Merge pull request #250 from mabarnes/multiple_sources

Multiple source functionality
mabarnes · Sep 13, 2024 · 3038940 · 3038940
2 parents db370d1 + 5ecabac
commit 3038940
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diff --git a/examples/fokker-planck/fokker-planck-relaxation-slowing-down-alphas.toml b/examples/fokker-planck/fokker-planck-relaxation-slowing-down-alphas.toml
@@ -46,7 +46,7 @@ sd_mi = 0.5 # mD/malpha
 sd_me = 0.000013616 # 0.25/1836.0 me/malpha
 sd_q = 1.0
 
-[ion_source]
+[ion_source_1]
 active=false
 source_strength=0.0
 source_T=0.005

diff --git a/examples/fokker-planck/fokker-planck-source-sink-slowing-down-alphas-no-self-collisions.toml b/examples/fokker-planck/fokker-planck-source-sink-slowing-down-alphas-no-self-collisions.toml
@@ -72,7 +72,7 @@ sd_mi = 0.5 # mD/malpha
 sd_me = 0.000013616 # 0.25/1836.0 me/malpha
 sd_q = 1.0
 
-[ion_source]
+[ion_source_1]
 active=true
 source_strength=1.0
 source_T=0.005

diff --git a/examples/fokker-planck/fokker-planck-source-sink-slowing-down-alphas.toml b/examples/fokker-planck/fokker-planck-source-sink-slowing-down-alphas.toml
@@ -73,7 +73,7 @@ sd_mi = 0.5 # mD/malpha
 sd_me = 0.000013616 # 0.25/1836.0 me/malpha
 sd_q = 1.0
 
-[ion_source]
+[ion_source_1]
 active=true
 source_strength=1.0
 source_T=0.005

diff --git a/examples/kinetic-electrons/wall-bc_recyclefraction0.5_split3_braginskii-vpadiss0-IMEX.toml b/examples/kinetic-electrons/wall-bc_recyclefraction0.5_split3_braginskii-vpadiss0-IMEX.toml
@@ -98,7 +98,7 @@ steady_state_residual = true
 converged_residual_value = 1.0e-3
 #write_after_fixed_step_count = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/kinetic-electrons/wall-bc_recyclefraction0.5_split3_kinetic-vpadiss0.toml b/examples/kinetic-electrons/wall-bc_recyclefraction0.5_split3_kinetic-vpadiss0.toml
@@ -104,7 +104,7 @@ minimum_dt = 1.0e-9
 initialization_residual_value = 2.5
 converged_residual_value = 0.1 #1.0e-3
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5-init.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5-init.toml
@@ -91,7 +91,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5.toml
@@ -96,7 +96,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split1.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split1.toml
@@ -96,7 +96,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split2.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split2.toml
@@ -97,7 +97,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3-init.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3-init.toml
@@ -92,7 +92,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3.toml
@@ -97,7 +97,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_SSPRK4.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_SSPRK4.toml
@@ -90,7 +90,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete104.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete104.toml
@@ -98,7 +98,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete42.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete42.toml
@@ -98,7 +98,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete64.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_fekete64.toml
@@ -98,7 +98,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_rkf54.toml b/examples/recycling-fraction/wall-bc_recyclefraction0.5_split3_rkf54.toml
@@ -98,7 +98,7 @@ converged_residual_value = 1.0e-3
 [krook_collisions]
 use_krook = true
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/wall-bc/wall-bc_no-neutrals.toml b/examples/wall-bc/wall-bc_no-neutrals.toml
@@ -60,7 +60,7 @@ nwrite = 5000
 nwrite_dfns = 5000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/wall-bc/wall-bc_no-neutrals_split1.toml b/examples/wall-bc/wall-bc_no-neutrals_split1.toml
@@ -60,7 +60,7 @@ nwrite = 5000
 nwrite_dfns = 5000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/wall-bc/wall-bc_no-neutrals_split2.toml b/examples/wall-bc/wall-bc_no-neutrals_split2.toml
@@ -60,7 +60,7 @@ nwrite = 5000
 nwrite_dfns = 5000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/wall-bc/wall-bc_no-neutrals_split3.toml b/examples/wall-bc/wall-bc_no-neutrals_split3.toml
@@ -60,7 +60,7 @@ nwrite = 5000
 nwrite_dfns = 5000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125

diff --git a/examples/wall-bc/wall-bc_volumerecycle.toml b/examples/wall-bc/wall-bc_volumerecycle.toml
@@ -86,14 +86,14 @@ nwrite = 10000
 nwrite_dfns = 10000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[neutral_source]
+[neutral_source_1]
 active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25

diff --git a/examples/wall-bc/wall-bc_volumerecycle_split1.toml b/examples/wall-bc/wall-bc_volumerecycle_split1.toml
@@ -86,14 +86,14 @@ nwrite = 10000
 nwrite_dfns = 10000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[neutral_source]
+[neutral_source_1]
 active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25

diff --git a/examples/wall-bc/wall-bc_volumerecycle_split2.toml b/examples/wall-bc/wall-bc_volumerecycle_split2.toml
@@ -86,14 +86,14 @@ nwrite = 10000
 nwrite_dfns = 10000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[neutral_source]
+[neutral_source_1]
 active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25

diff --git a/examples/wall-bc/wall-bc_volumerecycle_split3.toml b/examples/wall-bc/wall-bc_volumerecycle_split3.toml
@@ -86,14 +86,14 @@ nwrite = 10000
 nwrite_dfns = 10000
 split_operators = false
 
