Rename 'charged' to 'ion'

makie_post_processing/makie_post_processing/src/makie_post_processing.jl

@@ -303,7 +303,7 @@ function makie_post_process(run_dir::Union{String,Tuple},
         end
     end
 
-    plot_charged_pdf_2D_at_wall(run_info_dfns; plot_prefix=plot_prefix)
+    plot_ion_pdf_2D_at_wall(run_info_dfns; plot_prefix=plot_prefix)
     if has_neutrals
         plot_neutral_pdf_2D_at_wall(run_info_dfns; plot_prefix=plot_prefix)
     end
@@ -4302,9 +4302,9 @@ function animate_f_unnorm_vs_vpa_z(run_info; input=nothing, neutral=false, is=1,
 end
 
 """
-    plot_charged_pdf_2D_at_wall(run_info; plot_prefix)
+    plot_ion_pdf_2D_at_wall(run_info; plot_prefix)
 
-Make plots/animations of the charged particle distribution function at wall boundaries.
+Make plots/animations of the ion distribution function at wall boundaries.
 
 The information for the runs to plot is passed in `run_info` (as returned by
 [`get_run_info`](@ref)). If `run_info` is a Tuple, comparison plots are made where line
@@ -4318,7 +4318,7 @@ will be saved with the format `plot_prefix<some_identifying_string>.pdf`. When `
 is not a Tuple, `plot_prefix` is optional - plots/animations will be saved only if it is
 passed.
 """
-function plot_charged_pdf_2D_at_wall(run_info; plot_prefix)
+function plot_ion_pdf_2D_at_wall(run_info; plot_prefix)
     input = Dict_to_NamedTuple(input_dict_dfns["wall_pdf"])
     if !(input.plot || input.animate || input.advection_velocity)
         # nothing to do
@@ -4332,7 +4332,7 @@ function plot_charged_pdf_2D_at_wall(run_info; plot_prefix)
     z_lower = 1
     z_upper = run_info[1].z.n
     if !all(ri.z.n == z_upper for ri ∈ run_info)
-        println("Cannot run plot_charged_pdf_2D_at_wall() for runs with different "
+        println("Cannot run plot_ion_pdf_2D_at_wall() for runs with different "
                 * "z-grid sizes. Got $(Tuple(ri.z.n for ri ∈ run_info))")
         return nothing
     end
@@ -5772,7 +5772,7 @@ end
                    field_sym_label, norm_label, plot_dims, animate_dims)
 
 Utility function for making plots to avoid duplicated code in
-[`compare_charged_pdf_symbolic_test`](@ref) and
+[`compare_ion_pdf_symbolic_test`](@ref) and
 [`compare_neutral_pdf_symbolic_test`](@ref).
 
 The information for the run to analyse is passed in `run_info` (as returned by
@@ -5922,7 +5922,7 @@ function _MMS_pdf_plots(run_info, input, variable_name, plot_prefix, field_label
 end
 
 """
-    compare_charged_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
+    compare_ion_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
                                       input=nothing)
 
 Compare the computed and manufactured solutions for the ion distribution function.
@@ -5943,7 +5943,7 @@ Note: when calculating error norms, data is loaded only for 1 time point and for
 chunk that is the same size as computed by 1 block of the simulation at run time. This
 should prevent excessive memory requirements for this function.
 """
-function compare_charged_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
+function compare_ion_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
                                            input=nothing)
 
     field_label = L"\tilde{f}_i"
@@ -6473,7 +6473,7 @@ function manufactured_solutions_analysis_dfns(run_info; plot_prefix)
         println_to_stdout_and_file(io, "# ", run_info.run_name)
         println_to_stdout_and_file(io, join(run_info.time, " "), " # time / (Lref/cref): ")
 
