Merge pull request #237 from mabarnes/electrons

Kinetic electrons

.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'

examples/kinetic-electrons/periodic_split3_boltzmann.toml

@@ -0,0 +1,91 @@
+#runtime_plots = true
+n_ion_species = 1
+n_neutral_species = 1
+electron_physics = "boltzmann_electron_response"
+evolve_moments_density = true
+evolve_moments_parallel_flow = true
+evolve_moments_parallel_pressure = true
+evolve_moments_conservation = true
+recycling_fraction = 0.5
+T_e = 1.0
+T_wall = 0.1
+initial_density1 = 1.0
+initial_temperature1 = 1.0
+z_IC_option1 = "sinusoid"
+z_IC_density_amplitude1 = 0.1
+z_IC_density_phase1 = 0.0
+z_IC_upar_amplitude1 = 1.0
+z_IC_upar_phase1 = 0.0
+z_IC_temperature_amplitude1 = 0.1
+z_IC_temperature_phase1 = 1.0
+vpa_IC_option1 = "gaussian"
+vpa_IC_density_amplitude1 = 1.0
+vpa_IC_density_phase1 = 0.0
+vpa_IC_upar_amplitude1 = 0.0
+vpa_IC_upar_phase1 = 0.0
+vpa_IC_temperature_amplitude1 = 0.0
+vpa_IC_temperature_phase1 = 0.0
+initial_density2 = 1.0
+initial_temperature2 = 1.0
+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
+vpa_IC_option2 = "gaussian"
+vpa_IC_density_amplitude2 = 1.0
+vpa_IC_density_phase2 = 0.0
+vpa_IC_upar_amplitude2 = 0.0
+vpa_IC_upar_phase2 = 0.0
+vpa_IC_temperature_amplitude2 = 0.0
+vpa_IC_temperature_phase2 = 0.0
+charge_exchange_frequency = 0.75
+ionization_frequency = 0.0
+constant_ionization_rate = false
+nu_ei = 1000.0
+r_ngrid = 1
+r_nelement = 1
+z_ngrid = 17
+z_nelement = 16
+#z_nelement_local = 16
+z_bc = "periodic"
+z_discretization = "chebyshev_pseudospectral"
+vpa_ngrid = 6
+vpa_nelement = 31
+vpa_L = 12.0
+vpa_bc = "zero"
+vpa_discretization = "chebyshev_pseudospectral"
+vz_ngrid = 6
+vz_nelement = 31
+vz_L = 12.0
+vz_bc = "zero"
+vz_discretization = "chebyshev_pseudospectral"
+
+[timestepping]
+type = "Fekete4(3)"
+nstep = 1000000
+dt = 1.0e-6
+minimum_dt = 1.0e-7
+rtol = 1.0e-7
+nwrite = 10000
+nwrite_dfns = 100000
+steady_state_residual = true
+converged_residual_value = 1.0e-3
+
+[nonlinear_solver]
+nonlinear_max_iterations = 100
+#rtol = 1.0e-9
+#atol = 1.0e-12
+
+[ion_numerical_dissipation]
+vpa_dissipation_coefficient = 1.0e0
+force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+vz_dissipation_coefficient = 1.0e-1
+force_minimum_pdf_value = 0.0
+
+[krook_collisions]
+use_krook = true

examples/kinetic-electrons/periodic_split3_braginskii-IMEX.toml

@@ -0,0 +1,110 @@
+#runtime_plots = true
+n_ion_species = 1
+n_neutral_species = 1
+electron_physics = "braginskii_fluid"
+evolve_moments_density = true
+evolve_moments_parallel_flow = true
+evolve_moments_parallel_pressure = true
+evolve_moments_conservation = true
+recycling_fraction = 0.5
+T_e = 1.0
+T_wall = 0.1
+initial_density1 = 1.0
+initial_temperature1 = 1.0
+z_IC_option1 = "sinusoid"
+z_IC_density_amplitude1 = 0.1
+z_IC_density_phase1 = 0.0
+z_IC_upar_amplitude1 = 1.0
+z_IC_upar_phase1 = 0.0
+z_IC_temperature_amplitude1 = 0.1
+z_IC_temperature_phase1 = 1.0
+vpa_IC_option1 = "gaussian"
+vpa_IC_density_amplitude1 = 1.0
+vpa_IC_density_phase1 = 0.0
+vpa_IC_upar_amplitude1 = 0.0
+vpa_IC_upar_phase1 = 0.0
+vpa_IC_temperature_amplitude1 = 0.0
+vpa_IC_temperature_phase1 = 0.0
+initial_density2 = 1.0
+initial_temperature2 = 1.0
+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
+vpa_IC_option2 = "gaussian"
+vpa_IC_density_amplitude2 = 1.0
+vpa_IC_density_phase2 = 0.0
+vpa_IC_upar_amplitude2 = 0.0
+vpa_IC_upar_phase2 = 0.0
+vpa_IC_temperature_amplitude2 = 0.0
+vpa_IC_temperature_phase2 = 0.0
+charge_exchange_frequency = 0.75
+ionization_frequency = 0.0
+constant_ionization_rate = false
+nu_ei = 1000.0
+r_ngrid = 1
+r_nelement = 1
+z_ngrid = 17
+z_nelement = 16
+#z_nelement_local = 16
+z_bc = "periodic"
+z_discretization = "chebyshev_pseudospectral"
+vpa_ngrid = 6
+vpa_nelement = 31
+vpa_L = 12.0
+vpa_bc = "zero"
+vpa_discretization = "chebyshev_pseudospectral"
+vz_ngrid = 6
+vz_nelement = 31
+vz_L = 12.0
+vz_bc = "zero"
+vz_discretization = "chebyshev_pseudospectral"
+
+[timestepping]
+type = "KennedyCarpenterARK324"
+implicit_ion_advance = false
+implicit_vpa_advection = false
+implicit_braginskii_conduction = true
+nstep = 1000000
+dt = 1.0e-6
+minimum_dt = 1.0e-7
+rtol = 1.0e-7
+nwrite = 10000
+nwrite_dfns = 100000
+steady_state_residual = true
+converged_residual_value = 1.0e-3
+#[timestepping]
+#type = "KennedyCarpenterARK324"
+#implicit_ion_advance = false
+#implicit_vpa_advection = false
+#implicit_braginskii_conduction = true
+#nstep = 1000000
+#dt = 1.0e-6
+#minimum_dt = 1.0e-7
+#rtol = 1.0e-7
+#nwrite = 100
+#nwrite_dfns = 100
+#steady_state_residual = true
+#converged_residual_value = 1.0e-3
+#write_after_fixed_step_count = true
+#write_error_diagnostics = true
+#write_steady_state_diagnostics = true
+
+[nonlinear_solver]
+nonlinear_max_iterations = 100
+#rtol = 1.0e-9
+#atol = 1.0e-12
+
+[ion_numerical_dissipation]
+vpa_dissipation_coefficient = 1.0e0
+force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+vz_dissipation_coefficient = 1.0e-1
+force_minimum_pdf_value = 0.0
+
+[krook_collisions]
+use_krook = true

