpa_spectral = define_coordinate(vpa_input; ignore_MPI=true)
         vperp, vperp_spectral = define_coordinate(vperp_input; ignore_MPI=true)
         vz, vz_spectral = define_coordinate(vz_input; ignore_MPI=true)
diff --git a/moment_kinetics/test/wall_bc_tests.jl b/moment_kinetics/test/wall_bc_tests.jl
index 175251802..6c46e294e 100644
--- a/moment_kinetics/test/wall_bc_tests.jl
+++ b/moment_kinetics/test/wall_bc_tests.jl
@@ -140,6 +140,10 @@ function run_test(test_input, expected_phi, tolerance; args...)
     # by passing keyword arguments to run_test, args becomes a Dict which can be used to
     # update the default inputs
 
+    # Make a copy to make sure nothing modifies the input Dicts defined in this test
+    # script.
+    test_input = deepcopy(test_input)
+
     # Convert keyword arguments to a unique name
     name = test_input["run_name"] * ", with element spacing: " * test_input["z_element_spacing_option"]
     if length(args) > 0
diff --git a/plots_post_processing/plots_post_processing/src/plot_MMS_sequence.jl b/plots_post_processing/plots_post_processing/src/plot_MMS_sequence.jl
index 6181f1209..84bfcf21b 100644
--- a/plots_post_processing/plots_post_processing/src/plot_MMS_sequence.jl
+++ b/plots_post_processing/plots_post_processing/src/plot_MMS_sequence.jl
@@ -14,16 +14,16 @@ using SpecialFunctions: erfi
 using LaTeXStrings
 # modules
 using ..post_processing_input: pp
-using ..plots_post_processing: compare_charged_pdf_symbolic_test, compare_fields_symbolic_test
+using ..plots_post_processing: compare_ion_pdf_symbolic_test, compare_fields_symbolic_test
 using ..plots_post_processing: compare_moments_symbolic_test, compare_neutral_pdf_symbolic_test
-using ..plots_post_processing: allocate_global_zr_neutral_moments, allocate_global_zr_charged_moments
+using ..plots_post_processing: allocate_global_zr_neutral_moments, allocate_global_zr_ion_moments
 using ..plots_post_processing: allocate_global_zr_fields, get_composition
 using ..plots_post_processing: get_coords_nelement, get_coords_ngrid
 using moment_kinetics.array_allocation: allocate_float
 using moment_kinetics.type_definitions: mk_float, mk_int
 using moment_kinetics.load_data: open_readonly_output_file
 using moment_kinetics.load_data: load_fields_data, load_pdf_data
-using moment_kinetics.load_data: load_charged_particle_moments_data, load_neutral_particle_moments_data
+using moment_kinetics.load_data: load_ion_moments_data, load_neutral_particle_moments_data
 using moment_kinetics.load_data: load_neutral_pdf_data, load_time_data, load_species_data
 using moment_kinetics.load_data: load_block_data, load_coordinate_data, load_input
 using moment_kinetics.load_data: read_distributed_zr_data!, construct_global_zr_coords
@@ -198,7 +198,7 @@ function get_MMS_error_data(path_list,scan_type,scan_name)
         # allocate arrays to contain the global fields as a function of (z,r,t)
         phi, Ez, Er = allocate_global_zr_fields(z.n_global,r.n_global,ntime)
         density, parallel_flow, parallel_pressure, parallel_heat_flux,
-            thermal_speed = allocate_global_zr_charged_moments(z.n_global,r.n_global,n_ion_species,ntime)
+            thermal_speed = allocate_global_zr_ion_moments(z.n_global,r.n_global,n_ion_species,ntime)
         if n_neutral_species > 0
             neutral_density, neutral_uz, neutral_pz, 
              neutral_qz, neutral_thermal_speed = allocate_global_zr_neutral_moments(z.n_global,r.n_global,n_neutral_species,ntime)
@@ -216,7 +216,7 @@ function get_MMS_error_data(path_list,scan_type,scan_name)
         read_distributed_zr_data!(phi,"phi",run_names,"moments",nbs,z.n,r.n,iskip) 
         read_distributed_zr_data!(Ez,"Ez",run_names,"moments",nbs,z.n,r.n,iskip) 
         read_distributed_zr_data!(Er,"Er",run_names,"moments",nbs,z.n,r.n,iskip) 
-        # charged particle moments
+        # ion particle moments
         read_distributed_zr_data!(density,"density",run_names,"moments",nbs,z.n,r.n,iskip) 
         read_distributed_zr_data!(parallel_flow,"parallel_flow",run_names,"moments",nbs,z.n,r.n,iskip) 
         read_distributed_zr_data!(parallel_pressure,"parallel_pressure",run_names,"moments",nbs,z.n,r.n,iskip) 
@@ -298,7 +298,7 @@ function get_MMS_error_data(path_list,scan_type,scan_name)
         # use final time point for analysis
         ion_density_error_sequence[isim] = ion_density_error_t[end] 
         
