Merge pull request #306 from mabarnes/final_transfer_version

Final transfer version

.github/workflows/documentation.yml

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

docs/src/zz_collision_frequencies.md

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

examples/gk-ions/2D-periodic-gk.toml

@@ -45,7 +45,7 @@ discretization = "chebyshev_pseudospectral"
 n_ion_species = 1
 n_neutral_species = 0
 electron_physics = "boltzmann_electron_response"
-gyrokinetic_ions = true
+ion_physics = "gyrokinetic_ions"
 T_e = 1.0
 T_wall = 1.0
 

moment_kinetics/debug_test/gyroaverage_inputs.jl

@@ -6,7 +6,7 @@ test_input = OptionsDict(
     "output" => OptionsDict("run_name" => "gyroaverage"),
     "composition" => OptionsDict("n_ion_species" => 1,
                           "n_neutral_species" => 0,
-                          "gyrokinetic_ions" => true,
+                          "ion_physics" => "gyrokinetic_ions",
                           "T_e" => 1.0,
                           "T_wall" => 1.0),
     "evolve_moments" => OptionsDict("density" => false,

moment_kinetics/src/collision_frequencies.jl

@@ -0,0 +1,118 @@
+module collision_frequencies
+
+export get_collision_frequency_ii, get_collision_frequency_ee, get_collision_frequency_ei
+
+using ..reference_parameters: get_reference_collision_frequency_ii,
+                              get_reference_collision_frequency_ee,
+                              get_reference_collision_frequency_ei
+using ..reference_parameters: setup_reference_parameters
+
+"""
+    get_collision_frequency_ii(collisions, n, vth)
+
+Calculate the ion-ion collision frequency, depending on the settings/parameters in
+`collisions`, for the given density `n` and thermal speed `vth`.
+
+`n` and `vth` may be scalars or arrays, but should have shapes that can be broadcasted
+together.
+"""
+function get_collision_frequency_ii(collisions, n, vth)
+    # extract krook options from collisions struct
+    colk = collisions.krook
+    nuii0 = colk.nuii0
+    frequency_option = colk.frequency_option
+    if frequency_option ∈ ("reference_parameters", "collisionality_scan")
+        return @. nuii0 * n * vth^(-3)
+    elseif frequency_option == "manual"
+        # Include 0.0*n so that the result gets promoted to an array if n is an array,
+        # which hopefully means this function will have a fixed return type given the
+        # types of the arguments (we don't want to be 'type unstable' for array inputs by
+        # returning a scalar from this branch but an array from the "reference_parameters"
+        # branch).
+        return @. nuii0 + 0.0 * n
+    elseif frequency_option == "none"
+        # Include 0.0*n so that the result gets promoted to an array if n is an array,
+        # which hopefully means this function will have a fixed return type given the
+        # types of the arguments (we don't want to be 'type unstable' for array inputs by
+        # returning a scalar from this branch but an array from the "reference_parameters"
+        # branch).
+        return @. 0.0 * n
+    else
+        error("Unrecognised option [krook_collisions] "
+              * "frequency_option=$(frequency_option)")
+    end
+end
+
+"""
+    get_collision_frequency_ee(collisions, n, vthe)
+
+Calculate the electron-electron collision frequency, depending on the settings/parameters
+in `collisions`, for the given density `n` and electron thermal speed `vthe`.
+
+`n` and `vthe` may be scalars or arrays, but should have shapes that can be broadcasted
+together.
+"""
+function get_collision_frequency_ee(collisions, n, vthe)
+    # extract krook options from collisions struct
+    colk = collisions.krook
+    nuee0 = colk.nuee0
+    frequency_option = colk.frequency_option
+    if frequency_option == "reference_parameters"
+        return @. nuee0 * n * vthe^(-3)
+    elseif frequency_option == "manual"
+        # Include 0.0*n so that the result gets promoted to an array if n is an array,
+        # which hopefully means this function will have a fixed return type given the
+        # types of the arguments (we don't want to be 'type unstable' for array inputs by
+        # returning a scalar from this branch but an array from the "reference_parameters"
+        # branch).
+        return @. nuee0 + 0.0 * n
+    elseif frequency_option == "none"
+        # Include 0.0*n so that the result gets promoted to an array if n is an array,
+        # which hopefully means this function will have a fixed return type given the
+        # types of the arguments (we don't want to be 'type unstable' for array inputs by
+        # returning a scalar from this branch but an array from the "reference_parameters"
+        # branch).
+        return @. 0.0 * n
+    else
+        error("Unrecognised option [krook_collisions] "
+              * "frequency_option=$(frequency_option)")
+    end
+end
+
+"""
+    get_collision_frequency_ei(collisions, n, vthe)
+
+Calculate the electron-electron collision frequency, depending on the settings/parameters
+in `collisions`, for the given density `n` and electron thermal speed `vthe`.
+
+`n` and `vthe` may be scalars or arrays, but should have shapes that can be broadcasted
+together.
+"""
+function get_collision_frequency_ei(collisions, n, vthe)
+    # extract krook options from collisions struct
+    colk = collisions.krook
+    nuei0 = colk.nuei0
+    frequency_option = colk.frequency_option
+    if frequency_option == "reference_parameters"
+        return @. nuei0 * n * vthe^(-3)
+    elseif frequency_option == "manual"
+        # Include 0.0*n so that the result gets promoted to an array if n is an array,
+        # which hopefully means this function will have a fixed return type given the
+        # types of the arguments (we don't want to be 'type unstable' for array inputs by
+        # returning a scalar from this branch but an array from the "reference_parameters"
+        # branch).
+        return @. nuei0 + 0.0 * n
+    elseif frequency_option == "none"
+        # Include 0.0*n so that the result gets promoted to an array if n is an array,
+        # which hopefully means this function will have a fixed return type given the
+        # types of the arguments (we don't want to be 'type unstable' for array inputs by
+        # returning a scalar from this branch but an array from the "reference_parameters"
+        # branch).
+        return @. 0.0 * n
+    else
+        error("Unrecognised option [krook_collisions] "
+              * "frequency_option=$(frequency_option)")
+    end
+end
+
+end

moment_kinetics/src/electron_kinetic_equation.jl

@@ -46,9 +46,9 @@ using ..external_sources: total_external_electron_sources!,
                           add_total_external_electron_source_to_v_only_Jacobian!,
                           add_total_external_electron_source_to_z_only_Jacobian!
 using ..file_io: get_electron_io_info, write_electron_state, finish_electron_io
-using ..krook_collisions: electron_krook_collisions!, get_collision_frequency_ee,
-                          get_collision_frequency_ei,
-                          add_electron_krook_collisions_to_Jacobian!,
+using ..collision_frequencies: get_collision_frequency_ee,
+                                 get_collision_frequency_ei
+using ..krook_collisions: electron_krook_collisions!, add_electron_krook_collisions_to_Jacobian!,
                           add_electron_krook_collisions_to_v_only_Jacobian!,
                           add_electron_krook_collisions_to_z_only_Jacobian!
 using ..timer_utils

moment_kinetics/src/em_fields.jl

@@ -158,7 +158,7 @@ function update_phi!(fields, fvec, vperp, z, r, composition, collisions, moments
     end
 
     # get gyroaveraged field arrays for distribution function advance
-    gkions = composition.gyrokinetic_ions
+    gkions = composition.ion_physics == gyrokinetic_ions
     if gkions
         gyroaverage_field!(fields.gphi,fields.phi,gyroavs,vperp,z,r,composition)
         gyroaverage_field!(fields.gEz,fields.Ez,gyroavs,vperp,z,r,composition)