-        compare_charged_pdf_symbolic_test(run_info, plot_prefix; io=io, input=input)
+        compare_ion_pdf_symbolic_test(run_info, plot_prefix; io=io, input=input)
 
         if run_info.n_neutral_species > 0
             compare_neutral_pdf_symbolic_test(run_info, plot_prefix; io=io, input=input)

moment_kinetics/debug_test/README.md

@@ -96,7 +96,7 @@ Suggested debugging strategy for race conditions is:
   failure. Usually a failure should indicate where there is a missing
   `begin_*_region()` call. There may be places though where synchronization is
   required even though the type of loop macros used does not change (for
-  example when `phi` is calculated contributions from all charged species need
+  example when `phi` is calculated contributions from all ion species need
   to be summed, resulting in an unusual pattern of array accesses); in this
   case `_block_synchronize()` can be called directly.
     * The function `debug_check_shared_memory()` can be inserted between

moment_kinetics/ext/manufactured_solns_ext.jl

@@ -450,25 +450,25 @@ using IfElse
                                     geometry_input_data::geometry_input, composition, species, nr, nvperp)
         # calculate the geometry symbolically
         geometry = geometry_sym(geometry_input_data,Lz,Lr,nr)
-        charged_species = species.charged[1]
+        ion_species = species.ion[1]
         if composition.n_neutral_species > 0
             neutral_species = species.neutral[1]
         else
             neutral_species = nothing
         end
 
         densi = densi_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species)
+                          ion_species)
         upari = upari_sym(Lr, Lz, r_bc, z_bc, composition, geometry, nr, manufactured_solns_input,
-                          charged_species)
+                          ion_species)
         ppari = ppari_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species)
+                          ion_species)
         pperpi = pperpi_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species, nvperp)
+                          ion_species, nvperp)
         vthi = vthi_sym(Lr, Lz, r_bc, z_bc, composition, manufactured_solns_input,
-                          charged_species, nvperp)
+                          ion_species, nvperp)
         dfni = dfni_sym(Lr, Lz, r_bc, z_bc, composition, geometry, nr,
-                        manufactured_solns_input, charged_species)
+                        manufactured_solns_input, ion_species)
 
         densn = densn_sym(Lr, Lz, r_bc, z_bc, geometry,composition,
                           manufactured_solns_input, neutral_species)
@@ -538,7 +538,7 @@ using IfElse
             geometry_input_data::geometry_input, collisions,
             num_diss_params, species)
         geometry = geometry_sym(geometry_input_data,z_coord.L,r_coord.L,r_coord.n)
-        charged_species = species.charged[1]
+        ion_species = species.ion[1]
         if composition.n_neutral_species > 0
             neutral_species = species.neutral[1]
         else
@@ -547,16 +547,16 @@ using IfElse
 
         # ion manufactured solutions
         densi = densi_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition,
-                          manufactured_solns_input, charged_species)
-        upari = upari_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition, geometry, r_coord.n, manufactured_solns_input, charged_species)
+                          manufactured_solns_input, ion_species)
+        upari = upari_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition, geometry, r_coord.n, manufactured_solns_input, ion_species)
         vthi = vthi_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition, manufactured_solns_input,
-                          charged_species, vperp_coord.n)
+                          ion_species, vperp_coord.n)
         dfni = dfni_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc, composition,
-                        geometry, r_coord.n, manufactured_solns_input, charged_species)
+                        geometry, r_coord.n, manufactured_solns_input, ion_species)
         #dfni in vr vz vzeta coordinates
         vrvzvzeta_dfni = cartesian_dfni_sym(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc,
                                             composition, manufactured_solns_input,
-                                            charged_species)
+                                            ion_species)
 
         # neutral manufactured solutions
         densn = densn_sym(r_coord.L,z_coord.L, r_coord.bc, z_coord.bc, geometry,
@@ -604,7 +604,7 @@ using IfElse
         # calculate the electric fields and the potential
         Er, Ez, phi = electric_fields(r_coord.L, z_coord.L, r_coord.bc, z_coord.bc,
                                       composition, r_coord.n, manufactured_solns_input,
-                                      charged_species)
+                                      ion_species)
 
