Merge branch 'master' into final_transfer_version

.github/workflows/longtest.yml

@@ -15,7 +15,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, macOS-latest]
       fail-fast: false
-    timeout-minutes: 90
+    timeout-minutes: 120
 
     steps:
       - uses: actions/checkout@v4

examples/kinetic-electrons/wall-bc_recyclefraction0.5_split3_kinetic-coarse_tails-KennedyCarpenterARK324-time-evolving-ge-wall-Jac.toml

@@ -0,0 +1,165 @@
+[r]
+ngrid = 1
+nelement = 1
+
+[evolve_moments]
+parallel_pressure = true
+density = true
+moments_conservation = true
+parallel_flow = true
+
+[reactions]
+electron_ionization_frequency = 0.0
+ionization_frequency = 0.5
+charge_exchange_frequency = 0.75
+
+[vz]
+ngrid = 6
+discretization = "gausslegendre_pseudospectral"
+nelement = 31
+L = 36.0
+element_spacing_option = "coarse_tails"
+bc = "zero"
+
+[ion_species_1]
+initial_temperature = 0.1
+initial_density = 1.0
+
+[krook_collisions]
+use_krook = true
+
+[vpa]
+ngrid = 6
+discretization = "gausslegendre_pseudospectral"
+nelement = 31
+L = 30.0
+element_spacing_option = "coarse_tails"
+bc = "zero"
+
+[z]
+ngrid = 5
+discretization = "gausslegendre_pseudospectral"
+nelement = 32
+nelement_local = 4
+bc = "wall"
+element_spacing_option = "sqrt"
+
+[vpa_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 1.0
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 0.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+[z_IC_neutral_species_1]
+initialization_option = "gaussian"
+temperature_amplitude = 0.0
+density_amplitude = 0.001
+density_phase = 0.0
+upar_amplitude = -1.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+[composition]
+T_wall = 0.1
+T_e = 0.2
+electron_physics = "kinetic_electrons"
+recycling_fraction = 0.5
+n_ion_species = 1
+n_neutral_species = 1
+
+[vz_IC_neutral_species_1]
+initialization_option = "gaussian"
+density_amplitude = 1.0
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 0.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+[z_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 0.001
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 1.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+[neutral_species_1]
+initial_temperature = 1.0
+initial_density = 1.0
+
+[timestepping]
+type = "KennedyCarpenterARK324"
+implicit_electron_advance = false
+implicit_electron_time_evolving=true
+implicit_electron_ppar = false
+implicit_ion_advance = false
+implicit_vpa_advection = false
+nstep = 1000000
+dt = 1.0e-5
+nwrite = 10000
+nwrite_dfns = 10000
+steady_state_residual = true
+converged_residual_value = 1.0e-3
+
+#write_after_fixed_step_count = true
+#nstep = 1
+#nwrite = 1
+#nwrite_dfns = 1
+
+[electron_timestepping]
+nstep = 5000000
+#nstep = 1
+dt = 1.0e-5
+maximum_dt = 2.0e-5
+nwrite = 10000
+nwrite_dfns = 100000
+#type = "SSPRK4"
+type = "Fekete4(3)"
+rtol = 1.0e-3
+atol = 1.0e-14
+minimum_dt = 1.0e-9
+decrease_dt_iteration_threshold = 50
+increase_dt_iteration_threshold = 20
+cap_factor_ion_dt = 10.0
+initialization_residual_value = 2.5
+converged_residual_value = 1.0e-2
+include_wall_bc_in_preconditioner = true
+
+#debug_io = 1
+
+[nonlinear_solver]
+nonlinear_max_iterations = 100
+rtol = 1.0e-6 #1.0e-8
+atol = 1.0e-14 #1.0e-16
+linear_restart = 5
+preconditioner_update_interval = 25
+total_its_soft_limit = 30
+adi_precon_iterations = 3
+
+[ion_source_1]
+active = true
+z_profile = "gaussian"
+z_width = 0.125
+source_strength = 2.0
+source_T = 2.0
+
+[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
+
+[electron_numerical_dissipation]
+vpa_dissipation_coefficient = 2.0
+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

