Input Parameters

The following is a complete list of input parameters available in XGC. This list is generated with the Python script utils/document_inputs.py. Please help us improve the documentation for completeness, consistency and clarity. In the meantime, parameters labeled ‘See Fortran description’ may have more useful documentation here.

adios_param

bool adios_stage_3d = false

Enable/disable Adios stage mode for xgc.3d

bool adios_stage_escaped_ptls = false

Enable/disable Adios stage mode for escape particle diagnostic

bool adios_stage_f0 = false

Enable/disable Adios stage mode for xgc.f0

bool adios_stage_f0_df = false

Enable/disable Adios stage mode for xgc.fsourcediag

bool adios_stage_particle = false

Enable/disable Adios stage mode for xgc.particle

bool adios_stage_restart = false

Enable/disable Adios stage mode for checkpoint file

bool adios_stage_restartf0 = false

Enable/disable Adios stage mode for f0 checkpoint file

analytic_grid_param

double axis_r = 1.5

The r coordinate of the axis of the circular analytic magnetic equilibrium

int nsurfaces = 30

Number of surfaces in the analytic circular grid.

col_param

bool col_accel = false

Artificial collision amplifying.

double col_accel_factor1 = 10.0

Acceleration factor of Range 1

double col_accel_factor2 = 10.0

Acceleration factor of Range 2

int col_accel_n = 2

Number of psi regions to apply artifical accleration to. Maximum is 2.

double col_accel_pin1 = magnetic_field.inpsi

Inner psi value of acceleration Range 1

double col_accel_pin2 = magnetic_field.outpsi - 0.1*psi_range

Inner psi value of acceleration Range 2

double col_accel_pout1 = magnetic_field.inpsi + 0.1*psi_range

Outer psi value of acceleration Range 1

double col_accel_pout2 = magnetic_field.outpsi

Outer psi value of acceleration Range 2

int col_en_col_on = 1

Switch for energy collision

int col_mode = 0

Collision method. 0: No collisions. 1: uses the monte carlo non-conserving collisions. 4: uses the non-linear Fokker Planck Landau collision operator. 5: PETSc Landau AMR collisions.

double col_pin = magnetic_field.inpsi

Minimum of psi range where collisions are performed.

double col_pout = magnetic_field.outpsi

Maximum of psi range where collisions are performed.

int col_max_n_subcycles = 1

Enables collision subcycling. Collision time step of an unconverged vertex will be reduced, increasing the number of cycles of that vertex up to a maximum of col_max_n_subcycles. If it still does not converge, the vertex will not be attempted again.

int col_f_start = 1

The time step at which collisions begin

bool col_moving_frame = true

Switch for moving frame for collisions

int col_period = 3

Frequency of collisions

int col_varying_bg = 0

Switch for background plasma update

int col_vb_m = 50

Resolution of varying background

int col_vb_mtheta = 8

Resolution in theta direction of varying background

int col_vb_period = 1

Frequency of background update for collisions

double col_vb_pin = magnetic_field.inpsi

Inner psi boundary for varying background

double col_vb_pout = std::min(magnetic_field.outpsi, 1.03

Outer psi boundary for varying background

diag_param

bool diag_1d_on = true

Whether to write 1D diagnostics

int diag_1d_period = 10

Number of time steps between diag_1d diagnostic write

bool diag_3d_more = false

Write some additional moments in the diag_3d diagnostic

bool diag_3d_on = true

Whether to write 3D diagnostics

int diag_3d_period = default_period

Number of time steps between 3D diagnostic write

bool diag_col_convergence_stat_on = false

Switches file-output of convergence status of the collision operator on/off

[Used when col_param:col_mode=4]

bool diag_current_drive_on = false

Switches the loop voltage diagnostic on if dynamic current drive is on

int diag_current_drive_period = 1

Output frequency of loop_voltage_diagnostic

bool diag_diff_profiles_on = false

Description needed

int diag_diff_profiles_period = 1

Rate (multiples of sml_f_source_period) at which the profile data is sampled. (Must be compatible with diff_update_period!)

bool diag_f0_df_on = is_on_default

Switch for f0_df (grid-conservation) diagnostic

int diag_f0_df_period = period_default

Output interval for f0_df diagnostic

bool diag_f0_g = false

Whether to additionally write f0_g in the f0 diagnostic

bool diag_f0_n = false

Whether to additionally write f0_n in the f0 diagnostic

bool diag_f0_on = true

Whether to write f0 diagnostic

int diag_f0_period = default_period

Number of time steps between f0 diagnostic write

Make sure period is divisible by f_source_period

int diag_f3d_period = default_period

Number of time steps between f3d diagnostic write

int diag_heat_mode = 2

Heat diagnostic mode - 1 for old mode (rectangle based), 2 for new mode (wall segment based)

int diag_heat_nphi = 64

Number of phi bins for mode 2

int diag_heat_npsi = 1000

Number of psi bins for mode 1

int diag_heat_nr = 100

Number of radial bins in mode 1

int diag_heat_nsection = 1

Number of rectangular sections for mode 1

int diag_heat_nz = 100

Number of vertical bins in mode 1

bool diag_heat_on = false

Whether to write heat diagnostic.

double diag_heat_rmax1 = magnetic_field.bounds.max_r

Maximum r for the first section

double diag_heat_rmax2 = magnetic_field.bounds.max_r

Maximum r for the second section

double diag_heat_rmax3 = magnetic_field.bounds.max_r

Maximum r for the third section

double diag_heat_rmin1 = magnetic_field.bounds.min_r

Minimum r for the first section

double diag_heat_rmin2 = magnetic_field.bounds.min_r

Minimum r for the second section

double diag_heat_rmin3 = magnetic_field.bounds.min_r

Minimum r for the third section

double diag_heat_spacing = 5.0e-3

target spacing for wall segments

double diag_heat_zmax1 = magnetic_field.bounds.max_z

Maximum z for the first section

double diag_heat_zmax2 = magnetic_field.bounds.max_z

Maximum z for the second section

double diag_heat_zmax3 = magnetic_field.bounds.max_z

Maximum z for the third section

double diag_heat_zmin1 = magnetic_field.bounds.min_z

Minimum z for the first section

double diag_heat_zmin2 = magnetic_field.bounds.min_z

Minimum z for the second section

double diag_heat_zmin3 = magnetic_field.bounds.min_z

Minimum z for the third section

int diag_neutral_period = See Fortran description.

See Fortran description.

int diag_particle_mod = 1

Writes every Nth particle (based on GID)

bool diag_particle_on = false

Whether to write diag particles

int diag_particle_period = 1

Number of time steps between particle diagnostic write

int diag_poin_isp = See Fortran description.

See Fortran description.

int diag_poin_nrec = See Fortran description.