         # the adiabatic invariant (for compactness)
         mu = 0.5*(vperp^2)/Bmag

moment_kinetics/src/analysis.jl

@@ -13,7 +13,7 @@ using ..coordinates: coordinate
 using ..initial_conditions: vpagrid_to_dzdt
 using ..interpolation: interpolate_to_grid_1d
 using ..load_data: open_readonly_output_file, get_nranks, load_pdf_data, load_rank_data
-using ..load_data: load_distributed_charged_pdf_slice
+using ..load_data: load_distributed_ion_pdf_slice
 using ..looping
 using ..type_definitions: mk_int
 using ..velocity_moments: integrate_over_vspace
@@ -140,12 +140,12 @@ function check_Chodura_condition(r, z, vperp, vpa, dens, upar, vth, composition,
         end
     end
     if f_lower === nothing
-        f_lower = load_distributed_charged_pdf_slice(run_name, nblocks, t_range,
+        f_lower = load_distributed_ion_pdf_slice(run_name, nblocks, t_range,
                                                      composition.n_ion_species, r, z,
                                                      vperp, vpa; iz=1, ir=ir0)
     end
     if f_upper === nothing
-        f_upper = load_distributed_charged_pdf_slice(run_name, nblocks, t_range,
+        f_upper = load_distributed_ion_pdf_slice(run_name, nblocks, t_range,
                                                      composition.n_ion_species, r, z,
                                                      vperp, vpa; iz=z.n_global, ir=ir0)
     end

moment_kinetics/src/charge_exchange.jl

@@ -28,7 +28,7 @@ function charge_exchange_collisions_1V!(f_out, f_neutral_out, fvec_in, moments,
                 f_out[:,1,:,:,is], fvec_in.pdf[:,1,:,:,is],
                 fvec_in.pdf_neutral[:,1,1,:,:,is],
                 fvec_in.density_neutral[:,:,is], fvec_in.upar[:,:,is],
-                fvec_in.uz_neutral[:,:,is], moments.charged.vth[:,:,is],
+                fvec_in.uz_neutral[:,:,is], moments.ion.vth[:,:,is],
                 moments.neutral.vth[:,:,is], moments, vpa, vz, charge_exchange_frequency,
                 vz_spectral, dt)
         end
@@ -42,7 +42,7 @@ function charge_exchange_collisions_1V!(f_out, f_neutral_out, fvec_in, moments,
                 f_neutral_out[:,1,1,:,:,isn], fvec_in.pdf_neutral[:,1,1,:,:,isn],
                 fvec_in.pdf[:,1,:,:,isn], fvec_in.density[:,:,isn],
                 fvec_in.uz_neutral[:,:,isn], fvec_in.upar[:,:,isn],
-                moments.neutral.vth[:,:,isn], moments.charged.vth[:,:,isn], moments,
+                moments.neutral.vth[:,:,isn], moments.ion.vth[:,:,isn], moments,
                 vz, vpa, charge_exchange_frequency, vpa_spectral, dt)
         end
     else
@@ -135,7 +135,7 @@ function charge_exchange_collisions_single_species!(f_out, pdf_in, pdf_other,
     end
 end
 