-        ion_pdf_error_t = compare_charged_pdf_symbolic_test(run_name,manufactured_solns_list,"ion",
+        ion_pdf_error_t = compare_ion_pdf_symbolic_test(run_name,manufactured_solns_list,"ion",
          L"\widetilde{f}_i",L"\widetilde{f}^{sym}_i",L"\sum || \widetilde{f}_i - \widetilde{f}_i^{sym} ||^2","pdf")
         ion_pdf_error_sequence[isim] = ion_pdf_error_t[end]
         
diff --git a/plots_post_processing/plots_post_processing/src/plot_sequence.jl b/plots_post_processing/plots_post_processing/src/plot_sequence.jl
index 6035b1cc2..be090814f 100644
--- a/plots_post_processing/plots_post_processing/src/plot_sequence.jl
+++ b/plots_post_processing/plots_post_processing/src/plot_sequence.jl
@@ -10,7 +10,7 @@ using Statistics: mean
 using SpecialFunctions: erfi
 using LaTeXStrings
 # modules
-using ..plots_post_processing: allocate_global_zr_neutral_moments, allocate_global_zr_charged_moments
+using ..plots_post_processing: allocate_global_zr_neutral_moments, allocate_global_zr_ion_moments
 using ..plots_post_processing: allocate_global_zr_fields#, get_coords_nelement
 using moment_kinetics.array_allocation: allocate_float
 using moment_kinetics.type_definitions: mk_float, mk_int
diff --git a/plots_post_processing/plots_post_processing/src/plots_post_processing.jl b/plots_post_processing/plots_post_processing/src/plots_post_processing.jl
index f2a451fda..972b92620 100644
--- a/plots_post_processing/plots_post_processing/src/plots_post_processing.jl
+++ b/plots_post_processing/plots_post_processing/src/plots_post_processing.jl
@@ -3,12 +3,11 @@
 module plots_post_processing
 
 export analyze_and_plot_data
-export compare_charged_pdf_symbolic_test
 export compare_moments_symbolic_test
 export compare_neutral_pdf_symbolic_test
 export compare_fields_symbolic_test
 export construct_global_zr_coords
-export allocate_global_zr_charged_moments
+export allocate_global_zr_ion_moments
 export allocate_global_zr_neutral_moments
 export allocate_global_zr_fields
 export get_coords_nelement
@@ -43,9 +42,9 @@ using moment_kinetics.load_data: open_readonly_output_file, get_group, load_inpu
                                  load_time_data, construct_global_zr_coords
 using moment_kinetics.load_data: get_nranks
 using moment_kinetics.load_data: load_fields_data, load_pdf_data
-using moment_kinetics.load_data: load_charged_particle_moments_data,
+using moment_kinetics.load_data: load_ion_moments_data,
                                  load_neutral_particle_moments_data
-using moment_kinetics.load_data: load_distributed_charged_pdf_slice,
+using moment_kinetics.load_data: load_distributed_ion_pdf_slice,
                                  load_distributed_neutral_pdf_slice, iglobal_func
 using moment_kinetics.load_data: load_neutral_pdf_data
 using moment_kinetics.load_data: load_variable, read_distributed_zr_data!
@@ -193,7 +192,7 @@ function allocate_global_zr_fields(nz_global,nr_global,ntime)
     return phi, Ez, Er
 end
 
-function allocate_global_zr_charged_moments(nz_global,nr_global,n_ion_species,ntime)
+function allocate_global_zr_ion_moments(nz_global,nr_global,n_ion_species,ntime)
     density = allocate_float(nz_global,nr_global,n_ion_species,ntime)
     parallel_flow = allocate_float(nz_global,nr_global,n_ion_species,ntime)
     parallel_pressure = allocate_float(nz_global,nr_global,n_ion_species,ntime)
@@ -206,7 +205,7 @@ function allocate_global_zr_charged_moments(nz_global,nr_global,n_ion_species,nt
     return density, parallel_flow, parallel_pressure, perpendicular_pressure, parallel_heat_flux, thermal_speed, entropy_production, chodura_integral_lower, chodura_integral_upper
 end
 