See Fortran description.

double diag_ps_pin = 0.80

Psi range of selected particles

double diag_ps_pout = 0.81

Psi range of selected particles

int diag_ps_reset_period = 10

Number of time steps between particle stream diagnostic recording

bool diag_pseudo_inv_on = false

switches pseudo-inverse diagnostics on and off, only used if f0_velocity_interp_use_pseudo_inv = .true.

int diag_tracer_n = See Fortran description.

See Fortran description.

int diag_tracer_period = See Fortran description.

See Fortran description.

int diag_tracer_sp = See Fortran description.

See Fortran description.

bool diag_weight_stats = false

Write some particle weight statistics in the diag_3d diagnostic

diff_param

double diff_bd_in = magnetic_field.inpsi

Inner psi boundary for diffusion

double diff_bd_out = magnetic_field.outpsi

Outer psi boundary for diffusion

double diff_bd_shift_in = See Fortran description.

See Fortran description.

double diff_bd_shift_out = See Fortran description.

See Fortran description.

double diff_bd_width_in = See Fortran description.

See Fortran description.

double diff_bd_width_out = See Fortran description.

See Fortran description.

double diff_bd_width_priv = See Fortran description.

See Fortran description.

bool diff_nonlinear = See Fortran description.

See Fortran description.

bool diff_on = false

Switch for anomalous diffusion

bool diff_pol_peak = See Fortran description.

See Fortran description.

double diff_pol_peak_amp = See Fortran description.

See Fortran description.

double diff_pol_peak_angle = See Fortran description.

See Fortran description.

double diff_pol_peak_width = See Fortran description.

See Fortran description.

int diff_start_time = 1

Start time (in time steps) for anomalous diffusion

bool diff_update_on = 0

Switch for periodic updates of the diffusion coefficients

int diff_update_period = 500

Period in time steps between subsequent updates of the diffusion coefficients

bool diff_use_smoothing = 0

Whether apply poloidal smoothing to the fluid

moments before solving the diffusion equations.

eq_param

int eq_den_rsp_index = 0

Due to quasineutrality, the density of one species should be obtained from that of the others: specify its index here.

int eq_den_rsp_sample_num = 1024

density for the reduced spcies (rsp) is constructed from this number of samples

double eq_den_rsp_xmax = 1.3

normalized value of psi for domain setting psi_norm = [0, xmax], psi = psi_norm * eq_x_psi

std::string eq_dens_diff_file = See Fortran description.

See Fortran description.

int eq_dens_diff_shape = See Fortran description.

See Fortran description.

double eq_dens_diff_v1 = See Fortran description.

See Fortran description.

double eq_dens_diff_v2 = See Fortran description.

See Fortran description.

double eq_dens_diff_v3 = See Fortran description.

See Fortran description.

double eq_dens_diff_v4 = See Fortran description.

See Fortran description.

double eq_dens_diff_x1 = See Fortran description.

See Fortran description.

double eq_dens_diff_x2 = See Fortran description.

See Fortran description.

double eq_dens_diff_x3 = See Fortran description.

See Fortran description.

double eq_dens_diff_x4 = See Fortran description.

See Fortran description.

double eq_dens_diff_x5 = See Fortran description.

See Fortran description.

std::string eq_dens_file = "example.dat", ... [per species] ...

Filename for equilibrium density profile

int eq_dens_shape = 0, ... [per species] ...

Shape of equilibrium density profile

double eq_dens_v1 = 1.0e20, ... [per species] ...

Shape coefficients (m^-3)

double eq_dens_v2 = 0.0, ... [per species] ...

Shape coefficients (m^-3)

double eq_dens_v3 = 0.0, ... [per species] ...

Shape coefficients (m^-3)

double eq_dens_x1 = 0.0, ... [per species] ...

Shape coefficients

double eq_dens_x2 = 0.0, ... [per species] ...

Shape coefficients

double eq_dens_x3 = 0.0, ... [per species] ...

Shape coefficients

std::string eq_fg_flow_file = See Fortran description.

See Fortran description.

int eq_fg_flow_shape = See Fortran description.

See Fortran description.

int eq_fg_flow_type = See Fortran description.

See Fortran description.

double eq_fg_flow_v1 = See Fortran description.

See Fortran description.

double eq_fg_flow_v2 = See Fortran description.

See Fortran description.

double eq_fg_flow_v3 = See Fortran description.

See Fortran description.

double eq_fg_flow_x1 = See Fortran description.

See Fortran description.

double eq_fg_flow_x2 = See Fortran description.

See Fortran description.

double eq_fg_flow_x3 = See Fortran description.

See Fortran description.

std::string eq_fg_temp_file = See Fortran description.

See Fortran description.

int eq_fg_temp_shape = See Fortran description.

See Fortran description.

double eq_fg_temp_v1 = See Fortran description.

See Fortran description.

double eq_fg_temp_v2 = See Fortran description.

See Fortran description.

double eq_fg_temp_v3 = See Fortran description.

See Fortran description.

double eq_fg_temp_x1 = See Fortran description.

See Fortran description.

double eq_fg_temp_x2 = See Fortran description.

See Fortran description.

double eq_fg_temp_x3 = See Fortran description.

See Fortran description.

std::string eq_filename = "example_base.dat"

eq_filename is the name of the equilibrium input

std::string eq_flow_diff_file = See Fortran description.

See Fortran description.

int eq_flow_diff_shape = See Fortran description.

See Fortran description.

double eq_flow_diff_v1 = See Fortran description.

See Fortran description.

double eq_flow_diff_v2 = See Fortran description.

See Fortran description.

double eq_flow_diff_v3 = See Fortran description.

See Fortran description.

double eq_flow_diff_v4 = See Fortran description.

See Fortran description.

double eq_flow_diff_x1 = See Fortran description.

See Fortran description.

double eq_flow_diff_x2 = See Fortran description.

See Fortran description.

double eq_flow_diff_x3 = See Fortran description.

See Fortran description.

double eq_flow_diff_x4 = See Fortran description.

See Fortran description.

double eq_flow_diff_x5 = See Fortran description.

See Fortran description.

std::string eq_flow_file = "example.dat", ... [per species] ...

Filename for equilibrium flow profile

int eq_flow_shape = 0, ... [per species] ...

Shape of equilibrium flow profile

int eq_flow_type = 2, ... [per species] ...

How the flow term is calculated from the equilibrium flow profile. 0: flow = value; 1: flow = value*R; 2: flow = value*R*Bphi/B

double eq_flow_v1 = 0.0, ... [per species] ...

Shape coefficients

double eq_flow_v2 = 0.0, ... [per species] ...

Shape coefficients

double eq_flow_v3 = 0.0, ... [per species] ...

Shape coefficients

double eq_flow_x1 = 0.0, ... [per species] ...

Shape coefficients

double eq_flow_x2 = 0.0, ... [per species] ...

Shape coefficients

double eq_flow_x3 = 0.0, ... [per species] ...

Shape coefficients

std::string eq_g_filename = See Fortran description.

