Inputs refactor and extra checking

.github/workflows/test_scripts.yml

@@ -0,0 +1,25 @@
+# Based on example from https://github.com/julia-actions/julia-runtest
+name: Check test_scripts
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  examples:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+      fail-fast: false
+    timeout-minutes: 35
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.10'
+      - uses: julia-actions/cache@v1
+      - name: Test test_scripts
+        run: |
+          touch Project.toml
+          julia -O3 --project -e 'import Pkg; Pkg.develop(path="moment_kinetics/"); Pkg.add(["FastGaussQuadrature", "LaTeXStrings", "LegendrePolynomials", "Measures", "MPI", "Plots", "SpecialFunctions"]); Pkg.precompile()'
+          julia -O3 --project -e 'include("test_scripts/2D_FEM_assembly_test.jl"); run_assembly_test(); include("test_scripts/chebyshev_radau_test.jl"); chebyshevradau_test(); include("test_scripts/fkpl_direct_integration_test.jl"); test_rosenbluth_potentials_direct_integration(); include("test_scripts/GaussLobattoLegendre_test.jl"); gausslegendre_test(); include("test_scripts/gyroaverage_test.jl"); gyroaverage_test()'

docs/src/zz_electron_fluid_equations.md

@@ -0,0 +1,6 @@
+`electron_fluid_equations`
+==========================
+
+```@autodocs
+Modules = [moment_kinetics.electron_fluid_equations]
+```

docs/src/zz_electron_kinetic_equation.md

@@ -0,0 +1,6 @@
+`electron_kinetic_equation`
+===========================
+
+```@autodocs
+Modules = [moment_kinetics.electron_kinetic_equation]
+```

docs/src/zz_electron_vpa_advection.md

@@ -0,0 +1,6 @@
+`electron_vpa_advection`
+========================
+
+```@autodocs
+Modules = [moment_kinetics.electron_vpa_advection]
+```

docs/src/zz_electron_z_advection.md

@@ -0,0 +1,6 @@
+`electron_z_advection`
+======================
+
+```@autodocs
+Modules = [moment_kinetics.electron_z_advection]
+```

docs/src/zz_maxwell_diffusion.md

@@ -0,0 +1,6 @@
+`maxwell_diffusion`
+===================
+
+```@autodocs
+Modules = [moment_kinetics.maxwell_diffusion]
+```

docs/src/zz_nonlinear_solvers.md

@@ -0,0 +1,6 @@
+`nonlinear_solvers`
+===================
+
+```@autodocs
+Modules = [moment_kinetics.nonlinear_solvers]
+```

docs/src/zz_species_input.md

@@ -0,0 +1,6 @@
+`species_input`
+===============
+
+```@autodocs
+Modules = [moment_kinetics.species_input]
+```

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

@@ -1,35 +1,53 @@
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-charge_exchange_frequency = 0.0
-ionization_frequency = 1.0
-constant_ionization_rate = true
+[ion_source]
+z_profile = "constant"
+source_strength = 1.0
+source_T = 0.25
 
-z_ngrid = 5
-z_nelement = 16
-#z_nelement_local = 2
-z_bc = "wall"
-z_element_spacing_option = "sqrt"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 15
-vpa_L = 6.0
-vpa_bc = "zero"
-#vpa_discretization = "chebyshev_pseudospectral"
-vpa_discretization = "gausslegendre_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 4
-vperp_L = 3.0
-#vperp_bc = "periodic"
-#vperp_discretization = "finite_difference"
-#vperp_discretization = "chebyshev_pseudospectral"
-vperp_discretization = "gausslegendre_pseudospectral"
+[evolve_moments]
+density = false
+parallel_flow = false
+parallel_pressure = false
+moments_conservation = false
+
+[z]
+ngrid = 5
+nelement = 16
+#nelement_local = 2
+bc = "wall"
+element_spacing_option = "sqrt"
+discretization = "chebyshev_pseudospectral"
+
+[r]
+ngrid = 1
+nelement = 1
+nelement_local = 1
+bc = "periodic"
+discretization = "chebyshev_pseudospectral"
+
+[vpa]
+ngrid = 6
+nelement = 15
+L = 6.0
+bc = "zero"
+#discretization = "chebyshev_pseudospectral"
+discretization = "gausslegendre_pseudospectral"
+
+[vz]
+ngrid = 6
+nelement = 15
+L = 6.0
+bc = "zero"
+#discretization = "chebyshev_pseudospectral"
+discretization = "gausslegendre_pseudospectral"
+
+[vperp]
+ngrid = 5
+nelement = 4
+L = 3.0
+#bc = "periodic"
+#discretization = "finite_difference"
+#discretization = "chebyshev_pseudospectral"
+discretization = "gausslegendre_pseudospectral"
 