examples/kinetic-electrons/periodic_split3_braginskii.toml

@@ -0,0 +1,104 @@
+#runtime_plots = true
+n_ion_species = 1
+n_neutral_species = 1
+electron_physics = "braginskii_fluid"
+evolve_moments_density = true
+evolve_moments_parallel_flow = true
+evolve_moments_parallel_pressure = true
+evolve_moments_conservation = true
+recycling_fraction = 0.5
+T_e = 1.0
+T_wall = 0.1
+initial_density1 = 1.0
+initial_temperature1 = 1.0
+z_IC_option1 = "sinusoid"
+z_IC_density_amplitude1 = 0.1
+z_IC_density_phase1 = 0.0
+z_IC_upar_amplitude1 = 1.0
+z_IC_upar_phase1 = 0.0
+z_IC_temperature_amplitude1 = 0.1
+z_IC_temperature_phase1 = 1.0
+vpa_IC_option1 = "gaussian"
+vpa_IC_density_amplitude1 = 1.0
+vpa_IC_density_phase1 = 0.0
+vpa_IC_upar_amplitude1 = 0.0
+vpa_IC_upar_phase1 = 0.0
+vpa_IC_temperature_amplitude1 = 0.0
+vpa_IC_temperature_phase1 = 0.0
+initial_density2 = 1.0
+initial_temperature2 = 1.0
+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
+vpa_IC_option2 = "gaussian"
+vpa_IC_density_amplitude2 = 1.0
+vpa_IC_density_phase2 = 0.0
+vpa_IC_upar_amplitude2 = 0.0
+vpa_IC_upar_phase2 = 0.0
+vpa_IC_temperature_amplitude2 = 0.0
+vpa_IC_temperature_phase2 = 0.0
+charge_exchange_frequency = 0.75
+ionization_frequency = 0.0
+constant_ionization_rate = false
+nu_ei = 1000.0
+r_ngrid = 1
+r_nelement = 1
+z_ngrid = 17
+z_nelement = 16
+#z_nelement_local = 16
+z_bc = "periodic"
+z_discretization = "chebyshev_pseudospectral"
+vpa_ngrid = 6
+vpa_nelement = 31
+vpa_L = 12.0
+vpa_bc = "zero"
+vpa_discretization = "chebyshev_pseudospectral"
+vz_ngrid = 6
+vz_nelement = 31
+vz_L = 12.0
+vz_bc = "zero"
+vz_discretization = "chebyshev_pseudospectral"
+
+[timestepping]
+type = "Fekete4(3)"
+nstep = 1000000
+dt = 1.0e-6
+minimum_dt = 1.0e-9
+rtol = 1.0e-7
+nwrite = 10000
+nwrite_dfns = 100000
+steady_state_residual = true
+converged_residual_value = 1.0e-3
+#[timestepping]
+#type = "Fekete4(3)"
+#nstep = 1000000
+#dt = 1.0e-6
+#minimum_dt = 1.0e-9
+#rtol = 1.0e-7
+#nwrite = 1000
+#nwrite_dfns = 1000
+#steady_state_residual = true
+#converged_residual_value = 1.0e-3
+#write_after_fixed_step_count = true
+#write_error_diagnostics = true
+#write_steady_state_diagnostics = true
+
+[nonlinear_solver]
+nonlinear_max_iterations = 100
+#rtol = 1.0e-9
+#atol = 1.0e-12
+
+[ion_numerical_dissipation]
+vpa_dissipation_coefficient = 1.0e0
+force_minimum_pdf_value = 0.0
+
+[neutral_numerical_dissipation]
+vz_dissipation_coefficient = 1.0e-1
+force_minimum_pdf_value = 0.0
+
+[krook_collisions]
+use_krook = true