-[ion_source]
+[ion_source_1]
 active = true
 z_profile = "gaussian"
 z_width = 0.125
 source_strength = 2.0
 source_T = 2.0
 
-[neutral_source]
+[neutral_source_1]
 active = true
 source_type = "recycling"
 recycling_controller_fraction = 0.25

diff --git a/makie_post_processing/makie_post_processing/src/makie_post_processing.jl b/makie_post_processing/makie_post_processing/src/makie_post_processing.jl
@@ -40,7 +40,8 @@ using moment_kinetics.load_data: close_run_info, get_run_info_no_setup, get_vari
                                  neutral_moment_variables, all_moment_variables,
                                  ion_dfn_variables, electron_dfn_variables,
                                  neutral_dfn_variables, all_dfn_variables, ion_variables,
-                                 neutral_variables, all_variables
+                                 neutral_variables, all_variables, ion_source_variables,
+                                 neutral_source_variables, electron_source_variables
 using moment_kinetics.initial_conditions: vpagrid_to_dzdt
 using .shared_utils: calculate_and_write_frequencies
 using moment_kinetics.type_definitions: mk_float, mk_int
@@ -233,14 +234,6 @@ function makie_post_process(run_dir::Union{String,Tuple},
     # Plots from moment variables
     #############################
 
-    moment_variable_list = tuple(em_variables..., ion_moment_variables...)
-    if has_electrons
-        moment_variable_list = tuple(moment_variable_list..., electron_moment_variables...)
-    end
-    if has_neutrals
-        moment_variable_list = tuple(moment_variable_list..., neutral_moment_variables...)
-    end
-
     if any(ri !== nothing for ri ∈ run_info_moments)
         has_moments = true
 
@@ -276,7 +269,7 @@ function makie_post_process(run_dir::Union{String,Tuple},
     end
 
     do_steady_state_residuals = any(input_dict[v]["steady_state_residual"]
-                                    for v ∈ moment_variable_list)
+                                    for v ∈ all_moment_variables)
     if do_steady_state_residuals
         textoutput_files = Tuple(ri.run_prefix * "_residuals.txt"
                                  for ri in run_info if ri !== nothing)
@@ -299,7 +292,7 @@ function makie_post_process(run_dir::Union{String,Tuple},
         steady_state_residual_fig_axes = nothing
     end
 
-    for variable_name ∈ moment_variable_list
+    for variable_name ∈ all_moment_variables
         plots_for_variable(run_info, variable_name; plot_prefix=plot_prefix,
                            has_rdim=has_rdim, has_zdim=has_zdim, is_1V=is_1V,
                            steady_state_residual_fig_axes=steady_state_residual_fig_axes)
@@ -1030,8 +1023,18 @@ function plots_for_variable(run_info, variable_name; plot_prefix, has_rdim=true,
     elseif variable_name ∈ neutral_moment_variables ||
            variable_name ∈ neutral_dfn_variables
         species_indices = 1:maximum(ri.n_neutral_species for ri ∈ run_info)
-    else
+    elseif variable_name ∈ ion_moment_variables ||
+           variable_name ∈ ion_dfn_variables
         species_indices = 1:maximum(ri.n_ion_species for ri ∈ run_info)
+    elseif variable_name in ion_source_variables
+        species_indices = 1:maximum(length(ri.external_source_settings.ion) for ri ∈ run_info)
+    elseif variable_name in electron_source_variables
+        species_indices = 1:maximum(length(ri.external_source_settings.electron) for ri ∈ run_info)
+    elseif variable_name in neutral_source_variables
+        species_indices = 1:maximum(length(ri.external_source_settings.neutral) for ri ∈ run_info)
+    else
+        species_indices = 1:1
+        #error("variable_name=$variable_name not found in any defined group")
     end
     for is ∈ species_indices
         if is !== nothing

diff --git a/moment_kinetics/debug_test/kinetic_electron_inputs.jl b/moment_kinetics/debug_test/kinetic_electron_inputs.jl
@@ -82,7 +82,7 @@ test_input = OptionsDict("composition" => OptionsDict("n_ion_species" => 1,
                   "vz_L" => 6.0,
                   "vz_bc" => "zero",
                   "vz_discretization" => "chebyshev_pseudospectral",
-                  "ion_source" => OptionsDict("active" => true,
+                  "ion_source_1" => OptionsDict("active" => true,
                                                    "z_profile" => "gaussian",
                                                    "z_width" => 0.125,
                                                    "source_strength" => 2.0,

diff --git a/moment_kinetics/debug_test/recycling_fraction_inputs.jl b/moment_kinetics/debug_test/recycling_fraction_inputs.jl
@@ -74,7 +74,7 @@ test_input = OptionsDict("composition" => OptionsDict("n_ion_species" => 1,
                   "vz_L" => 6.0,
                   "vz_bc" => "zero",
                   "vz_discretization" => "chebyshev_pseudospectral",
-                  "ion_source" => OptionsDict("active" => true,
+                  "ion_source_1" => OptionsDict("active" => true,
                                        "z_profile" => "gaussian",
                                        "z_width" => 0.125,
                                        "source_strength" => 2.0,