 [composition]
 n_ion_species = 1

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

@@ -1,32 +1,41 @@
 # cheap input file for a 0D2V relaxation to a collisional Maxwellian distribution with self-ion collisions.
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
+[reactions]
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-constant_ionization_rate = false
 
-z_ngrid = 1
-z_nelement = 1
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 8
-vpa_L = 6.0
-vpa_bc = "zero"
-vpa_discretization = "gausslegendre_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 4
-vperp_L = 3.0
-vperp_discretization = "gausslegendre_pseudospectral"
-vperp_bc = "zero"
+[evolve_moments]
+density = false
+parallel_flow = false
+parallel_pressure = false
+moments_conservation = false
+
+[z]
+ngrid = 1
+nelement = 1
+nelement_local = 1
+bc = "wall"
+discretization = "chebyshev_pseudospectral"
+
+[r]
+ngrid = 1
+nelement = 1
+nelement_local = 1
+bc = "periodic"
+discretization = "chebyshev_pseudospectral"
+
+[vpa]
+ngrid = 5
+nelement = 8
+L = 6.0
+bc = "zero"
+discretization = "gausslegendre_pseudospectral"
+
+[vperp]
+ngrid = 5
+nelement = 4
+L = 3.0
+discretization = "gausslegendre_pseudospectral"
+bc = "zero"
 # Fokker-Planck operator requires the "gausslegendre_pseudospectral
 # options for the vpa and vperp grids
 

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

@@ -1,33 +1,41 @@
 # 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.
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-
+[reactions]
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-constant_ionization_rate = false
 
-z_ngrid = 1
-z_nelement = 1
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 32
-vpa_L = 3.0
-vpa_bc = "zero"
-vpa_discretization = "gausslegendre_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 16
-vperp_L = 1.5
-vperp_discretization = "gausslegendre_pseudospectral"
-vperp_bc = "zero"
+[evolve_moments]
+density = false
+parallel_flow = false
+parallel_pressure = false
+moments_conservation = false
+
+[z]
+ngrid = 1
+nelement = 1
+nelement_local = 1
+bc = "wall"
+discretization = "chebyshev_pseudospectral"
+
+[r]
+ngrid = 1
+nelement = 1
+nelement_local = 1
+bc = "periodic"
+discretization = "chebyshev_pseudospectral"
+
+[vpa]
+ngrid = 5
+nelement = 32
+L = 3.0
+bc = "zero"
+discretization = "gausslegendre_pseudospectral"
+
+[vperp]
+ngrid = 5
+nelement = 16
+L = 1.5
+discretization = "gausslegendre_pseudospectral"
+bc = "zero"
 # Fokker-Planck operator requires the "gausslegendre_pseudospectral
 # options for the vpa and vperp grids
 

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

@@ -1,30 +1,40 @@
 # cheap input file for a 0D2V relaxation to a collisional Maxwellian distribution with self-ion collisions.
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
+[reactions]
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-constant_ionization_rate = false
-z_ngrid = 1
-z_nelement = 1
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 32
-vpa_L = 6.0
-vpa_bc = "zero"
-vpa_discretization = "gausslegendre_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 16
-vperp_L = 3.0
-vperp_discretization = "gausslegendre_pseudospectral"
+
+[evolve_moments]
+density = false
+parallel_flow = false
+parallel_pressure = false
+moments_conservation = false
+
+[z]
+ngrid = 1
+nelement = 1
+nelement_local = 1
+bc = "wall"
+discretization = "chebyshev_pseudospectral"
+
+[r]
+ngrid = 1
+nelement = 1
+nelement_local = 1
+bc = "periodic"
+discretization = "chebyshev_pseudospectral"
+
+[vpa]
+ngrid = 5
+nelement = 32
+L = 6.0
+bc = "zero"
+discretization = "gausslegendre_pseudospectral"
+
+[vperp]
+ngrid = 5
+nelement = 16
+L = 3.0
+discretization = "gausslegendre_pseudospectral"
 # Fokker-Planck operator requires the "gausslegendre_pseudospectral
 # options for the vpa and vperp grids