First pull request LM_sandbox to electrons-jto-debug

examples/kinetic-electrons/wall+sheath-bc_boltzmann_loworder.toml

@@ -49,10 +49,10 @@ ionization_frequency = 2.0
 #electron_ionization_frequency = 2.0
 #ionization_energy = 1.0
 constant_ionization_rate = false
-nstep = 1000000
+nstep = 1000
 #nstep = 1
 dt = 1.0e-5
-nwrite = 10000
+nwrite = 100
 nwrite_dfns = 10000
 use_semi_lagrange = false
 n_rk_stages = 4
@@ -85,8 +85,8 @@ ascii_output = true
 [numerical_dissipation]
 #moment_dissipation_coefficient = 0.0001
 #moment_dissipation_coefficient = 1.0
-vpa_dissipation_coefficient = 0.002
-#vpa_dissipation_coefficient = 0.1
+#vpa_dissipation_coefficient = 0.002
+ion_vpa_dissipation_coefficient = 0.1
 #vpa_dissipation_coefficient = 0.2
 #vpa_dissipation_coefficient = 2.0
 #vpa_dissipation_coefficient = 20.0

moment_kinetics/src/numerical_dissipation.jl

@@ -19,7 +19,7 @@ using ..type_definitions: mk_float
 Base.@kwdef struct numerical_dissipation_parameters
     vpa_boundary_buffer_damping_rate::mk_float = -1.0
     vpa_boundary_buffer_diffusion_coefficient::mk_float = -1.0
-    vpa_dissipation_coefficient::mk_float = -1.0
+    ion_vpa_dissipation_coefficient::mk_float = -1.0
     vz_dissipation_coefficient::mk_float = -1.0
     vperp_dissipation_coefficient::mk_float = -1.0
     z_dissipation_coefficient::mk_float = -1.0
@@ -29,12 +29,12 @@ Base.@kwdef struct numerical_dissipation_parameters
 end
 
 function setup_numerical_dissipation(input_section::Dict, is_1V)
-    if is_1V && "vpa_dissipation_coefficient" ∈ keys(input_section)
+    if is_1V && "ion_vpa_dissipation_coefficient" ∈ keys(input_section)
         # Set default for vz_dissipation_coefficient the same as
-        # vpa_dissipation_coefficient for 1V case
+        # ion_vpa_dissipation_coefficient for 1V case
         input_section["vz_dissipation_coefficient"] =
             get(input_section, "vz_dissipation_coefficient",
-                input_section["vpa_dissipation_coefficient"])
+                input_section["ion_vpa_dissipation_coefficient"])
     end
 
     input = Dict(Symbol(k)=>v for (k,v) in input_section)
@@ -243,9 +243,8 @@ vpa_dissipation_coefficient = 0.1
 ```
 """
 function vpa_dissipation!(f_out, f_in, vpa, spectral::T_spectral, dt,
-        num_diss_params::numerical_dissipation_parameters) where T_spectral
+        diffusion_coefficient) where T_spectral
 
-    diffusion_coefficient = num_diss_params.vpa_dissipation_coefficient
     if diffusion_coefficient <= 0.0 || vpa.n == 1
         return nothing
     end
@@ -534,7 +533,7 @@ function r_dissipation_neutral!(f_out, f_in, r, r_spectral::T_spectral, dt,
 end
 
 """
-    force_minimum_pdf_value!(f, num_diss_paras::numerical_dissipation_parameters)
+    force_minimum_pdf_value!(f, num_diss_params::numerical_dissipation_parameters)
 
 Set a minimum value for the pdf-sized array `f`. Any points less than the minimum are
 set to the minimum. By default, no minimum is applied. The minimum value can be set by

moment_kinetics/src/time_advance.jl

@@ -685,7 +685,7 @@ function setup_advance_flags(moments, composition, t_input, collisions,
         # flag to determine if a d^2/dr^2 operator is present
         r_diffusion = (advance_numerical_dissipation && num_diss_params.r_dissipation_coefficient > 0.0)
         # flag to determine if a d^2/dvpa^2 operator is present
-        vpa_diffusion = ((advance_numerical_dissipation && num_diss_params.vpa_dissipation_coefficient > 0.0) || explicit_weakform_fp_collisions)
+        vpa_diffusion = ((advance_numerical_dissipation && num_diss_params.ion_vpa_dissipation_coefficient > 0.0) || explicit_weakform_fp_collisions)
         vz_diffusion = (advance_numerical_dissipation && num_diss_params.vz_dissipation_coefficient > 0.0)
     end
 
@@ -1863,7 +1863,7 @@ function euler_time_advance!(fvec_out, fvec_in, pdf, fields, moments,
     # add numerical dissipation
     if advance.numerical_dissipation
         vpa_dissipation!(fvec_out.pdf, fvec_in.pdf, vpa, vpa_spectral, dt,
-                         num_diss_params)
+                         num_diss_params.ion_vpa_dissipation_coefficient)
         vperp_dissipation!(fvec_out.pdf, fvec_in.pdf, vperp, vperp_spectral, dt,
                          num_diss_params)
         z_dissipation!(fvec_out.pdf, fvec_in.pdf, z, z_spectral, dt,