-function allocate_global_zr_charged_dfns(nvpa_global, nvperp_global, nz_global, nr_global,
+function allocate_global_zr_ion_dfns(nvpa_global, nvperp_global, nz_global, nr_global,
                                          n_ion_species, ntime)
     f = allocate_float(nvpa_global, nvperp_global, nz_global, nr_global, n_ion_species,
                        ntime)
@@ -434,11 +433,11 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
                                              Tuple(this_r.n_global for this_r ∈ r),
                                              ntime)
     density, parallel_flow, parallel_pressure, perpendicular_pressure, parallel_heat_flux, thermal_speed, entropy_production, chodura_integral_lower, chodura_integral_upper =
-        get_tuple_of_return_values(allocate_global_zr_charged_moments,
+        get_tuple_of_return_values(allocate_global_zr_ion_moments,
                                    Tuple(this_z.n_global for this_z ∈ z),
                                    Tuple(this_r.n_global for this_r ∈ r),
                                    n_ion_species, ntime)
-    if has_neutrals
+    if any(n_neutral_species .> 0)
         neutral_density, neutral_uz, neutral_pz, neutral_qz, neutral_thermal_speed =
             get_tuple_of_return_values(allocate_global_zr_neutral_moments,
                                        Tuple(this_z.n_global for this_z ∈ z),
@@ -463,7 +462,7 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
                                nblocks,
                                Tuple(this_z.n for this_z ∈ z),
                                Tuple(this_r.n for this_r ∈ r), iskip)
-    # charged particle moments
+    # ion particle moments
     get_tuple_of_return_values(read_distributed_zr_data!, density, "density", run_names,
                                "moments", nblocks,
                                Tuple(this_z.n for this_z ∈ z),
@@ -556,7 +555,7 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
     perpendicular_pressure_at_pdf_timse, parallel_heat_flux_at_pdf_times,
     thermal_speed_at_pdf_times, entropy_production_at_pdf_times,
     chodura_integral_lower_at_pdf_times, chodura_integral_upper_at_pdf_times =
-        get_tuple_of_return_values(allocate_global_zr_charged_moments,
+        get_tuple_of_return_values(allocate_global_zr_ion_moments,
                                    Tuple(this_z.n_global for this_z ∈ z),
                                    Tuple(this_r.n_global for this_r ∈ r), n_ion_species,
                                    ntime_pdfs)
@@ -581,7 +580,7 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
                                run_names, "dfns", nblocks,
                                Tuple(this_z.n for this_z ∈ z),
                                Tuple(this_r.n for this_r ∈ r), iskip_pdfs)
-    # charged particle moments
+    # ion particle moments
     get_tuple_of_return_values(read_distributed_zr_data!, density_at_pdf_times, "density",
                                run_names, "dfns", nblocks,
                                Tuple(this_z.n for this_z ∈ z),
@@ -663,7 +662,7 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
                    (vr === nothing ? true : (this_vr.n == 1 for this_vr ∈ vr))...])
     if is_1D1V && false
         # load full (vpa,z,r,species,t) particle distribution function (pdf) data
-        ff = get_tuple_of_return_values(load_distributed_charged_pdf_slice, run_names,
+        ff = get_tuple_of_return_values(load_distributed_ion_pdf_slice, run_names,
                                         nblocks, itime_min_pdfs:iskip_pdfs:itime_max_pdfs,
                                         n_ion_species, r, z, vperp, vpa)
         if has_neutrals
@@ -1031,26 +1030,26 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
 
     if !is_1D1V || true
         # make plots and animations of the phi, Ez and Er
-        plot_charged_moments_2D(density, parallel_flow, parallel_pressure, 
-                                perpendicular_pressure, thermal_speed, entropy_production,
-                                chodura_integral_lower, chodura_integral_upper, time,
-                                z_global.grid, r_global.grid, iz0, ir0, n_ion_species,
-                                itime_min, itime_max, nwrite_movie, run_name_label, pp)
+        plot_ion_moments_2D(density, parallel_flow, parallel_pressure, 
+                            perpendicular_pressure, thermal_speed, entropy_production,
+                            chodura_integral_lower, chodura_integral_upper, time,
+                            z_global.grid, r_global.grid, iz0, ir0, n_ion_species,
+                            itime_min, itime_max, nwrite_movie, run_name_label, pp)
         # make plots and animations of the phi, Ez and Er
         plot_fields_2D(phi, Ez, Er, time, z_global.grid, r_global.grid, iz0, ir0, itime_min,
                        itime_max, nwrite_movie, run_name_label, pp, "")
 