See Fortran description.

std::string eq_m3dc1_filename = See Fortran description.

See Fortran description.

std::string eq_mk_flow_file = See Fortran description.

See Fortran description.

int eq_mk_flow_shape = See Fortran description.

See Fortran description.

int eq_mk_flow_type = See Fortran description.

See Fortran description.

double eq_mk_flow_v1 = See Fortran description.

See Fortran description.

double eq_mk_flow_v2 = See Fortran description.

See Fortran description.

double eq_mk_flow_v3 = See Fortran description.

See Fortran description.

double eq_mk_flow_x1 = See Fortran description.

See Fortran description.

double eq_mk_flow_x2 = See Fortran description.

See Fortran description.

double eq_mk_flow_x3 = See Fortran description.

See Fortran description.

std::string eq_mk_temp_file = See Fortran description.

See Fortran description.

int eq_mk_temp_shape = See Fortran description.

See Fortran description.

double eq_mk_temp_v1 = See Fortran description.

See Fortran description.

double eq_mk_temp_v2 = See Fortran description.

See Fortran description.

double eq_mk_temp_v3 = See Fortran description.

See Fortran description.

double eq_mk_temp_x1 = See Fortran description.

See Fortran description.

double eq_mk_temp_x2 = See Fortran description.

See Fortran description.

double eq_mk_temp_x3 = See Fortran description.

See Fortran description.

double eq_out_decay_factor = 0.1

Profiles decay exponentially to f(sml_outpsi)/decay_factor for psi>sml_outpsi

double eq_out_decay_width = 0.03

Width for exponential decay for psi>sml_outpsi

std::string eq_pinch_v_file = See Fortran description.

See Fortran description.

int eq_pinch_v_shape = See Fortran description.

See Fortran description.

double eq_pinch_v_v1 = See Fortran description.

See Fortran description.

double eq_pinch_v_v2 = See Fortran description.

See Fortran description.

double eq_pinch_v_v3 = See Fortran description.

See Fortran description.

double eq_pinch_v_v4 = See Fortran description.

See Fortran description.

double eq_pinch_v_x1 = See Fortran description.

See Fortran description.

double eq_pinch_v_x2 = See Fortran description.

See Fortran description.

double eq_pinch_v_x3 = See Fortran description.

See Fortran description.

double eq_pinch_v_x4 = See Fortran description.

See Fortran description.

double eq_pinch_v_x5 = See Fortran description.

See Fortran description.

double eq_priv_flux_decay_factor = 0.05

Profiles decay exponentially to f(sml_outpsi)/decay_factor in priv. flux region

double eq_priv_flux_decay_width = 0.015

Width for exponential decay in private flux region

bool eq_set_x2 = false

Determine if there is second (upper) X-point to consider. It does not have to be set unless using the old flx.aif format.

std::string eq_t_diff_file = See Fortran description.

See Fortran description.

int eq_t_diff_shape = See Fortran description.

See Fortran description.

double eq_t_diff_v1 = See Fortran description.

See Fortran description.

double eq_t_diff_v2 = See Fortran description.

See Fortran description.

double eq_t_diff_v3 = See Fortran description.

See Fortran description.

double eq_t_diff_v4 = See Fortran description.

See Fortran description.

double eq_t_diff_x1 = See Fortran description.

See Fortran description.

double eq_t_diff_x2 = See Fortran description.

See Fortran description.

double eq_t_diff_x3 = See Fortran description.

See Fortran description.

double eq_t_diff_x4 = See Fortran description.

See Fortran description.

double eq_t_diff_x5 = See Fortran description.

See Fortran description.

std::string eq_temp_file = "example.dat", ... [per species] ...

Filename for equilibrium temperature profile

int eq_temp_shape = 0, ... [per species] ...

Shape of equilibrium temperature profile

double eq_temp_v1 = 1.0e3, ... [per species] ...

Shape coefficients (ev)

double eq_temp_v2 = 0.0, ... [per species] ...

Shape coefficients (ev)

double eq_temp_v3 = 0.0, ... [per species] ...

Shape coefficients (ev)

double eq_temp_x1 = 0.0, ... [per species] ...

Shape coefficients

double eq_temp_x2 = 0.0, ... [per species] ...

Shape coefficients

double eq_temp_x3 = 0.0, ... [per species] ...

Shape coefficients

double eq_x2_r = 1.7

R value of second (upper) X-point

double eq_x2_z = 10.0

Z value of second (upper) X-point

std::string eq_zeff_file = "zeff.dat"

Filename for Z-effective profile for radiation source

int eq_zeff_shape = 0

Shape of analytic Z-effective profile

double eq_zeff_v1 = 1.0

Shape coefficients for analytic Z-effective profile

double eq_zeff_v2 = 1.0

Shape coefficients for analytic Z-effective profile

double eq_zeff_v3 = 1.0

Shape coefficients for analytic Z-effective profile

double eq_zeff_x1 = 1.0

Shape coefficients for analytic Z-effective profile

double eq_zeff_x2 = 0.1

Shape coefficients for analytic Z-effective profile

double eq_zeff_x3 = 0.0

Shape coefficients for analytic Z-effective profile

f0_param

double f0_coarse_graining_alpha = 1.0e-3

Description needed

bool f0_coarse_graining_on = false

Description needed

int f0_nmu = 31

Resolution of velocity space in perpendicular direction. Total perpendicular grid points is f0_nmu+1

int f0_nvp = 15

Resolution of velocity space in parallel direcion. Total parallel grid points is 2*f0_nvp+1

double f0_smu_max = 3.0

Maximum perpendicular velocity of velocity space grid, normalized to thermal velocity

bool f0_update_analytic = false

Switch on/off the update of the analytic part of the distribution function

double f0_update_analytic_alpha = f0_grid_alpha

Separate alpha from sml_f0_grid_alpha for Maxwellian contribution

bool f0_update_analytic_local = false

If .false. –> flux-surface average update, .true. –> local

double f0_update_analytic_damp_width = 0.5

For width of \(\exp^{-(x/w)^2}\) damping factor for updating density/temperature of the analytical f0

bool f0_upsample = See Fortran description.

See Fortran description.

int f0_upsample_cell_target = See Fortran description.

See Fortran description.

int f0_upsample_corner_cell_target = See Fortran description.

See Fortran description.

int f0_upsample_rate = See Fortran description.

See Fortran description.

bool f0_upsample_skip_full_bins = See Fortran description.

See Fortran description.

int f0_upsample_tile_size = See Fortran description.

See Fortran description.

bool f0_velocity_interp_force_pseudo_inv = See Fortran description.

See Fortran description.

bool f0_velocity_interp_pseudo_inv_delta_grid = See Fortran description.

See Fortran description.

int f0_velocity_interp_pseudo_inv_order = 2

1 (linear) or 2 (quadratic) pseudo-inverse interpolation, only used if f0_velocity_interp_use_pseudo_inv = .true.

bool f0_velocity_interp_pseudo_inv_particles_to_grid_petsc = See Fortran description.

