Merge pull request #200 from mabarnes/cross-species-collisions

Cross species collisions

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

@@ -30,13 +30,6 @@ charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
 constant_ionization_rate = false
 
-nstep = 200000
-dt = 1.0e-3
-nwrite = 50
-nwrite_dfns = 50
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 1
 z_nelement = 1
 z_nelement_local = 1
@@ -64,3 +57,9 @@ use_fokker_planck = true
 # nuii sets the normalised input C[F,F] Fokker-Planck collision frequency
 nuii = 1.0
 frequency_option = "manual"
+
+[timestepping]
+nstep = 200000
+dt = 1.0e-3
+nwrite = 50
+nwrite_dfns = 50

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

@@ -0,0 +1,91 @@
+# 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
+
+z_ngrid = 1
+z_nelement = 1
+z_nelement_local = 1
+z_bc = "wall"
+z_discretization = "chebyshev_pseudospectral"
+r_ngrid = 1
+r_nelement = 1
+r_nelement_local = 1
+r_bc = "periodic"
+r_discretization = "chebyshev_pseudospectral"
+vpa_ngrid = 5
+vpa_nelement = 32
+vpa_L = 3.0
+vpa_bc = "zero"
+vpa_discretization = "gausslegendre_pseudospectral"
+vperp_ngrid = 5
+vperp_nelement = 16
+vperp_L = 1.5
+vperp_discretization = "gausslegendre_pseudospectral"
+vperp_bc = "zero"
+# Fokker-Planck operator requires the "gausslegendre_pseudospectral
+# options for the vpa and vperp grids
+
+[fokker_planck_collisions]
+# nuii sets the normalised input C[F,F] Fokker-Planck collision frequency
+nuii = 1.876334222e-3 #(1/nu_alphae, as computed from input diagnostic)
+Zi = 2.0
+self_collisions = true
+slowing_down_test = true
+frequency_option = "manual"
+use_fokker_planck = true
+sd_density = 1.0
+sd_temp = 0.0025 # TD/Ealpha
+sd_mi = 0.5 # mD/malpha
+sd_me = 0.000013616 # 0.25/1836.0 me/malpha
+sd_q = 1.0
+
+[ion_source]
+active=true
+source_strength=1.0
+source_T=0.005
+source_n=1.0
+r_profile="constant"
+r_width=1.0
+r_relative_minimum=0.0
+z_profile="gaussian"
+z_width=0.1
+z_relative_minimum=0.0
+source_v0 = 1.0
+#source_type="alphas"
+source_type="alphas-with-losses"
+#source_type="beam-with-losses"
+#source_vpa0 = 1.0
+#source_vperp0 = 1.0
+sink_strength = 1.0
+sink_vth=0.07071067811865475                     
+
+[timestepping]
+nstep = 50000
+dt = 5.0e-4
+nwrite = 100
+nwrite_dfns = 100

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

@@ -0,0 +1,71 @@
+# 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
+vpa_IC_option1 = "isotropic-beam"
+#vpa_IC_option1 = "directed-beam"
+#vpa_IC_v01 = 
+#vpa_IC_vth0 =
+#vpa_IC_vpa0 =
+#vpa_IC_vperp0 =
+charge_exchange_frequency = 0.0
+ionization_frequency = 0.0
+constant_ionization_rate = false
+z_ngrid = 1
+z_nelement = 1
+z_nelement_local = 1
+z_bc = "wall"
+z_discretization = "chebyshev_pseudospectral"
+r_ngrid = 1
+r_nelement = 1
+r_nelement_local = 1
+r_bc = "periodic"
+r_discretization = "chebyshev_pseudospectral"
+vpa_ngrid = 5
+vpa_nelement = 32
+vpa_L = 6.0
+vpa_bc = "zero"
+vpa_discretization = "gausslegendre_pseudospectral"
+vperp_ngrid = 5
+vperp_nelement = 16
+vperp_L = 3.0
+vperp_discretization = "gausslegendre_pseudospectral"
+# Fokker-Planck operator requires the "gausslegendre_pseudospectral
+# options for the vpa and vperp grids
+
+[fokker_planck_collisions]
+# nuii sets the normalised input C[F,F] Fokker-Planck collision frequency
+nuii = 1.0
+slowing_down_test = true
+frequency_option = "manual"
+use_fokker_planck = true
+
+[timestepping]
+nstep = 1000
+dt = 1.0e-5
+nwrite = 50
+nwrite_dfns = 50

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

@@ -0,0 +1,65 @@
+# 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
+z_ngrid = 1
+z_nelement = 1
+z_nelement_local = 1
+z_bc = "wall"
+z_discretization = "chebyshev_pseudospectral"
+r_ngrid = 1
+r_nelement = 1
+r_nelement_local = 1
+r_bc = "periodic"
+r_discretization = "chebyshev_pseudospectral"
+vpa_ngrid = 5
+vpa_nelement = 32
+vpa_L = 6.0
+vpa_bc = "zero"
+vpa_discretization = "gausslegendre_pseudospectral"
+vperp_ngrid = 5
+vperp_nelement = 16
+vperp_L = 3.0
+vperp_discretization = "gausslegendre_pseudospectral"
+# Fokker-Planck operator requires the "gausslegendre_pseudospectral
+# options for the vpa and vperp grids
+
+[fokker_planck_collisions]
+# nuii sets the normalised input C[F,F] Fokker-Planck collision frequency
+nuii = 1.0
+slowing_down_test = true
+frequency_option = "manual"
+use_fokker_planck = true
+
+[timestepping]
+nstep = 1000
+dt = 1.0e-5
+nwrite = 50
+nwrite_dfns = 50

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

@@ -63,4 +63,3 @@ nstep = 5000
 dt = 1.0e-2
 nwrite = 5000
 nwrite_dfns = 5000
-split_operators = false

moment_kinetics/src/communication.jl

@@ -120,7 +120,7 @@ function __init__()
     if !MPI.Initialized()
         MPI.Init()
     end
-
+    
     comm_world.val = MPI.COMM_WORLD.val
 
     global_rank[] = MPI.Comm_rank(comm_world)

moment_kinetics/src/coordinates.jl

@@ -192,7 +192,8 @@ function define_coordinate(input, parallel_io::Bool=false; run_directory=nothing
         cell_width, igrid, ielement, imin, imax, igrid_full, input.discretization, input.fd_option, input.cheb_option,
         input.bc, wgts, uniform_grid, duniform_dgrid, scratch, copy(scratch), copy(scratch), scratch_shared, scratch_shared2,
         scratch_2d, copy(scratch_2d), advection, send_buffer, receive_buffer, input.comm,
-        local_io_range, global_io_range, element_scale, element_shift, input.element_spacing_option, element_boundaries)
+        local_io_range, global_io_range, element_scale, element_shift, input.element_spacing_option,
+        element_boundaries)
 
     if coord.n == 1 && occursin("v", coord.name)
         spectral = null_velocity_dimension_info()