Merge branch 'master' into fokker-planck-vperp-bc-experiment

.github/workflows/debug_checks.yml

@@ -23,25 +23,23 @@ jobs:
           version: '1.10'
           arch: x64
       - uses: julia-actions/cache@v1
-      - uses: julia-actions/julia-buildpkg@v1
-        with:
-          project: 'moment_kinetics/'
       - name: Debug test
         run: |
-          cd moment_kinetics
-
           # Hard code the debug level so that we can run without using the
           # `--compiled-modules=no` flag, which breaks Symbolics.jl at the
           # moment.
-          sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" src/debugging.jl
+          sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" moment_kinetics/src/debugging.jl
 
-          julia --project -e 'using MPIPreferences; MPIPreferences.use_system_binary(); using Pkg; Pkg.precompile()'
+          touch Project.toml
+          julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "PackageCompiler", "Symbolics"]); using MPIPreferences; MPIPreferences.use_system_binary()'
+          julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.develop(path="moment_kinetics/"); Pkg.precompile()'
+          julia --project -O3 --check-bounds=yes precompile.jl --debug 2
 
           # Need to use openmpi so that the following arguments work:
           # * `--mca rmaps_base_oversubscribe 1` allows oversubscription (more processes
           #   than physical cores).
           # * `--mca mpi_yield_when_idle 1` changes a setting to prevent excessively
           #   terrible performance when oversubscribing.
           ## Don't use --compiled-modules=no for now, as it currently breaks Symbolics.jl
-          #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no debug_test/sound_wave_tests.jl --debug 2
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes debug_test/runtests.jl --debug 2
+          #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no moment_kinetics/debug_test/sound_wave_tests.jl --debug 2
+          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project -Jmoment_kinetics.so -O3 --check-bounds=yes moment_kinetics/debug_test/runtests.jl --debug 2

.github/workflows/examples.yml

@@ -23,4 +23,8 @@ jobs:
           touch Project.toml
           julia -O3 --project -e 'import Pkg; Pkg.develop(path="moment_kinetics/"); Pkg.add("NCDatasets"); Pkg.precompile()'
           # Reduce nstep for each example to 10 to avoid the CI job taking too long
-          julia -O3 --project -e 'using moment_kinetics; for (root, dirs, files) in walkdir("examples") for file in files if endswith(file, ".toml") filename = joinpath(root, file); println(filename); input = moment_kinetics.moment_kinetics_input.read_input_file(filename); t_input = get(input, "timestepping", Dict{String,Any}()); t_input["nstep"] = 10; t_input["dt"] = 1.0e-10; pop!(input, "z_nelement_local", ""); pop!(input, "r_nelement_local", ""); run_moment_kinetics(input) end end end'
+          # Note we skip the example `if (occursin("ARK", get(t_input, "type", "") && Sys.isapple())`
+          # because the way we use MINPACK.jl (needed for nonlinear solvers
+          # used for implicit parts of timestep) doesn't currently work on
+          # macOS.
+          julia -O3 --project -e 'using moment_kinetics; for (root, dirs, files) in walkdir("examples") for file in files if endswith(file, ".toml") filename = joinpath(root, file); println(filename); input = moment_kinetics.moment_kinetics_input.read_input_file(filename); t_input = get(input, "timestepping", Dict{String,Any}()); if (occursin("ARK", get(t_input, "type", "")) && Sys.isapple()) continue end; t_input["nstep"] = 10; t_input["dt"] = 1.0e-12; input["timestepping"] = t_input; pop!(input, "z_nelement_local", ""); pop!(input, "r_nelement_local", ""); electron_t_input = get(input, "electron_timestepping", Dict{String,Any}()); electron_t_input["initialization_residual_value"] = 1.0e8; electron_t_input["converged_residual_value"] = 1.0e8; input["electron_timestepping"] = electron_t_input; nl_solver_input = get(input, "nonlinear_solver", Dict{String,Any}()); nl_solver_input["rtol"] = 1.0e6; nl_solver_input["atol"] = 1.0e6; input["nonlinear_solver"] = nl_solver_input; run_moment_kinetics(input) end end end'

.github/workflows/parallel_test.yml

@@ -10,7 +10,7 @@ permissions:
 jobs:
   test-ubuntu:
     runs-on: ubuntu-latest
-    timeout-minutes: 120
+    timeout-minutes: 150
 
     steps:
       - uses: actions/checkout@v4

examples/fokker-planck-1D2V/fokker-planck-1D2V-even_nz-shorttest-nstep200.toml

@@ -1,47 +1,11 @@
-#use_manufactured_solns_for_init = true
-#use_manufactured_solns_for_advance = false
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
-#force_Er_zero_at_wall = false #true
-#epsilon_offset = 0.1
-#use_vpabar_in_mms_dfni = true
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 1.0
 constant_ionization_rate = true
 