-function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in, f_charged_vrvzvzeta_in, fvec_in, composition, vz, vr, vzeta, vpa, vperp, z, r,
+function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in, f_ion_vrvzvzeta_in, fvec_in, composition, vz, vr, vzeta, vpa, vperp, z, r,
                                      charge_exchange_frequency, dt)
     # This routine assumes a 3V model with:
     @boundscheck vz.n == size(f_neutral_out,1) || throw(BoundsError(f_neutral_out))
@@ -144,12 +144,12 @@ function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in,
     @boundscheck z.n == size(f_neutral_out,4) || throw(BoundsError(f_neutral_out))
     @boundscheck r.n == size(f_neutral_out,5) || throw(BoundsError(f_neutral_out))
     @boundscheck composition.n_neutral_species == size(f_neutral_out,6) || throw(BoundsError(f_neutral_out))
-    @boundscheck vz.n == size(f_charged_vrvzvzeta_in,1) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck vr.n == size(f_charged_vrvzvzeta_in,2) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck vzeta.n == size(f_charged_vrvzvzeta_in,3) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck z.n == size(f_charged_vrvzvzeta_in,4) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck r.n == size(f_charged_vrvzvzeta_in,5) || throw(BoundsError(f_charged_vrvzvzeta_in))
-    @boundscheck composition.n_neutral_species == size(f_charged_vrvzvzeta_in,6) || throw(BoundsError(f_charged_vrvzvzeta_in))
+    @boundscheck vz.n == size(f_ion_vrvzvzeta_in,1) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck vr.n == size(f_ion_vrvzvzeta_in,2) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck vzeta.n == size(f_ion_vrvzvzeta_in,3) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck z.n == size(f_ion_vrvzvzeta_in,4) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck r.n == size(f_ion_vrvzvzeta_in,5) || throw(BoundsError(f_ion_vrvzvzeta_in))
+    @boundscheck composition.n_neutral_species == size(f_ion_vrvzvzeta_in,6) || throw(BoundsError(f_ion_vrvzvzeta_in))
     @boundscheck vpa.n == size(f_out,1) || throw(BoundsError(f_out))
     @boundscheck vperp.n == size(f_out,2) || throw(BoundsError(f_out))
     @boundscheck z.n == size(f_out,3) || throw(BoundsError(f_out))
@@ -181,7 +181,7 @@ function charge_exchange_collisions_3V!(f_out, f_neutral_out, f_neutral_gav_in,
         for is ∈ 1:composition.n_ion_species
             f_neutral_out[ivz,ivr,ivzeta,iz,ir,isn] +=
                 dt*charge_exchange_frequency*(
-                    f_charged_vrvzvzeta_in[ivz,ivr,ivzeta,iz,ir,is]*fvec_in.density_neutral[iz,ir,isn]
+                    f_ion_vrvzvzeta_in[ivz,ivr,ivzeta,iz,ir,is]*fvec_in.density_neutral[iz,ir,isn]
                     - fvec_in.pdf_neutral[ivz,ivr,ivzeta,iz,ir,isn]*fvec_in.density[iz,ir,is])
         end
     end

moment_kinetics/src/continuity.jl

@@ -8,7 +8,7 @@ using ..calculus: derivative!
 using ..looping
 
 """
-use the continuity equation dn/dt + d(n*upar)/dz to update the density n for all charged
+use the continuity equation dn/dt + d(n*upar)/dz to update the density n for all ion
 species
 """
 function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spectral,
@@ -18,8 +18,8 @@ function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spect
     @loop_s_r_z is ir iz begin
         # Use ddens_dz is upwinded using upar
         dens_out[iz,ir,is] -=
-            dt*(fvec_in.upar[iz,ir,is]*moments.charged.ddens_dz_upwind[iz,ir,is] +
-                fvec_in.density[iz,ir,is]*moments.charged.dupar_dz[iz,ir,is])
+            dt*(fvec_in.upar[iz,ir,is]*moments.ion.ddens_dz_upwind[iz,ir,is] +
+                fvec_in.density[iz,ir,is]*moments.ion.dupar_dz[iz,ir,is])
     end
 
     # update the density to account for ionization collisions;
@@ -31,7 +31,7 @@ function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spect
     end
 
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_density_amplitude
+        source_amplitude = moments.ion.external_source_density_amplitude
         @loop_s_r_z is ir iz begin
             dens_out[iz,ir,is] +=
                 dt * source_amplitude[iz,ir]
@@ -42,7 +42,7 @@ function continuity_equation!(dens_out, fvec_in, moments, composition, dt, spect
     diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_s_r_z is ir iz begin
-            dens_out[iz,ir,is] += dt*diffusion_coefficient*moments.charged.d2dens_dz2[iz,ir,is]
+            dens_out[iz,ir,is] += dt*diffusion_coefficient*moments.ion.d2dens_dz2[iz,ir,is]
         end
     end
 end

moment_kinetics/src/derivatives.jl

@@ -19,7 +19,7 @@ using ..looping
 Centered derivatives
 df/dr group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -87,7 +87,7 @@ function derivative_r!(dfdr::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
 end
 