See Fortran description.

bool f0_velocity_interp_use_pseudo_inv = false

Whether to use pseudo-inverse interpolation between particles and velocity grid

double f0_vp_max = 3.0

Maximum parallel velocity of velocity space grid, normalized to thermal velocity

field_decomp_param

int n_ghost_planes = 1

Number of ghost planes on each side of a subdomain. Toroidal overlap is not required, but may be useful for performance since it reduces the need to shift particles between ranks.

int n_ghost_vertices = 3000

Number of ghost vertices on each side of the subdomain within the poloidal plane. It must be large enough to ensure that all neighboring vertices of the subdomain are present. However, this depends entirely on the grid since there is no guarantee on the order of vertices in an XGC grid.

int n_phi_domains = n_ranks

Number of subdomains in the toroidal direction. By default, there is no poloidal decomposition.

int n_ranks = 6

Number of ranks across which the fields are decomposed. The larger this number, the less memory is used per rank. However, for best performance, this number should be as small as possible.

init_cond

bool ic_add_zonal = false

Include a n=0 component

double ic_amp = 1.0e-4

Amplitude of the n!=0 initial perturbation

double ic_amp_0 = 0.0

Amplitude of the n=0 initial perturbation

int ic_delta_n = wedge_n

Spacing between toroidal modes

int ic_n_modes = (int

Number of toroidal modes

double ic_phi_sign = magnetic_field.bp_sign*magnetic_field.bt_sign

Invert the sign of toridal direction in the eikonal

bool ic_poloidal_gaussian = false

Apply a gaussian modulation to the poloidal profile

double ic_psi_0 = 0.0

Center of radial gaussian modulation

double ic_q_sign = magnetic_field.bp_sign

Invert the sign of q in the eikonal

bool ic_radial_gaussian = false

Apply a gaussian modulation to the radial profile

bool ic_resonant_modes = true

use field aligned resonant modes

int ic_resonant_nmax_real = 1

Maximal (real, not wedge) toroidal mode number in initial density when using sml_field_aligned_initial=.true. and ic_resonant_modes=.true.

int ic_resonant_nmin_real = 1

Minimal (real, not wedge) toroidal mode number in initial density when using sml_field_aligned_initial=.true. and ic_resonant_modes=.true.

double ic_sigma_psi = 0.5

Width of radial gaussian modulation

double ic_sigma_theta = 0.784

Width of poloidal gaussian

double ic_theta_0 = 0.0

Center of poloidal gaussian

load_balance_param

double max_mem_redist_gb = 10.0

Sets the maximum amount of memory per rank that can be allocated to particles, in gigabytes.

double threshold_to_rebalance = 0.02

How much better the projected timing of a proposed load redistribution must be than the current distribution in order to adopt the new one. e.g. 0.02 sets a threshold of 2% better.

std::string update_method = "NoHistory"

Methods for updating internal model of load distribution. “NoHistory” uses only the most recent time step, while “ExpHistory” averages the existing model with the new step’s timing information. Does not apply when weighting_algorithm is “Fortran”.

bool verbose = false

Verbose output of the internal load distribution model and load balancing decisions.

std::string weighting_algorithm = "Fortran"

Load balancing method. “Fortran” is the default since the newer methods are experimental. “ParticleBalance” does not incorporate timing data, but only tries to equally distribute particles. “SingleRegionBalance” currently tries to balance the push.

mon_param

int mon_flush_count = 12

Number of timing files to write. Set to 0 to use mon_flush_freq

int mon_flush_freq = 0

Frequency of timing files, if mon_flush_count is set to 0

mr_param

int mr_factor1 = 1

Unused

int mr_factor2 = 1

Unused

int mr_factor3 = 1

Unused

int mr_factor4 = 1

Unused

int mr_factor5 = 1

multirate timestepping for core region ions; mr_ratio (> 1) is the

factor used to accelerate the core region physics.

double mr_psi_max5 = 0.0

maximum normalized psi value of each multirate region

neu_param

bool neu_adjust_n0 = See Fortran description.

See Fortran description.

int neu_background_period = See Fortran description.

See Fortran description.

double neu_delta_n = See Fortran description.

See Fortran description.

double neu_delta_theta = See Fortran description.

See Fortran description.

double neu_dt = See Fortran description.

See Fortran description.

bool neu_ebin_log = true

Description needed

double neu_ebin_max = 100.0

Description needed

double neu_ebin_min = 0.1

Description needed

int neu_ebin_num = 1

Description needed

bool neu_exclude_private = See Fortran description.

See Fortran description.

double neu_inpsi = See Fortran description.

See Fortran description.

int neu_istep_max = See Fortran description.

See Fortran description.

double neu_lost_rate_max = See Fortran description.

See Fortran description.

double neu_n0 = See Fortran description.

See Fortran description.

int neu_num = See Fortran description.

See Fortran description.

double neu_peak_theta = See Fortran description.

See Fortran description.

double neu_recycle_rate = See Fortran description.

See Fortran description.

bool neu_source_match_flux = See Fortran description.

See Fortran description.

int neu_start_time = 2

Start time of neutral recycling in ion time steps

double neu_temp0 = See Fortran description.

See Fortran description.

double neu_theta_x = See Fortran description.

See Fortran description.

performance_param

bool backup_particles_on_device = false

Whether to store backup of electrons in device memory. Saves on host-device communication, but uses significantly more device memory.

bool calculate_phi_ff_on_device = false

With this option, potential is communicated and the electric field is calculated on every MPI process. This means additional computation, but less communication. This tradeoff is probably beneficial on all current flagship platforms, but this has not been verified.

bool col_async_reassign = false

Asynchronously transfer collision workload between MPI ranks

[Used when col_param:col_mode=4]

std::string collisions_solver = "lapack"

Which collisions solver to use.

“lapack” is always used for CPU-only simulations

“ginkgo” is available for GPU and improves performance

[Used when col_param:col_mode=4]

double ginkgo_residual_reduction = 1.0e-16

For the Ginkgo solver, the residual reduction

int ginkgo_max_iterations = 300

For the Ginkgo solver, the maximum number of iterations

bool decompose_fields = false

Not ready for use. This option splits field quantities used for the electron push kernel so that not every MPI process contains the field information of the entire simulation domain.

std::string gyro_comm_method = "PlaneComm"

Different methods for storing gyroaverage matrices.

“PlaneComm” assigns each gyromatrix to a separate MPI process on each plane

“PackedPlaneComm” assigns each gyromatrix to multiple MPI process on each plane and communicates the results locally. This is not currently supported

“SelfComm” stores every gyromatrix on each MPI process, reducing communication but increasing storage requirements and computation.

double initial_ptl_res_margin = 1.1

The particles are allocated with this initial buffer factor to delay or avoid having to reallocate these large arrays later in the simulation

int mesh_batch_size = default_batch_size

Collisions are batched (multiple vertices run in parallel) for better performance. The best value may vary by platform. Typically higher is better (for GPU simulations) but memory usage is linearly proportional to this value.