         # load full (vpa,z,r,species,t) particle distribution function (pdf) data
         spec_type = "ion"
-        plot_charged_pdf(run_name, run_name_label, vpa, vperp, z_global, r_global, z, r,
-                         ivpa0, ivperp0, iz0, ir0, spec_type, n_ion_species, ntime_pdfs,
-                         nblocks, itime_min_pdfs, itime_max_pdfs, iskip_pdfs,
-                         nwrite_movie_pdfs, pp)
+        plot_ion_pdf(run_name, run_name_label, vpa, vperp, z_global, r_global, z, r,
+                     ivpa0, ivperp0, iz0, ir0, spec_type, n_ion_species, ntime_pdfs,
+                     nblocks, itime_min_pdfs, itime_max_pdfs, iskip_pdfs,
+                     nwrite_movie_pdfs, pp)
         Maxwellian_diagnostic = true
         if Maxwellian_diagnostic
             pressure = copy(parallel_pressure)
             @. pressure = (2.0*perpendicular_pressure + parallel_pressure)/3.0
-            ff = load_distributed_charged_pdf_slice(run_name, nblocks, 1:ntime, n_ion_species, r,
+            ff = load_distributed_ion_pdf_slice(run_name, nblocks, 1:ntime, n_ion_species, r,
                                                    z, vperp, vpa; iz=iz0, ir=ir0)
             plot_Maxwellian_diagnostic(ff[:,:,:,:], density[iz0,ir0,:,:],
              parallel_flow[iz0,ir0,:,:], thermal_speed[iz0,ir0,:,:], vpa.grid, vpa.wgts, 
@@ -1066,9 +1065,9 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
         end
         # plot ion pdf data near the wall boundary
         if pp.plot_wall_pdf
-            plot_charged_pdf_2D_at_wall(run_name, run_name_label, r_global, z_global,
-                                        nblocks, n_ion_species, r, z, vperp, vpa,
-                                        ntime_pdfs)
+            plot_ion_pdf_2D_at_wall(run_name, run_name_label, r_global, z_global,
+                                    nblocks, n_ion_species, r, z, vperp, vpa,
+                                    ntime_pdfs)
         end
     end
 
@@ -1157,7 +1156,7 @@ function analyze_and_plot_data(prefix...; run_index=nothing)
         compare_moments_symbolic_test(run_name_label,thermal_speed,vthi_sym,"ion",z_global.grid,r_global.grid,time,z_global.n,r_global.n,ntime,
          L"\widetilde{v}_{th,i}",L"\widetilde{v}_{th,i}^{sym}",L"\varepsilon(\widetilde{v}_{th,i})","vthi")
 
-        compare_charged_pdf_symbolic_test(run_name_label,manufactured_solns_list,"ion",
+        compare_ion_pdf_symbolic_test(run_name_label,manufactured_solns_list,"ion",
           L"\widetilde{f}_i",L"\widetilde{f}^{sym}_i",L"\varepsilon(\widetilde{f}_i)","pdf")
         if n_neutral_species > 0
             # neutral test
@@ -1253,7 +1252,7 @@ function calculate_differences(prefix...)
                                              ntime)
     density, parallel_flow, parallel_pressure, parallel_heat_flux, thermal_speed,
     chodura_integral_lower, chodura_integral_upper =
-        get_tuple_of_return_values(allocate_global_zr_charged_moments,
+        get_tuple_of_return_values(allocate_global_zr_ion_moments,
                                    Tuple(this_z.n_global for this_z ∈ z),
                                    Tuple(this_r.n_global for this_r ∈ r),
                                    n_ion_species, ntime)
@@ -1282,7 +1281,7 @@ function calculate_differences(prefix...)
                                nblocks,
                                Tuple(this_z.n for this_z ∈ z),
                                Tuple(this_r.n for this_r ∈ r))
-    # charged particle moments
+    # ion particle moments
     get_tuple_of_return_values(read_distributed_zr_data!, density, "density", run_names,
                                "moments", nblocks,
                                Tuple(this_z.n for this_z ∈ z),
@@ -1358,7 +1357,7 @@ function calculate_differences(prefix...)
     density_at_pdf_times, parallel_flow_at_pdf_times, parallel_pressure_at_pdf_times,
     parallel_heat_flux_at_pdf_times, thermal_speed_at_pdf_times, chodura_integral_lower_at_pdf_times,
     chodura_integral_upper_at_pdf_times =
-        get_tuple_of_return_values(allocate_global_zr_charged_moments,
+        get_tuple_of_return_values(allocate_global_zr_ion_moments,
                                    Tuple(this_z.n_global for this_z ∈ z),
                                    Tuple(this_r.n_global for this_r ∈ r), n_ion_species,
                                    ntime_pdfs)
@@ -1383,7 +1382,7 @@ function calculate_differences(prefix...)
                                run_names, "dfns", nblocks,
                                Tuple(this_z.n for this_z ∈ z),
                                Tuple(this_r.n for this_r ∈ r))
-    # charged particle moments
+    # ion moments
     get_tuple_of_return_values(read_distributed_zr_data!, density_at_pdf_times, "density",
                                run_names, "dfns", nblocks,
                                Tuple(this_z.n for this_z ∈ z),
@@ -1431,7 +1430,7 @@ function calculate_differences(prefix...)
     end
 