 #df/dr
-#5D version for f[vpa,vperp,z,r,s] -> charged particle dfn (species indexing taken outside this loop)
+#5D version for f[vpa,vperp,z,r,s] -> ion particle dfn
 function derivative_r!(dfdr::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         dfdr_lower_endpoints::AbstractArray{mk_float,4},
         dfdr_upper_endpoints::AbstractArray{mk_float,4},
@@ -139,7 +139,7 @@ end
 Centered derivatives
 df/dz group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -206,7 +206,7 @@ function derivative_z!(dfdz::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
     end
 end
 
-#5D version for f[vpa,vperp,z,r,s] -> dfn charged particles
+#5D version for f[vpa,vperp,z,r,s] -> dfn ions
 function derivative_z!(dfdz::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         dfdz_lower_endpoints::AbstractArray{mk_float,4},
         dfdz_upper_endpoints::AbstractArray{mk_float,4},
@@ -258,7 +258,7 @@ end
 Upwind derivatives
 df/dr group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -335,7 +335,7 @@ function derivative_r!(dfdr::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
 end
 
 #df/dr
-#5D version for f[vpa,vperp,z,r,s] -> charged particle dfn (species indexing taken outside this loop)
+#5D version for f[vpa,vperp,z,r,s] -> ion particle dfn
 function derivative_r!(dfdr::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         advect, adv_fac_lower_buffer::AbstractArray{mk_float,4},
         adv_fac_upper_buffer::AbstractArray{mk_float,4},
@@ -398,7 +398,7 @@ end
 Upwind derivatives
 df/dz group of rountines for
 fields & moments -> [z,r]
-dfns (charged) -> [vpa,vperp,z,r,s]
+dfns (ion) -> [vpa,vperp,z,r,s]
 dfns (neutrals) -> [vz,vr,vzeta,z,r,sn]
 """
 
@@ -472,7 +472,7 @@ function derivative_z!(dfdz::AbstractArray{mk_float,3}, f::AbstractArray{mk_floa
     end
 end
 
-#5D version for f[vpa,vperp,z,r,s] -> dfn charged particles
+#5D version for f[vpa,vperp,z,r,s] -> dfn ion particles
 function derivative_z!(dfdz::AbstractArray{mk_float,5}, f::AbstractArray{mk_float,5},
         advect, adv_fac_lower_buffer::AbstractArray{mk_float,4},
         adv_fac_upper_buffer::AbstractArray{mk_float,4},

moment_kinetics/src/energy_equation.jl

@@ -17,13 +17,14 @@ function energy_equation!(ppar, fvec, moments, collisions, dt, spectral, composi
     begin_s_r_z_region()
 
     @loop_s_r_z is ir iz begin
-        ppar[iz,ir,is] += dt*(-fvec.upar[iz,ir,is]*moments.charged.dppar_dz_upwind[iz,ir,is]
-                              - moments.charged.dqpar_dz[iz,ir,is]
-                              - 3.0*fvec.ppar[iz,ir,is]*moments.charged.dupar_dz[iz,ir,is])
+        ppar[iz,ir,is] += dt*(-fvec.upar[iz,ir,is]*moments.ion.dppar_dz_upwind[iz,ir,is]
+                              - moments.ion.dqpar_dz[iz,ir,is]
+                              - 3.0*fvec.ppar[iz,ir,is]*moments.ion.dupar_dz[iz,ir,is])
     end
 
+
     if ion_source_settings.active
-        source_amplitude = moments.charged.external_source_pressure_amplitude
+        source_amplitude = moments.ion.external_source_pressure_amplitude
         @loop_s_r_z is ir iz begin
             ppar[iz,ir,is] += dt * source_amplitude[iz,ir]
         end
@@ -32,7 +33,7 @@ function energy_equation!(ppar, fvec, moments, collisions, dt, spectral, composi
     diffusion_coefficient = num_diss_params.moment_dissipation_coefficient
     if diffusion_coefficient > 0.0
         @loop_s_r_z is ir iz begin
-            ppar[iz,ir,is] += dt*diffusion_coefficient*moments.charged.d2ppar_dz2[iz,ir,is]
+            ppar[iz,ir,is] += dt*diffusion_coefficient*moments.ion.d2ppar_dz2[iz,ir,is]
         end
     end