[Used when col_param:col_mode=4]

bool particles_resident_on_device = default_residence_option(

Sets particle information to reside in device memory. This improves performance by reducing host-device communication. Particles are still sent back to host memory for some operations. This option can and should be used on platforms with sufficient device memory, which includes all flagship platforms as of 2024.

bool stream_particles = default_streaming_option(

Streams particles in chunks to hide time spent on host-device communication while not increasing device memory usage. This probably isn’t currently very helpful for performance, and is not actively supported.

bool use_unfused_electron_push_kernel = false

Use unfused electron push kernel. This algorithm may be faster than the default push algorithm

ptb_3db_param

int ptb_3db_dasdt_opt = 1

Selector for how to compute dAs/dt for RMP penetration

double ptb_3db_em_bd_width = 0.05

Blending width between A_s and full A representation

bool ptb_3db_em_full_spec = false

If false, only modes |m/q-n|<=sml_mode_select_mres_q are retained,

if true, the remaining modes are retained in toroidal Fourier representation

but without RMP response (Always true for ES).

double ptb_3db_em_inpsi = -1.0

Inner boundary of RMP representation in A_s

double ptb_3db_em_outpsi = 1.1

Outer boundary of RMP representation in A_s

int ptb_3db_es_to_em_dt_ratio = 1

Ratio of ES to EM time step size in RMP penetration calculation with ptb_3db_mode==2

(also: the number of time steps over which the perturbed current is averaged)

int ptb_3db_file_format = 1

Format of input file with perturbed field data: (0) toroidal Fourier coefficients in R,Z, (1) read from M3D-C1 file using fusion-io (2) Generic test data (no file)

std::string ptb_3db_filename = See Fortran description.

See Fortran description.

int ptb_3db_m3dc1_timeslice = See Fortran description.

See Fortran description.

int ptb_3db_mode = 0

Mode of operation: (0) static RMP field (ES), or fully self-consistent RMP field (EM version)

(2) self-consistent RMP field with time-averaged field-equations (EM version)

int ptb_3db_mstep_em = mstep

Number of EM time steps in RMP penetration calculation with ptb_3db_mode==2

int ptb_3db_mstep_es = 0

Number of ES time steps in RMP penetration calculation with ptb_3db_mode==2

double ptb_3db_mult_factor = See Fortran description.

See Fortran description.

int ptb_3db_nr = See Fortran description.

See Fortran description.

int ptb_3db_ntor_min = See Fortran description.

See Fortran description.

int ptb_3db_num_mpol = See Fortran description.

See Fortran description.

int ptb_3db_num_ntor = 1

Number of toroidal mode numbers (<= sml_nphi_total)

int ptb_3db_nz = See Fortran description.

See Fortran description.

int ptb_3db_rampup_time = 1000

Number of time steps over which the perturbed field is ramped up

bool ptb_3db_rampup_vac = true

(.true.) Ramp up perturbed field slowly, (.false.) turn on perturbed field abruptly

double ptb_3db_screening_fac1 = See Fortran description.

See Fortran description.

double ptb_3db_screening_fac2 = See Fortran description.

See Fortran description.

bool ptb_3db_screening_on = See Fortran description.

See Fortran description.

double ptb_3db_screening_psi1 = See Fortran description.

See Fortran description.

double ptb_3db_screening_width1 = See Fortran description.

See Fortran description.

double ptb_3db_screening_width2 = See Fortran description.

See Fortran description.

bool ptb_3db_single_mode_input = See Fortran description.

See Fortran description.

int ptb_3db_single_mode_ntor = See Fortran description.

See Fortran description.

int ptb_3db_start_time = 1

Time step in which perturbed field is switched on

double ptb_3db_update_alpha = See Fortran description.

See Fortran description.

ptl_param

double ptl_charge_eu = -1.0, ... [per species] ...

Particle charge in EU

int ptl_collision_grid_index = nonadiabatic_idx, ... [per species] ...

Which collision grid to use. This option can be used to assign species to share a collision grid, improving performance of the collision operator. By default, each species has its own collision grid. ptl_collision_grid_index = 0, 1, 2, 2 would mean the third and fourth species share a collision grid.

bool ptl_dynamic_f0 = default_dynamic_f0, ... [per species] ...

Whether f0 can evolve in time

std::string ptl_f_analytic_shape = default_f_analytic_shape, ... [per species] ...

f_analytic_shape shape: Maxwellian, SlowingDown or None

std::string ptl_f_init_file = "i_initial_f.bp", ... [per species] ...

Input file name for initial distribution

std::string ptl_input_file_dir = "./"

Directory of input file for loading initial distribution

bool ptl_is_gyrokinetic = !species_is_electron, ... [per species] ...

Whether particles of this species are gyrokinetic or drift kinetic

std::string ptl_marker_type = "TotalF", ... [per species] ...

Marker type: ‘ReducedDeltaF’, ‘TotalF’, ‘FullF’, or ‘None’ (placeholder for adiabatic species). excluding the neoclassical terms in the gyrokinetic equation

double ptl_mass_au = 2.0e-2, ... [per species] ...

Particle mass in AU

bool ptl_maxwellian_init = true, ... [per species] ...

whether initial distribution is maxwellian

int ptl_nsp = 1

Number of ion species in the simulation

int ptl_num = 0

Initial number of particles per species per OpenMP thread per MPI rank. This method is an alternative to ptl_num_per_vertex. All species have the same value.

int ptl_num_per_vertex = 10000, MAIN_ION

Initial number of particles of each species per vertex per plane. e.g. Doubling the number of planes will double the number of particles in the simulation. The value refers to the average number of particles per vertex. It does not imply that each vertex has this number of associated particles initialized; the spatial distribution is controlled by other parameters.

double ptl_special_en_ev = 7205.0

Initial energy of particle if using sml_load_single_ptl

double ptl_special_phi = 0.0

Initial phi coordinate of particle if using sml_load_single_ptl

double ptl_special_pitch = 0.276

Initial pitch angle of particle if using sml_load_single_ptl

double ptl_special_r = magnetic_field.equil.axis.r

Initial r coordinate of particle if using sml_load_single_ptl

double ptl_special_z = magnetic_field.equil.axis.z

Initial z coordinate of particle if using sml_load_single_ptl

std::string ptl_weight_evo_eq = default_weight_evo_eq, ... [per species] ...

Specifies the weight evolution equation method: Direct, PDE, or None.

- Direct integration: Is used in the Total-F method, where the source term and particle contributions are evaluated separately.

Refer to Section II C of Hager et al., Phys. Plasmas 29, 112308 (2022) for more details.

- PDE: The PDE (Partial Differential Equation) method, where the source term and particle contributions are evaluated together (delta-f).