     # load full (vpa,z,r,species,t) particle distribution function (pdf) data
-    ff = get_tuple_of_return_values(load_distributed_charged_pdf_slice, run_names,
+    ff = get_tuple_of_return_values(load_distributed_ion_pdf_slice, run_names,
                                     nblocks, Tuple(1:nt for nt ∈ ntime_pdfs),
                                     n_ion_species, r, z, vperp, vpa)
     if maximum(n_neutral_species) > 0
@@ -2658,7 +2657,7 @@ function compare_moments_symbolic_test(run_name,moment,moment_sym,spec_string,z,
 
 end
 
-function compare_charged_pdf_symbolic_test(run_name,manufactured_solns_list,spec_string,
+function compare_ion_pdf_symbolic_test(run_name,manufactured_solns_list,spec_string,
     pdf_label,pdf_sym_label,norm_label,file_string)
     fid = open_readonly_output_file(run_name,"dfns", printout=false)
     # load block data on iblock=0
@@ -2672,7 +2671,7 @@ function compare_charged_pdf_symbolic_test(run_name,manufactured_solns_list,spec
     # load time data (unique to pdf, may differ to moment values depending on user nwrite_dfns value)
     ntime, time, _ = load_time_data(fid, printout=false)
     close(fid)
-    # get the charged particle pdf
+    # get the ion pdf
     dfni_func = manufactured_solns_list.dfni_func
     is = 1 # only one species supported currently
 
@@ -2754,7 +2753,7 @@ function compare_neutral_pdf_symbolic_test(run_name,manufactured_solns_list,spec
     # load time data (unique to pdf, may differ to moment values depending on user nwrite_dfns value)
     ntime, time, _ = load_time_data(fid, printout=false)
     close(fid)
-    # get the charged particle pdf
+    # get the ion pdf
     dfnn_func = manufactured_solns_list.dfnn_func
     is = 1 # only one species supported currently
 
@@ -2837,7 +2836,7 @@ end
 """
 plots various slices of the ion pdf (1d and 2d, stills and animations)
 """
-function plot_charged_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r_local,
+function plot_ion_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r_local,
                           ivpa0, ivperp0, iz0, ir0, spec_type, n_species, n_time_pdfs,
                           nblocks, itime_min, itime_max, iskip, nwrite_movie, pp)
 
@@ -2860,7 +2859,7 @@ function plot_charged_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r
     end
     # make a gif animation of f(vpa,z,t) at a given (vperp,r) location
     if pp.animate_f_vs_vpa_z
-        pdf = load_distributed_charged_pdf_slice(run_name, nblocks,
+        pdf = load_distributed_ion_pdf_slice(run_name, nblocks,
                                                  itime_min:iskip:itime_max, n_species,
                                                  r_local, z_local, vperp, vpa;
                                                  ivperp=ivperp0, ir=ir0)
@@ -2878,10 +2877,10 @@ function plot_charged_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r
     end
     # make a gif animation of f(vpa,r,t) at a given (vperp,z) location
     if pp.animate_f_vs_vpa_r
-        pdf = load_distributed_charged_pdf_slice(run_name, nblocks,
-                                                 itime_min:iskip:itime_max, n_species,
-                                                 r_local, z_local, vperp, vpa;
-                                                 ivperp=ivperp0, iz=iz0)
+        pdf = load_distributed_ion_pdf_slice(run_name, nblocks,
+                                             itime_min:iskip:itime_max, n_species,
+                                             r_local, z_local, vperp, vpa;
+                                             ivperp=ivperp0, iz=iz0)
         for is ∈ 1:n_species
             anim = @animate for i ∈ itime_min:nwrite_movie:itime_max
                 @views heatmap(r.grid, vpa.grid, pdf[:,:,is,i], xlabel="r", ylabel="vpa", c = :deep, interpolation = :cubic)
@@ -2896,7 +2895,7 @@ function plot_charged_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r
     end
     # make a gif animation of f(vperp,z,t) at a given (vpa,r) location
     if pp.animate_f_vs_vperp_z
-        pdf = load_distributed_charged_pdf_slice(run_name, nblocks,
+        pdf = load_distributed_ion_pdf_slice(run_name, nblocks,
                                                  itime_min:iskip:itime_max, n_species,
                                                  r_local, z_local, vperp, vpa; ivpa=ivpa0,
                                                  ir=ir0)
@@ -2910,7 +2909,7 @@ function plot_charged_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r
     end
     # make a gif animation of f(vperp,r,t) at a given (vpa,z) location
     if pp.animate_f_vs_vperp_r
-        pdf = load_distributed_charged_pdf_slice(run_name, nblocks,
+        pdf = load_distributed_ion_pdf_slice(run_name, nblocks,
                                                  itime_min:iskip:itime_max, n_species,
                                                  r_local, z_local, vperp, vpa; ivpa=ivpa0,
                                                  iz=iz0)
@@ -2924,7 +2923,7 @@ function plot_charged_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r
     end
     # make a gif animation of f(vpa,vperp,t) at a given (z,r) location
     if pp.animate_f_vs_vperp_vpa
-        pdf = load_distributed_charged_pdf_slice(run_name, nblocks,
+        pdf = load_distributed_ion_pdf_slice(run_name, nblocks,
                                                  itime_min:iskip:itime_max, n_species,
                                                  r_local, z_local, vperp, vpa; iz=iz0,
                                                  ir=ir0)
@@ -2972,10 +2971,10 @@ function plot_charged_pdf(run_name, run_name_label, vpa, vperp, z, r, z_local, r
     end
     # make a gif animation of f(z,r,t) at a given (vpa,vperp) location
     if pp.animate_f_vs_r_z
-        pdf = load_distributed_charged_pdf_slice(run_name, nblocks,
-                                                 itime_min:iskip:itime_max, n_species,
-                                                 r_local, z_local, vperp, vpa; ivpa=ivpa0,
-                                                 ivperp=ivperp0)
+        pdf = load_distributed_ion_pdf_slice(run_name, nblocks,
+                                             itime_min:iskip:itime_max, n_species,
+                                             r_local, z_local, vperp, vpa; ivpa=ivpa0,
+                                             ivperp=ivperp0)
         for is ∈ 1:n_species
             anim = @animate for i ∈ itime_min:nwrite_movie:itime_max
                 @views heatmap(r.grid, z.grid, pdf[:,:,is,i], xlabel="r", ylabel="z", c = :deep, interpolation = :cubic)
@@ -3154,14 +3153,14 @@ function plot_fields_2D(phi, Ez, Er, time, z, r, iz0, ir0,
     println("done.")
 end
 