-nstep = 200
-dt = 1.0e-4
-nwrite = 1000
-nwrite_dfns = 1000
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 5
 z_nelement = 16
 #z_nelement_local = 2
@@ -67,31 +31,34 @@ vperp_L = 3.0
 #vperp_discretization = "chebyshev_pseudospectral"
 vperp_discretization = "gausslegendre_pseudospectral"
 
-#vz_ngrid = 17
-#vz_nelement = 4
-#vz_L = 12.0
-#vz_bc = "periodic"
-#vz_discretization = "chebyshev_pseudospectral"
-
-#vr_ngrid = 17
-#vr_nelement = 4
-#vr_L = 12.0
-#vr_bc = "periodic"
-#vr_discretization = "chebyshev_pseudospectral"
+[composition]
+n_ion_species = 1
+n_neutral_species = 0
+electron_physics = "boltzmann_electron_response"
+#electron_physics = "boltzmann_electron_response_with_simple_sheath"
+T_e = 1.0
+T_wall = 1.0
 
-#vzeta_ngrid = 17
-#vzeta_nelement = 4
-#vzeta_L = 12.0
-#vzeta_bc = "periodic"
-#vzeta_discretization = "chebyshev_pseudospectral"
+[ion_species_1]
+initial_density = 0.5
+initial_temperature = 1.0
 
-#[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.0
-#vperp_dissipation_coefficient = 0.0
-#z_dissipation_coefficient = 0.1
-#r_dissipation_coefficient = 0.0
+[z_IC_ion_species_1]
+initialization_option = "sinusoid"
+density_amplitude = 0.001
+density_phase = 0.0
+upar_amplitude = 0.0
+upar_phase = 0.0
+temperature_amplitude = 0.0
+temperature_phase = 0.0
 
 [fokker_planck_collisions]
 use_fokker_planck = true
 nuii = 1.0
 frequency_option = "manual"
+
+[timestepping]
+nstep = 50
+dt = 1.0e-4
+nwrite = 10
+nwrite_dfns = 10

examples/fokker-planck/fokker-planck-relaxation-report-resolutions.toml

@@ -1,31 +1,8 @@
 # cheap input file for a 0D2V relaxation to a collisional Maxwellian distribution with self-ion collisions.
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
 constant_ionization_rate = false
@@ -53,6 +30,27 @@ vperp_bc = "zero"
 # Fokker-Planck operator requires the "gausslegendre_pseudospectral
 # options for the vpa and vperp grids
 
+[composition]
+n_ion_species = 1
+n_neutral_species = 0
+electron_physics = "boltzmann_electron_response"
+T_e = 1.0
+T_wall = 1.0
+
+[ion_species_1]
+initial_density = 0.5
+initial_temperature = 1.0
+
+[z_IC_ion_species_1]
+initialization_option = "sinusoid"
+density_amplitude = 0.001
+density_phase = 0.0
+upar_amplitude = 0.0
+upar_phase = 0.0
+temperature_amplitude = 0.0
+temperature_phase = 0.0
+
+
 [fokker_planck_collisions]
 use_fokker_planck = true
 # nuii sets the normalised input C[F,F] Fokker-Planck collision frequency

examples/fokker-planck/fokker-planck-relaxation-slowing-down-alphas.toml

@@ -1,28 +1,9 @@
 # cheap input file for a 0D2V relaxation to a collisional Maxwellian distribution with self-ion collisions and collisions with fixed Maxwellian background of cold ions and electrons.
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 1.0
-initial_temperature1 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.0
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-vpa_IC_option1 = "isotropic-beam"
-vpa_IC_v01 = 1.0
-vpa_IC_vth01 = 0.1
-#vpa_IC_option1 = "directed-beam"
-#vpa_IC_vpa01 = -1.5
-#vpa_IC_vperp01 = 0.0
+
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
 constant_ionization_rate = false
@@ -90,3 +71,31 @@ nstep = 50000
 dt = 2.5e-4
 nwrite = 100
 nwrite_dfns = 100
+
+[composition]
+n_ion_species = 1
+n_neutral_species = 0
+electron_physics = "boltzmann_electron_response"
+T_e = 1.0
+T_wall = 1.0
+
+[ion_species_1]
+initial_density = 0.5
+initial_temperature = 1.0
+
+[z_IC_ion_species_1]
+initialization_option = "sinusoid"
+density_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 0.0
+upar_phase = 0.0
+temperature_amplitude = 0.0
+temperature_phase = 0.0
+
+[vpa_IC_ion_species_1]
+initialization_option = "isotropic-beam"
+#initialization_option = "directed-beam"
+v0 = 1.0
+vth0 = 0.1
+#vpa0 = -1.5
+#vperp0 = 0.0