- None: No weight evolution is applied.

rad_param

std::string rad_filename = "mist_adas_xgc1.dat"

Filename containing radiation information

double rad_impurity_fraction = 0.1

simplest model : n_imp / n_e is constant

double rad_inpsi = magnetic_field.inpsi

Inner boundary for impurity radiation

double rad_outpsi = magnetic_field.outpsi

Outer boundary for impurity radiation

int rad_species = -1

Which species to use for density if not using a Z-effective profile

int rad_start_time = 1

Start time for impurity radiation in time steps

bool rad_use_fix_charge = true

Use fixed Z for impurity

bool rad_use_zeff_profile = false

Use a psi-dependent Z-effective for radiation.

double rad_z = 6.0

! fixed Z for impurity - Z_Carbon –> 6, Z^2 –> 36

resamp_param

bool resamp_discard_var_bins = false

Discard resampled bins that increase the variance by factor of resamp_var_limit

bool resamp_distribute_evenly_subbins = false

Whether to fill/remove evenly in 1x1 velocity cells in the bin when resamp_tile_size > 1 and upsampling/downsampling

std::string resamp_down_choice = "weight"

option arg for downsampled new particle selection: ‘random’,’weight’,’weight+replace’,’volume’

weight: keep particles with largest w0*w1 absolute weight, deterministic

weight+replace: keep particles with largest w0*w1 absolute weight, allow multiple copies of same particle

if split weight is still larger than next unsplit particle

volume: keep particles with largest phase space volume, deterministic

bool resamp_fill_empty = false

Whether to fill empty bins

bool resamp_fullf_on = false

Whether to resample the full-f weights in addition to delta-f weights

bool resamp_grid_ineq_on = false

Switch for using inequality constraints for the grid charge for resampling

double resamp_highv_max = 10.0

energy cutoff of the high velocity bins v_para>f0_vp_max and v_perp>f0_smu_max

double resamp_highv_max_ratio = 4.0

Downsampling threshold for high-velocity bins

double resamp_ineq_tol = 1.0e-4

Threshold for relative error in the inequality constraints in the QP optimization

double resamp_ineq_tol_max = 1.0e-3

Maximal threshold for relative error in inequality constraints for retried bins

bool resamp_keep_downsamples = false

Retain downsampling results with high variance, mainly for preventing buildup. Only relevant if resamp_discard_var_bins is .true.

bool resamp_keep_upsamples = false

Retain upsampling results with high variance, for filling for pseudoinverse. Only relevant if resamp_discard_var_bins is .true.

double resamp_max_ratio = 1.5

max ratio of (# of ptl)/(target # of ptl) in bin for auto-downsample

double resamp_max_shift = 0.1

maximum shift in local coordinates for ‘copy’, ‘weight+replace’

int resamp_max_target = 4

Overrides the number of constraints in determining the target # of ptl of a bin

double resamp_min_ratio = 0.5

min ratio of (# of ptl)/(target # of ptl) in bin for auto-upsample

std::string resamp_node_file = "resample.node"

File containing the vertex positions of the mesh for which to resample

int resamp_nphi_new = 1

Number of poloidal planes in simulation with new mesh

bool resamp_output_problem_bins = false

Switch to output failed or high-variance bins as to .bp files

int resamp_rate = 2

timesteps between subsequent resamples, placedholder, in practice ~ sml_f_source_period

bool resamp_restart = false

Perform resampling before dumping the final restart file

bool resamp_restart_read = false

Whether to read a restart file written from a simulation with different grid

bool resamp_retry = false

Retry QP optimization for failed bins with relaxed inequality constraints

int resamp_tile_size = 2

Bin size on the velocity space grid in cells (not vertices) (input parameter)

std::string resamp_up_choice = "random"

option arg for upsampled new particle selection: ‘random’,’copy’,’poisson’ currently added

random: random velocity coordinates for new particles in bin

copy: add new particles as copies of old particles with largest absolute w0*w1 weight

poision: add new particles as poisson disc samples generated from the old particle set.

double resamp_var = 1.0e4

threshold for relative standard deviation in bin for auto-resample

double resamp_var_limit = 3.0

Increase in relative bin variance for flagging for possible rejection

sml_param

bool f0_update_analytic = false

Switch on/off the update of the analytic part of the distribution function

bool f0_update_analytic_local = false

If .false. –> flux-surface average update, .true. –> local

bool sml_00_efield = true

Flux-surface averaged potential not used for calculating the electric field if .false.

int sml_00_npsi = 150

Size of the uniform 1D psi-grid

bool sml_0m_efield = true

The axisymmetric potential variation \(\langle \phi-\langle\phi\rangle\rangle_T\) is

set to zero if .false.

bool sml_3db_on = false

Toggle for ptb_3db

int sml_add_pot0 = 0

Additional electrostatic potential: (0) for off, (1) for reading data from file

(2) for simple neoclassical axisymmetric field (not operational)

std::string sml_add_pot0_file = See Fortran description.

See Fortran description.

int sml_add_pot0_mixing_time = See Fortran description.

See Fortran description.

bool sml_adiabatic_from_poisson = See Fortran description.

See Fortran description.

bool sml_ampere_natural_boundary = false

Ampere counterpart of sml_poisson_natural_boundary.

When using this option .true., should we force sml_poisson_natural_boundary to .true.?

double sml_bd_ext_delta1 = 0.01

Outward shift of the inner boundary of the axisymmetric

Poisson solver relative to sml_inpsi (in norm. pol. flux)

double sml_bd_ext_delta1h = bd_ext_delta1

Outward shift of the inner boundary of the non-axisymmetric

Poisson solver relative to sml_inpsi (in norm. pol. flux)

double sml_bd_ext_delta2 = 0.02

Outward shift of the inner boundary of the RHS of the axisymmetric

Poisson solver relative to sml_inpsi (in norm. pol. flux)

double sml_bd_ext_delta2h = bd_ext_delta2

Outward shift of the inner boundary of the RHS of the non-axisymmetric

Poisson solver relative to sml_inpsi (in norm. pol. flux)

double sml_bd_ext_delta3 = bd_ext_delta1

Inward shift of the outer boundary of the axisymmetric

Poisson solver relative to sml_outpsi (in norm. pol. flux)

double sml_bd_ext_delta3h = bd_ext_delta3

Inward shift of the outer boundary of the non-axisymmetric

Poisson solver relative to sml_outpsi (in norm. pol. flux)

double sml_bd_ext_delta4 = bd_ext_delta2

Inward shift of the outer boundary of the RHS of the axisymmetric

Poisson solver relative to sml_outpsi (in norm. pol. flux)

double sml_bd_ext_delta4h = bd_ext_delta4

Inward shift of the outer boundary of the RHS of the non-axisymmetric

Poisson solver relative to sml_outpsi (in norm. pol. flux)

double sml_bd_ext_delta_ai = 0.0

Shift of inner boundary of n!=0 Ampere solver (LHS) outwards relative to sml_inpsi

double sml_bd_ext_delta_ao = 0.0

Shift of outer boundary of n!=0 Ampere solver (LHS) inwards relative to sml_outpsi

bool sml_bd_ext_delta_in_simple00 = false

If .true., the outer boundary of the simple 1D Poisson solver that provides the initial guess of the flux-surface averaged potential is determined as the minimum of [sml_outpsi-sml_bd_ext_delta3,psi_xpt-sml_bd_ext_delta4] instead of [sml_outpsi-sml_bd_ext_delta3,psi_xpt].