-function plot_charged_moments_2D(density, parallel_flow, parallel_pressure,
+function plot_ion_moments_2D(density, parallel_flow, parallel_pressure,
     perpendicular_pressure, thermal_speed, 
     entropy_production,chodura_integral_lower, chodura_integral_upper,
     time, z, r, iz0, ir0, n_ion_species,
     itime_min, itime_max, nwrite_movie, run_name, pp)
     nr = size(r,1)
     ntime = size(time,1)
-    print("Plotting charged moments data...")
+    print("Plotting ion moments data...")
     for is in 1:n_ion_species
 		description = "_ion_spec"*string(is)*"_"
 		# the density
@@ -3427,9 +3426,9 @@ function plot_Maxwellian_diagnostic(ff, density, parallel_flow, thermal_speed, v
     end
     return nothing
 end
-function plot_charged_pdf_2D_at_wall(run_name, run_name_label, r_global, z_global,
+function plot_ion_pdf_2D_at_wall(run_name, run_name_label, r_global, z_global,
                                      nblocks, n_ion_species, r, z, vperp, vpa, ntime)
-    print("Plotting charged pdf data at wall boundaries...")
+    print("Plotting ion pdf data at wall boundaries...")
 
     # plot a thermal vpa on line plots
     ivpa0 = floor(mk_int,vpa.n/3)
@@ -3441,10 +3440,10 @@ function plot_charged_pdf_2D_at_wall(run_name, run_name_label, r_global, z_globa
     # Note only need final time point, so only load the one time point
     itime0 = 1
     # pdf at lower wall
-    pdf_lower = load_distributed_charged_pdf_slice(run_name, nblocks, ntime:ntime, n_ion_species, r,
+    pdf_lower = load_distributed_ion_pdf_slice(run_name, nblocks, ntime:ntime, n_ion_species, r,
                                                    z, vperp, vpa; iz=1)
     # pdf at upper wall
-    pdf_upper = load_distributed_charged_pdf_slice(run_name, nblocks, ntime:ntime, n_ion_species, r,
+    pdf_upper = load_distributed_ion_pdf_slice(run_name, nblocks, ntime:ntime, n_ion_species, r,
                                                    z, vperp, vpa; iz=z.n_global)
     for (pdf, zlabel) ∈ ((pdf_lower, "wall-"), (pdf_upper, "wall+"))
         for is in 1:n_ion_species
@@ -3474,7 +3473,7 @@ function plot_charged_pdf_2D_at_wall(run_name, run_name_label, r_global, z_globa
             outfile = string(run_name_label, "_pdf(vpa,vperp,iz_"*zlabel*",ir0)"*description*"vs_vperp_vpa.pdf")
             trysavefig(outfile)
 
