Merge pull request #234 from mabarnes/refactor-composition

Refactor composition and species inputs

examples/fokker-planck-1D2V/fokker-planck-1D2V-even_nz-shorttest-nstep200.toml

@@ -1,47 +1,11 @@
-#use_manufactured_solns_for_init = true
-#use_manufactured_solns_for_advance = false
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
-#force_Er_zero_at_wall = false #true
-#epsilon_offset = 0.1
-#use_vpabar_in_mms_dfni = true
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 1.0
 constant_ionization_rate = true
 
-nstep = 200
-dt = 1.0e-4
-nwrite = 1000
-nwrite_dfns = 1000
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 5
 z_nelement = 16
 #z_nelement_local = 2
@@ -67,31 +31,34 @@ vperp_L = 3.0
 #vperp_discretization = "chebyshev_pseudospectral"
 vperp_discretization = "gausslegendre_pseudospectral"
 
-#vz_ngrid = 17
-#vz_nelement = 4
-#vz_L = 12.0
-#vz_bc = "periodic"
-#vz_discretization = "chebyshev_pseudospectral"
-
-#vr_ngrid = 17
-#vr_nelement = 4
-#vr_L = 12.0
-#vr_bc = "periodic"
-#vr_discretization = "chebyshev_pseudospectral"
+[composition]
+n_ion_species = 1
+n_neutral_species = 0
+electron_physics = "boltzmann_electron_response"
+#electron_physics = "boltzmann_electron_response_with_simple_sheath"
+T_e = 1.0
+T_wall = 1.0
 
-#vzeta_ngrid = 17
-#vzeta_nelement = 4
-#vzeta_L = 12.0
-#vzeta_bc = "periodic"
-#vzeta_discretization = "chebyshev_pseudospectral"
+[ion_species_1]
+initial_density = 0.5
+initial_temperature = 1.0
 
-#[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.0
-#vperp_dissipation_coefficient = 0.0
-#z_dissipation_coefficient = 0.1
-#r_dissipation_coefficient = 0.0
+[z_IC_ion_species_1]
+initialization_option = "sinusoid"
+density_amplitude = 0.001
+density_phase = 0.0
+upar_amplitude = 0.0
+upar_phase = 0.0
+temperature_amplitude = 0.0
+temperature_phase = 0.0
 
 [fokker_planck_collisions]
 use_fokker_planck = true
 nuii = 1.0
 frequency_option = "manual"
+
+[timestepping]
+nstep = 50
+dt = 1.0e-4
+nwrite = 10
+nwrite_dfns = 10

examples/fokker-planck/fokker-planck-relaxation-report-resolutions.toml

@@ -1,31 +1,8 @@
 # cheap input file for a 0D2V relaxation to a collisional Maxwellian distribution with self-ion collisions.
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
 constant_ionization_rate = false
@@ -53,6 +30,27 @@ vperp_bc = "zero"
 # Fokker-Planck operator requires the "gausslegendre_pseudospectral
 # options for the vpa and vperp grids
 
+[composition]
+n_ion_species = 1
+n_neutral_species = 0
+electron_physics = "boltzmann_electron_response"
+T_e = 1.0
+T_wall = 1.0
+
+[ion_species_1]
+initial_density = 0.5
+initial_temperature = 1.0
+
+[z_IC_ion_species_1]
+initialization_option = "sinusoid"
+density_amplitude = 0.001
+density_phase = 0.0
+upar_amplitude = 0.0
+upar_phase = 0.0
+temperature_amplitude = 0.0
+temperature_phase = 0.0
+
+
 [fokker_planck_collisions]
 use_fokker_planck = true
 # nuii sets the normalised input C[F,F] Fokker-Planck collision frequency

examples/fokker-planck/fokker-planck-relaxation-slowing-down-alphas.toml

@@ -1,28 +1,9 @@
 # cheap input file for a 0D2V relaxation to a collisional Maxwellian distribution with self-ion collisions and collisions with fixed Maxwellian background of cold ions and electrons.
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 1.0
-initial_temperature1 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.0
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-vpa_IC_option1 = "isotropic-beam"
-vpa_IC_v01 = 1.0
-vpa_IC_vth01 = 0.1
-#vpa_IC_option1 = "directed-beam"
-#vpa_IC_vpa01 = -1.5
-#vpa_IC_vperp01 = 0.0
+
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
 constant_ionization_rate = false
@@ -90,3 +71,31 @@ nstep = 50000
 dt = 2.5e-4
 nwrite = 100
 nwrite_dfns = 100
+
+[composition]
+n_ion_species = 1
+n_neutral_species = 0
+electron_physics = "boltzmann_electron_response"
+T_e = 1.0
+T_wall = 1.0
+
+[ion_species_1]
+initial_density = 0.5
+initial_temperature = 1.0
+
+[z_IC_ion_species_1]
+initialization_option = "sinusoid"
+density_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 0.0
+upar_phase = 0.0
+temperature_amplitude = 0.0
+temperature_phase = 0.0
+
+[vpa_IC_ion_species_1]
+initialization_option = "isotropic-beam"
+#initialization_option = "directed-beam"
+v0 = 1.0
+vth0 = 0.1
+#vpa0 = -1.5
+#vperp0 = 0.0

examples/fokker-planck/fokker-planck-relaxation-slowing-down.toml

@@ -1,31 +1,8 @@
 # cheap input file for a 0D2V relaxation to a collisional Maxwellian distribution with self-ion collisions.
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
 constant_ionization_rate = false
@@ -51,6 +28,27 @@ vperp_discretization = "gausslegendre_pseudospectral"
 # Fokker-Planck operator requires the "gausslegendre_pseudospectral
 # options for the vpa and vperp grids
 
+[composition]
+n_ion_species = 1
+n_neutral_species = 0
+electron_physics = "boltzmann_electron_response"
+T_e = 1.0
+T_wall = 1.0
+
+[ion_species_1]
+initial_density = 0.5
+initial_temperature = 1.0
+
+[z_IC_ion_species_1]
+initialization_option = "sinusoid"
+density_amplitude = 0.001
+density_phase = 0.0
+upar_amplitude = 0.0
+upar_phase = 0.0
+temperature_amplitude = 0.0
+temperature_phase = 0.0
+
+
 [fokker_planck_collisions]
 # nuii sets the normalised input C[F,F] Fokker-Planck collision frequency
 nuii = 1.0