Include all input files that I made for transfer, and the files that …

…I used to generate input files/ make plots.

examples/lucas_transfer_input_files/ion_braginskii_rf100/braginskii_T1.0Te0.5_n1.0_rf100.toml

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+[r]
+ngrid = 1
+nelement = 1
+
+[evolve_moments]
+parallel_pressure = true
+density = true
+moments_conservation = true
+parallel_flow = true
+
+[ion_species_1]
+initial_temperature = 1.0
+initial_density = 1.0
+
+[krook_collisions]
+use_krook = true
+frequency_option = "reference_parameters"
+nuii0 = 1.0
+
+[vpa]
+ngrid = 6
+discretization = "chebyshev_pseudospectral"
+nelement = 63
+L = 36.0
+bc = "zero"
+element_spacing_option = "coarse_tails"
+
+[z]
+ngrid = 5
+discretization = "chebyshev_pseudospectral"
+#element_spacing_option = "sqrt"
+nelement = 32
+bc = "wall"
+
+[vpa_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 1.0
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 0.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+#[z_IC_neutral_species_1]
+#initialization_option = "gaussian"
+#temperature_amplitude = 0.0
+#density_amplitude = 0.001
+#density_phase = 0.0
+#upar_amplitude = -1.0
+#temperature_phase = 0.0
+#upar_phase = 0.0
+
+[composition]
+#T_wall = 0.1
+T_e = 0.5
+electron_physics = "boltzmann_electron_response"
+n_ion_species = 1
+n_neutral_species = 0
+ion_physics = "coll_krook_ions"
+
+#[vz_IC_neutral_species_1]
+#initialization_option = "gaussian"
+#density_amplitude = 1.0
+#temperature_amplitude = 0.0
+#density_phase = 0.0
+#upar_amplitude = 0.0
+#temperature_phase = 0.0
+#upar_phase = 0.0
+
+[z_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 0.001
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 1.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+#[neutral_species_1]
+#initial_temperature = 1.0
+#initial_density = 1.0
+
+[ion_source_1]
+source_T = 1.0
+active = true
+source_strength = 1.0
+source_type = "energy"
+z_profile = "super_gaussian_4"
+z_width = 0.275816
+
+[ion_source_2]
+source_T = 0.1
+active = true
+source_strength = 1.0
+z_profile = "wall_exp_decay"
+z_width = 0.15
+
+[timestepping]
+nstep = 60000
+steady_state_residual = true
+dt = 0.000012
+nwrite = 3000
+type = "SSPRK4"
+nwrite_dfns = 3000

examples/lucas_transfer_input_files/ion_braginskii_rf100/braginskii_T1.0Te0.5_n2.0_rf100.toml

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+[r]
+ngrid = 1
+nelement = 1
+
+[evolve_moments]
+parallel_pressure = true
+density = true
+moments_conservation = true
+parallel_flow = true
+
+[ion_species_1]
+initial_temperature = 1.0
+initial_density = 2.0
+
+[krook_collisions]
+use_krook = true
+frequency_option = "reference_parameters"
+nuii0 = 1.0
+
+[vpa]
+ngrid = 6
+discretization = "chebyshev_pseudospectral"
+nelement = 63
+L = 36.0
+bc = "zero"
+element_spacing_option = "coarse_tails"
+
+[z]
+ngrid = 5
+discretization = "chebyshev_pseudospectral"
+#element_spacing_option = "sqrt"
+nelement = 32
+bc = "wall"
+
+[vpa_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 1.0
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 0.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+#[z_IC_neutral_species_1]
+#initialization_option = "gaussian"
+#temperature_amplitude = 0.0
+#density_amplitude = 0.001
+#density_phase = 0.0
+#upar_amplitude = -1.0
+#temperature_phase = 0.0
+#upar_phase = 0.0
+
+[composition]
+#T_wall = 0.1
+T_e = 0.5
+electron_physics = "boltzmann_electron_response"
+n_ion_species = 1
+n_neutral_species = 0
+ion_physics = "coll_krook_ions"
+
+#[vz_IC_neutral_species_1]
+#initialization_option = "gaussian"
+#density_amplitude = 1.0
+#temperature_amplitude = 0.0
+#density_phase = 0.0
+#upar_amplitude = 0.0
+#temperature_phase = 0.0
+#upar_phase = 0.0
+
+[z_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 0.001
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 1.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+#[neutral_species_1]
+#initial_temperature = 1.0
+#initial_density = 1.0
+
+[ion_source_1]
+source_T = 1.0
+active = true
+source_strength = 2.0
+source_type = "energy"
+z_profile = "super_gaussian_4"
+z_width = 0.275816
+
+[ion_source_2]
+source_T = 0.1
+active = true
+source_strength = 2.0
+z_profile = "wall_exp_decay"
+z_width = 0.15
+
+[timestepping]
+nstep = 80000
+steady_state_residual = true
+dt = 0.00005
+nwrite = 4000
+type = "SSPRK4"
+nwrite_dfns = 4000

examples/lucas_transfer_input_files/ion_braginskii_rf100/braginskii_T1.0Te0.5_n3.0_rf100.toml

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+[r]
+ngrid = 1
+nelement = 1
+
+[evolve_moments]
+parallel_pressure = true
+density = true
+moments_conservation = true
+parallel_flow = true
+
+[ion_species_1]
+initial_temperature = 1.0
+initial_density = 2.0
+
+[krook_collisions]
+use_krook = true
+frequency_option = "reference_parameters"
+nuii0 = 1.0
+
+[vpa]
+ngrid = 6
+discretization = "chebyshev_pseudospectral"
+nelement = 63
+L = 36.0
+bc = "zero"
+element_spacing_option = "coarse_tails"
+
+[z]
+ngrid = 5
+discretization = "chebyshev_pseudospectral"
+#element_spacing_option = "sqrt"
+nelement = 32
+bc = "wall"
+
+[vpa_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 1.0
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 0.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+#[z_IC_neutral_species_1]
+#initialization_option = "gaussian"
+#temperature_amplitude = 0.0
+#density_amplitude = 0.001
+#density_phase = 0.0
+#upar_amplitude = -1.0
+#temperature_phase = 0.0
+#upar_phase = 0.0
+
+[composition]
+#T_wall = 0.1
+T_e = 0.5
+electron_physics = "boltzmann_electron_response"
+n_ion_species = 1
+n_neutral_species = 0
+ion_physics = "coll_krook_ions"
+
+#[vz_IC_neutral_species_1]
+#initialization_option = "gaussian"
+#density_amplitude = 1.0
+#temperature_amplitude = 0.0
+#density_phase = 0.0
+#upar_amplitude = 0.0
+#temperature_phase = 0.0
+#upar_phase = 0.0
+
+[z_IC_ion_species_1]
+initialization_option = "gaussian"
+density_amplitude = 0.001
+temperature_amplitude = 0.0
+density_phase = 0.0
+upar_amplitude = 1.0
+temperature_phase = 0.0
+upar_phase = 0.0
+
+#[neutral_species_1]
+#initial_temperature = 1.0
+#initial_density = 1.0
+
+[ion_source_1]
+source_T = 1.0
+active = true
+source_strength = 3.0
+source_type = "energy"
+z_profile = "super_gaussian_4"
+z_width = 0.275816
+
+[ion_source_2]
+source_T = 0.1
+active = true
+source_strength = 3.0
+z_profile = "wall_exp_decay"
+z_width = 0.15
+
+[timestepping]
+nstep = 20000
+steady_state_residual = true
+dt = 0.0001
+nwrite = 1000
+type = "SSPRK4"
+nwrite_dfns = 1000