-            # Skip this because load_distributed_charged_pdf_slice() currently only
+            # Skip this because load_distributed_ion_pdf_slice() currently only
             # handles selecting a single value like `iz=1`, not a sub-slice like
             # `iz=1:n_local`, so we only have data for one point in z here, so we can't
             # plot vs z.
@@ -3486,7 +3485,7 @@ function plot_charged_pdf_2D_at_wall(run_name, run_name_label, r_global, z_globa
 
             # plot f(ivpa0,ivperp0,z,r,is,itime) near the wall
             if r.n > 1
-                # Skip this because load_distributed_charged_pdf_slice() currently only
+                # Skip this because load_distributed_ion_pdf_slice() currently only
                 # handles selecting a single value like `iz=1`, not a sub-slice like
                 # `iz=1:n_local`, so we only have data for one point in z here, so we
                 # can't plot vs z.
diff --git a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5.toml b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5.toml
index ec657ade1..8943ac402 100644
--- a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5.toml
+++ b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5.toml
@@ -82,8 +82,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 #force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+#force_minimum_pdf_value = 0.0
diff --git a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split1.toml b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split1.toml
index c819bb71c..f7a1484d7 100644
--- a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split1.toml
+++ b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split1.toml
@@ -82,8 +82,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 #force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+#force_minimum_pdf_value = 0.0
diff --git a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split2.toml b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split2.toml
index 702fd6b0c..ef1a221cb 100644
--- a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split2.toml
+++ b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split2.toml
@@ -82,8 +82,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
diff --git a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split3.toml b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split3.toml
index cc6c15f4b..79c01a3be 100644
--- a/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split3.toml
+++ b/publication_inputs/2023_EFTC_jto-poster/wall-bc/wall-bc_recyclefraction0.5_split3.toml
@@ -82,8 +82,14 @@ z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 1.0e-1
 #vpa_dissipation_coefficient = 1.0e-2
 #vpa_dissipation_coefficient = 1.0e-3
 force_minimum_pdf_value = 0.0
+
+[ion_numerical_dissipation]
+#vz_dissipation_coefficient = 1.0e-1
+#vz_dissipation_coefficient = 1.0e-2
+#vz_dissipation_coefficient = 1.0e-3
+force_minimum_pdf_value = 0.0
diff --git a/runs/1D-mirror_MMS_new_nel_r_1_z_16_vpa_16_vperp_8_diss.toml b/runs/1D-mirror_MMS_new_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
index 45d596904..9a475346b 100644
--- a/runs/1D-mirror_MMS_new_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
+++ b/runs/1D-mirror_MMS_new_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
@@ -91,7 +91,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/1D-mirror_MMS_new_nel_r_1_z_6_vpa_6_vperp_3_diss.toml b/runs/1D-mirror_MMS_new_nel_r_1_z_6_vpa_6_vperp_3_diss.toml
index a465d248c..347dd2b04 100644
--- a/runs/1D-mirror_MMS_new_nel_r_1_z_6_vpa_6_vperp_3_diss.toml
+++ b/runs/1D-mirror_MMS_new_nel_r_1_z_6_vpa_6_vperp_3_diss.toml
@@ -92,7 +92,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
index 6a89faab1..cb8ce6cf2 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
index a90350f22..6d9c31403 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml
index 92a8aa331..c0ec6f8f5 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml
index 5f63e0aec..dff2bf452 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.0
 #z_dissipation_coefficient = 0.1
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml
index c8e8df9ee..a5be20d0d 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
index d6851c2bf..e28b4b068 100644
--- a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
+++ b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
@@ -87,7 +87,7 @@ split_operators = false
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.0
diff --git a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
index 2edf54dc2..f45c8828d 100644
--- a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
+++ b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
@@ -88,7 +88,7 @@ split_operators = false
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = -1.0
 z_dissipation_coefficient = -1.0
 r_dissipation_coefficient = -1.0
diff --git a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml
index aa6b849d5..9ec02fede 100644
--- a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml
+++ b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml
@@ -88,7 +88,7 @@ split_operators = false
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = -1.0
 z_dissipation_coefficient = -1.0
 r_dissipation_coefficient = -1.0
diff --git a/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml b/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
index a300c9a56..cf3eb5d19 100644
--- a/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
+++ b/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml b/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml
index c98077d3a..5bd48c14b 100644
--- a/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml
+++ b/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/2D-mirror_MMS_ngrid_5_nel_r_4_z_4_vpa_4_vperp_2_diss.toml b/runs/2D-mirror_MMS_ngrid_5_nel_r_4_z_4_vpa_4_vperp_2_diss.toml
index 3ec12c9fe..b13205d70 100644
--- a/runs/2D-mirror_MMS_ngrid_5_nel_r_4_z_4_vpa_4_vperp_2_diss.toml
+++ b/runs/2D-mirror_MMS_ngrid_5_nel_r_4_z_4_vpa_4_vperp_2_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml b/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml
index e936ef06e..d011761cb 100644
--- a/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml
+++ b/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml
@@ -87,7 +87,7 @@ vzeta_discretization = "chebyshev_pseudospectral"
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 vpa_dissipation_coefficient = 0.001
 vperp_dissipation_coefficient = 0.001
 #z_dissipation_coefficient = 0.1
diff --git a/runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml
index b3aa7eff8..3fb456895 100644
--- a/runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml
+++ b/runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml
@@ -78,7 +78,7 @@ nwrite_dfns = 200
 n_rk_stages = 4
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.01
diff --git a/runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml
index eaeecff96..ee1765bf4 100644
--- a/runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml
+++ b/runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml
@@ -78,7 +78,7 @@ nwrite_dfns = 200
 n_rk_stages = 4
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.01
diff --git a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml
index 19c6593b8..38bc4655a 100644
--- a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml
+++ b/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml
@@ -87,7 +87,7 @@ split_operators = false
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.1
diff --git a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml b/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml
index 6b9bfc86d..16c5ca77a 100644
--- a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml
+++ b/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml
@@ -78,7 +78,7 @@ nwrite_dfns = 200
 n_rk_stages = 4
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.01
diff --git a/runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml
index 3307b52b2..2211ef9a6 100644
--- a/runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml
+++ b/runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml
@@ -78,7 +78,7 @@ nwrite_dfns = 200
 n_rk_stages = 4
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.01
diff --git a/runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml
index 78f3e95b7..095f8d86e 100644
--- a/runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml
+++ b/runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml
@@ -78,7 +78,7 @@ nwrite_dfns = 200
 n_rk_stages = 4
 split_operators = false
 
