Merge branch 'master' into cross-species-collisions

.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

.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: |

.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:

.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:

.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:

.gitignore

@@ -26,3 +26,4 @@ makie_postproc.so
 plots_postproc.so
 precompile-temp
 post_processing_input.toml
+.DS_Store

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}
 ```
 

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}} \\

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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"

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"

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"

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"