machines/generic-batch-template/compile_dependencies.sh

@@ -77,10 +77,10 @@ if [[ $BUILDHDF5 == "y" && -d hdf5-build ]]; then
 fi
 
 if [[ $BUILDHDF5 == "y" ]]; then
-  HDF5=hdf5-1.14.5
+  HDF5=hdf5-1.14.3
   # Download and extract the source
-  wget -O ${HDF5}.tar.gz https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz
-  tar xjf ${HDF5}.tar.gz
+  wget -O ${HDF5}.tar.bz2 https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.3/src/hdf5-1.14.3.tar.bz2
+  tar xjf ${HDF5}.tar.bz2
 
   cd $HDF5
 

machines/generic-pc/compile_dependencies.sh

@@ -77,10 +77,10 @@ else
 fi
 
 if [[ $BUILDHDF5 == "y" ]]; then
-  HDF5=hdf5-1.14.5
+  HDF5=hdf5-1.14.3
   # Download and extract the source
-  wget -O ${HDF5}.tar.gz https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz
-  tar xzf ${HDF5}.tar.gz
+  wget -O ${HDF5}.tar.bz2 https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.3/src/hdf5-1.14.3.tar.bz2
+  tar xjf ${HDF5}.tar.bz2
 
   cd $HDF5
 

machines/marconi/compile_dependencies.sh

@@ -30,10 +30,10 @@ if [ -d hdf5-build ]; then
 fi
 
 if [ $BUILDHDF5 -eq 0 ]; then
-  HDF5=hdf5-1.14.5
+  HDF5=hdf5-1.14.3
   # Download and extract the source
-  wget -O ${HDF5}.tar.gz https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz
-  tar xjf ${HDF5}.tar.gz
+  wget -O ${HDF5}.tar.bz2 https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.3/src/hdf5-1.14.3.tar.bz2
+  tar xjf ${HDF5}.tar.bz2
 
   cd $HDF5
 

machines/shared/add_dependencies_to_project.jl

@@ -186,8 +186,7 @@ if mk_preferences["use_system_mpi"] == "y"
             local_hdf5_install_dir = realpath(local_hdf5_install_dir)
             # We have downloaded and compiled HDF5, so link that
             hdf5_dir = local_hdf5_install_dir
-            hdf5_lib = joinpath(local_hdf5_install_dir, "libhdf5.so")
-            hdf5_lib_hl = joinpath(local_hdf5_install_dir, "libhdf5_hl.so")
+            hdf5_lib, hdf5_lib_hl = get_hdf5_lib_names(local_hdf5_install_dir)
         elseif !prompt_for_lib_paths
             hdf5_dir = mk_preferences["hdf5_dir"]
             if hdf5_dir != "default"
@@ -207,9 +206,10 @@ if mk_preferences["use_system_mpi"] == "y"
                 global hdf5_dir, hdf5_lib, hdf5_lib_hl
                 hdf5_dir = get_input_with_path_completion(
                     "\nAn HDF5 installation compiled with your system MPI is required to use\n"
-                    * "parallel I/O. Enter the directory where the libhdf5.so and libhdf5_hl.so are\n"
-                    * "located (enter 'default' to use the Julia-provided HDF5, which does not\n"
-                    * "support parallel I/O): [$default_hdf5_dir]")
+                    * "parallel I/O. Enter the directory where the libhdf5.so and\n"
+                    * "libhdf5_hl.so (or libhdf5.dylib and libhdf5_hl.dylib on macOS)\n"
+                    * "are located (enter 'default' to use the Julia-provided HDF5, which\n"
+                    * "is not compatible with using the system MPI): [$default_hdf5_dir]")
 
                 if hdf5_dir == ""
                     hdf5_dir = default_hdf5_dir
@@ -222,8 +222,7 @@ if mk_preferences["use_system_mpi"] == "y"
                 if isdir(hdf5_dir)
                     hdf5_dir = realpath(hdf5_dir)
                 end
-                hdf5_lib = joinpath(hdf5_dir, "libhdf5.so")
-                hdf5_lib_hl = joinpath(hdf5_dir, "libhdf5_hl.so")
+                hdf5_lib, hdf5_lib_hl = get_hdf5_lib_names(hdf5_dir)
                 if isfile(hdf5_lib) && isfile(hdf5_lib_hl)
                     break
                 else