-[numerical_dissipation]
+[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.01
diff --git a/runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml b/runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml
index 3d9efefcb..543739bed 100644
--- a/runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml
+++ b/runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml
@@ -90,7 +90,7 @@ nwrite_dfns = 5000
 n_rk_stages = 4
 split_operators = false
 
-#[numerical_dissipation]
+#[ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.0
 #vperp_dissipation_coefficient = 0.0
 #z_dissipation_coefficient = 0.1
diff --git a/util/compare_collision_frequencies.jl b/util/compare_collision_frequencies.jl
index 8396e5cb7..a1fac065e 100644
--- a/util/compare_collision_frequencies.jl
+++ b/util/compare_collision_frequencies.jl
@@ -27,10 +27,10 @@ function compare_collision_frequencies(input_file::String,
     # v_∥ dissipation term is D d^2f/dv_∥^2. Inserting factors of c_ref, this is a bit like
     # pitch angle scattering D cref^2 d^2f/dv_∥^2 ~ D d^2f/dξ^2, so D is similar to a
     # (normalised) collision frequency.
-    if num_diss_params.vpa_dissipation_coefficient < 0.0
+    if num_diss_params.ion.vpa_dissipation_coefficient < 0.0
         nu_vpa_diss = 0.0
     else
-        nu_vpa_diss = num_diss_params.vpa_dissipation_coefficient /
+        nu_vpa_diss = num_diss_params.ion.vpa_dissipation_coefficient /
                       dimensional_parameters["timenorm"]
     end
 
@@ -89,17 +89,17 @@ function compare_collision_frequencies(input_file::String,
     println("classical heat chi_i0 with effective rho_i ", effective_classical_heat_chi_i0)
 
     # Get numerical diffusion parameters
-    if num_diss_params.r_dissipation_coefficient < 0.0
+    if num_diss_params.ion.r_dissipation_coefficient < 0.0
         D_r = 0.0
     else
-        D_r = Unitful.upreferred(num_diss_params.r_dissipation_coefficient *
+        D_r = Unitful.upreferred(num_diss_params.ion.r_dissipation_coefficient *
                                  dimensional_parameters["Lnorm"]^2 /
                                  dimensional_parameters["timenorm"])
     end
-    if num_diss_params.z_dissipation_coefficient < 0.0
+    if num_diss_params.ion.z_dissipation_coefficient < 0.0
         D_z = 0.0
     else
-        D_z = Unitful.upreferred(num_diss_params.z_dissipation_coefficient *
+        D_z = Unitful.upreferred(num_diss_params.ion.z_dissipation_coefficient *
                                  dimensional_parameters["Lnorm"]^2 /
                                  dimensional_parameters["timenorm"])
     end