double sml_bd_ext_delta_ji = 0.0

Shift of inner boundary of n!=0 Ampere solver (RHS=current density) outwards relative to sml_inpsi

double sml_bd_ext_delta_jo = 0.0

Shift of outer boundary of n!=0 Ampere solver (RHS) inwards relative to sml_outpsi

double sml_bd_ext_near_wall = 0.0

To move the outer boundary of the Poisson solver away from the inner wall (in m)

double sml_bd_max_r = 1.0e3

Minimum R of simulation

double sml_bd_max_z = 1.0e3

Maximum Z of simulation

double sml_bd_min_r = 1.0e-4

Minimum R of simulation

double sml_bd_min_z = -1.0e3

Maximum Z of simulation

int sml_bounce = is_core_simulation ? 2 : 1

Bounce routine switch 0 for off, 1 for inner boundary, 2 for both boundaries

double sml_bounce_buffer = 0.0

Buffer width between sml_outpsi and where the particle actually bounces (must be >=0)

int sml_bounce_zero_weight = 0

If ==1 and bounce>0, set particle weights to zero after bouncing from the outer boundary

double sml_bp_sign = 1.0

Option to flip sign of poloidal field

double sml_bt_sign = -1.0

Option to flip sign of toroidal field

double sml_core_ptl_fac = See Fortran description.

See Fortran description.

double sml_core_ptl_psi = See Fortran description.

See Fortran description.

bool sml_create_analytic_equil = false

Creates a simple analytic magnetic field instead of reading from a file

bool sml_create_analytic_grid = false

Option to use a generated grid instead of reading a grid from file. The grid is composed of concentric circles of vertices. analytic_grid_param can be used to control basic grid properties.

Keep analytic grid options simple: number of surfaces, and axis_r

bool sml_current_drive_on = false

Whether to use dynamic current drive via adjustments of the loop voltage

The controller output is implemented as

:math:`V_{loop} = 2pi R eta_parallel P left[Delta j_parallel + I int_0^t Delta j_parallel mathrm{d}tau + D frac{partial Delta j_parallel}{partial t} right] `

Time integral and derivative are with respect to the ion time step instead of time, so \(1/I\) is the integration time scale,

and \(D\) is the derivative time scale

bool sml_dpot_bd_apply = false

Damp (n=0,m>0) potential towards the magnetic axis

double sml_dpot_bd_width = 0.02

Decay length (normalized flux) for (n=0,m>0) potential towards the magnetic axis

double sml_dpot_te_limit = 64.0

Max absolute value of dpot/temp in getf0

double sml_dpot_te_limit_n0 = 64.0

Limits the magnitude of the normalized axisymmetric potential e*dphi_0/T_e

bool sml_drift_on = true

Toggle for using drift

double sml_dt = 0.001

Time step (s)

bool sml_dwdt_exb_only = false

excluding grad-b drift in dwdt

bool sml_dwdt_fix_bg = false

1-w factor in dwdt

std::string sml_ele_file = "example_file.ele"

The element file

bool sml_electron_on = false

Use kinetic electrons

bool sml_em_b_para_eff = false

Effective dB_|| via a modified grad-B drift (Joiner et al., PoP, 2010)

bool sml_em_control_variate = false

Switch for use of control variate method

int sml_em_control_variate_niter = 1

Number of iterations for Ampere solve with control-variate method

bool sml_em_dasdt_filter_on = false

Switch for applying Fourier filters on RHS of dAs/dt equation (pullback mode 4)

bool sml_em_dasdt_hypvis = false

Use radial hyperviscosity in dA_s/dt (push_As)

bool sml_em_exclude_private = true

Makes the private flux region electrostatic if .true.

bool sml_em_mixed_variable = true

Switch for use of mixed-variable formulation

bool sml_em_n0 = false

Include n=0 electromagnetic mode

double sml_em_pullback_dampfac = 1.0

Damping term gamma on -b.grad(phi) in pullback mode 4

std::string sml_em_pullback_method = "Electrostatic"

“Electrostatic”: mixed-variable pullback with dA_s/dt=0,

“IdealMHD”: pullback using Ohm’s law dA_s/dt + b.grad(phi) = 0

int sml_em_pullback_mode = 3

(3) mixed-variable pullback with dA_s/dt=0,

(4) pullback using Ohm’s law dA_s/dt + b.grad(phi) = 0

bool sml_em_use_dpot_te_limit = false

In EM simulation: whether to force usage of the min-max limiter on the turbulent potential fluctuation

double sml_en_order_kev = 0.2

Characteristic ion energy (keV) –> controls reference time (toroidal ion transit time)

bool sml_exclude_private = false

This is already in Simulation class; should consolidate

bool sml_exclude_private_turb = true

If .true. the private-flux region has no turbulence

double sml_f0_grid_alpha = 0.0

Fraction of the particle weight that is transferred to the background

distribution function (particle noise control) every

sml_f_source_period time steps. As a rule of thumb,

sml_f0_grid_alpha=sml_dt*sml_f_source_period can be used.

int sml_f0_grid_alpha_start = 1

For delayed onset of total-f particle noise control. (must be >=1)

Values >1 cause a linear ramp-up of sml_f0_grid_alpha from 0

to its input value from time step 1 to sml_f0_grid_alpha_start

double sml_f0_grid_init_ptl_imbal = See Fortran description.

See Fortran description.

int sml_f0_grid_lbal_period = See Fortran description.

See Fortran description.

double sml_f0_grid_max_ptl_imbal = See Fortran description.

See Fortran description.

double sml_f0_grid_min_ptl_imbal = See Fortran description.

See Fortran description.

int sml_f_source_period = 1

Period (in time steps) of when f_source is called

bool sml_ff_boundary_zero_p = false

zero out p for non-exist field following position.

int sml_ff_order = 4

Order of RK scheme used for field following. Can be 1, 2, or 4.

int sml_ff_step = 2

Number of steps taken when projecting the particle location onto the midplane

bool sml_field_aligned_initial = false

Use field aligned initial condition

bool sml_field_solver = true

Whether to solve for fields. Scatter and solve are skipped if set to false

bool sml_flat_electron_density = false

In case of adiabatic electrons, whether to use a uniform electron background density

bool sml_flat_marker = true

Use flat marker distribution function when set to .true.

