Merge branch 'master' into ion_flags

.github/workflows/debug_checks.yml

@@ -22,7 +22,7 @@ jobs:
         with:
           version: '1.10'
           arch: x64
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Debug test
         run: |
           # Hard code the debug level so that we can run without using the
@@ -31,7 +31,8 @@ jobs:
           sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" moment_kinetics/src/debugging.jl
 
           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.add(["MPI", "MPIPreferences", "PackageCompiler", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
+          julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
           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
 
@@ -42,4 +43,4 @@ jobs:
           #   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 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
+          ./mpiexecjl -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/documentation.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Install dependencies
         run: |
           # Version 3.9.0 of matplotlib causes an error with PyPlot.jl, so pin

.github/workflows/examples.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Test examples
         run: |
           touch Project.toml

.github/workflows/longtest.yml

@@ -22,7 +22,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         with:
           project: 'moment_kinetics/'

.github/workflows/parallel_test.yml

@@ -21,20 +21,21 @@ jobs:
         with:
           version: '1.10'
           arch: x64
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - run: |
           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(["NCDatasets", "Random", "SpecialFunctions", "Test"]); Pkg.develop(path="moment_kinetics/")'
+          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
+          julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
+          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["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:
           # * `--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.
-          mpiexec -np 3 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1 --force-optional-dependencies
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1 --force-optional-dependencies
-          mpiexec -np 2 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1 --long --force-optional-dependencies
+          ./mpiexecjl -np 3 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1
+          ./mpiexecjl -np 4 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1
+          ./mpiexecjl -np 2 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1 --long
           # Note: MPI.jl's default implementation is mpich, which has a similar option
           # `--with-device=ch3:sock`, but that needs to be set when compiling mpich.
         shell: bash
@@ -52,19 +53,19 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - run: |
-          export MPILIBPATH=$(find /opt/homebrew/Cellar/open-mpi/ -name libmpi.dylib)
           touch Project.toml
-          julia --project -O3 --check-bounds=no -e "import Pkg; Pkg.add([\"MPI\", \"MPIPreferences\"]); using MPIPreferences; MPIPreferences.use_system_binary(library_names=\"$MPILIBPATH\")"
-          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.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
+          julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
+          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["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:
           # * `--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.
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1 --force-optional-dependencies
+          ./mpiexecjl -np 4 --mca rmaps_base_oversubscribe 1 julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --debug 1
           # Note: MPI.jl's default implementation is mpich, which has a similar option
           # `--with-device=ch3:sock`, but that needs to be set when compiling mpich.
         shell: bash

.github/workflows/test.yml

@@ -21,7 +21,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         with:
           project: 'moment_kinetics/'

.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@v2
+      - 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/make.jl

@@ -9,10 +9,19 @@ Pkg.instantiate()
 using Documenter
 using moment_kinetics, makie_post_processing, plots_post_processing
 
+if get(ENV, "CI", nothing) == "true"
+    # On the CI, run in strict mode to turn warnings into errors, so that we don't deploy
+    # documentation with formatting bugs.
+    strict = true
+else
+    strict = false
+end
+
 makedocs(
     sitename = "moment_kinetics",
     format = Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true"),
-    modules = [moment_kinetics, makie_post_processing, plots_post_processing]
+    modules = [moment_kinetics, makie_post_processing, plots_post_processing],
+    strict = strict,
 )
 
 if get(ENV, "CI", nothing) == "true"

docs/src/developing.md

@@ -28,6 +28,20 @@ julia> run_moment_kinetics("input.toml")
 It might be convenient to add `using Revise` to your `startup.jl` file (`~/julia/config/startup.jl`) so it's always loaded.
 
 
+## Input options and defaults
+
+The input is read from a `.toml` file. It is also written to the output HDF5
+(or NetCDF) file, after all defaults are applied, both as a TOML-formatted
+String and as a tree of HDF5 variables.
+
+!!! warning
+    Neither TOML nor HDF5 have a 'null' type, so there is no convenient way to
+    store Julia's `nothing` when writing to TOML or HDF5.  Therefore `nothing`
+    should not be used as a default for any input option. If the code should
+    use `nothing` as a default for some setting, that is fine, but must be done
+    after the input is read, and not stored in the `input_dict`.
+
+
 ## Array types
 
 Most arrays in `moment_kinetics` are declared using a custom array type

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_1]
+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