Marker distribution g is constant up to v<= sml_flat_marker_decay_start[1/2]

and decays exponentially from there up to v<= sml_flat_marker_cutoff. The decay

length is sml_flat_marker_width.

Does not applied to FullF

double sml_flat_marker_cutoff1 = 4.0

Normalized (to \(v_{th}\)) parallel velocity cutoff of flat marker distribution

double sml_flat_marker_cutoff2 = flat_marker_cutoff1

Like sml_flat_marker_cutoff1 but for the perpendicular velocity

double sml_flat_marker_decay_start1 = 3.5

Normalized (to \(v_{th}\)) velocity at which the marker distribution decays exponentially

double sml_flat_marker_decay_start2 = flat_marker_decay_start1

Like sml_flat_marker_decay_start1 but for the perpendicular velocity

double sml_flat_marker_width1 = 0.5

Decay length of flat marker distribution in the normalized (to \(v_{th}\)) parallel velocity

double sml_flat_marker_width2 = flat_marker_width1

Like sml_flat_marker_width1 but for the perpendicular velocity

bool sml_grad_psitheta = false

This is already in Simulation class; should consolidate

double sml_gradpsi_limit = 1.0e-3

If \(|\nabla\psi|\) is smaller than this threshold, \(\nabla\psi\) is computed

int sml_grid_nrho = 6

Size of the gyroradius grid (should be such that the resolution is >= 0.5 rho_i)

int sml_guess_table_size = 500

Size of the hash table used to narrow down the number of triangles in which to search a particle

bool sml_helmholtz_spectral = false

Whether to solve Helmholtz-type equations with toroidally spectral solver

bool sml_heuristic_priv_pot = false

Override the Poisson solver in the private region and replace the solution by

the separatrix potential scaled with the initial electron temperature

bool sml_ignore_f0g = false

Ignore f0g in f0 calculation. When true, it skips the update of den_f0_h, instead

using the initialized value (which is zero). This is helpful to density conservation

of heating when f0g is noisy due to insufficient number of particles

int sml_increase_ptl_factor_int = 1

the factor to increase when sml_increase_ptl_tor

double sml_increase_ptl_rand_mu = 1.0e-4

random noise to rho_parallel (v_parallel) - to avoid identical marker of sml_increase_ptl_factor_int

double sml_increase_ptl_rand_phi = 1.0e-1

random noise to phi (applied to core only) to avoid identical marker of sml_increase_ptl_factor_int

double sml_increase_ptl_rand_vp = 1.0e-4

random noise to mu - to avoid identical marker of sml_increase_ptl_factor_int

double sml_increase_ptl_rand_w0 = 1.0e-4

random noise to w0 - to avoid identical marker of sml_increase_ptl_factor_int

double sml_increase_ptl_rand_w1 = 1.0e-4

random noise to w1 - to avoid identical marker of sml_increase_ptl_factor_int

bool sml_increase_ptl_tor = false

increase # of particle with different toroidal angle when reading restart file

double sml_initial_deltaf_noise = 1.0e-3

Delta-f particle weights are initialized with this level of noise

double sml_inpsi = 0.0

Inner psi boundary for the simulation

std::string sml_input_file_dir = "./"

Directory containing the grid files

bool sml_iter_solver = true

Split Poisson equation into axisymmetric and

non-axisymmetric parts. The axisymmetric part has the

flux-surface averaged potential on the RHS. Solve

iteratively by lagging the RHS potential by one

iteration. Stop after sml_iter_solver_niter iterations.

If .false., split Poisson equation into

flux-surface averaged part and rest (assuming that the

polarization term commutes with the flux-surface

average) and the rest; solve in two steps.

double sml_iter_solver_atol = See Fortran description.

See Fortran description.

bool sml_iter_solver_converge = false

If .true., keep taking iterations in PETSc until termination criteria is met,

i.e. until a residual tolerance is reached or it is determined that the iterations

have diverged or exceeded sml_iter_solver_max_it. If .false., take a fixed number

of iterations set from sml_iter_solver_niter.

int sml_iter_solver_max_it = See Fortran description.

See Fortran description.

int sml_iter_solver_niter = See Fortran description.

See Fortran description.

int sml_iter_solver_precond_type = See Fortran description.

See Fortran description.

double sml_iter_solver_rtol = See Fortran description.

See Fortran description.

bool sml_limit_marker_den = false

Whether to limit marker density

double sml_limit_marker_den_fac = See Fortran description.

See Fortran description.

bool sml_load_single_ptl = false

Option to run simulation with a single particle. The particle’s initial phase is determined by the inputs ptl_special_r etc. This option overrides ptl_num and ptl_num_per_vertex

bool sml_loop_voltage_fsa = true

Make loop voltage and current drive flux-functions if true (default: true)

bool sml_loop_voltage_on = false

Inductive current drive: loop voltage (from Faraday’s law curl(E)=-dB/dt)

double sml_low_mu_fill_population = 0.0

Used for filling the low-mu range of velocity space if sml_marker_temp_factor3>1

0.0 –> all markers in low-mu range, 1.0 –> no low-mu filling (only if sml_flat_marker=.false.)

double sml_marker_min_temp = 10.0

minimum temperature of markers (only if sml_flat_marker=.false.)

double sml_marker_temp_factor = 1.0

Initial loading with Maxwellian marker distribution with virtual temperature

\(T_{marker} = \alpha*T_{plasma}\) (only if sml_flat_marker=.false.)

double sml_marker_temp_factor2 = See Fortran description.

See Fortran description.

double sml_max_imbalance = See Fortran description.

See Fortran description.

double sml_max_loading_factor = 10.0

Upper limit for loading factor (default is conservative, might need higher value)

double sml_min_loading_factor = 0.1

Lower limit for loading factor (default is conservative, might need lower value; lower values increase time for loading)

bool sml_mms = See Fortran description.

See Fortran description.

double sml_mms_alpha = See Fortran description.

See Fortran description.

double sml_mms_beta = See Fortran description.

See Fortran description.

double sml_mms_gamma = See Fortran description.

See Fortran description.

bool sml_mod_adiabatic = See Fortran description.

See Fortran description.

double sml_mod_adiabatic_psi_in = See Fortran description.

See Fortran description.

double sml_mod_adiabatic_psi_out = See Fortran description.

See Fortran description.

bool sml_mode_select_bands_on = false

Determine the number of side bands to include by using grid%m_max_surf(i)

double sml_mode_select_bd_width = 0.01

width of boundary envelope

int sml_mode_select_cutoff = 2

Factor for cutoff in Fourier space, determines grid%m_max_surf(i)

The default is the Nyquist limit sml_mode_select_cutoff=2

int sml_mode_select_cutoff_mode = See Fortran description.

See Fortran description.

double sml_mode_select_damp_width = See Fortran description.

See Fortran description.

bool sml_mode_select_div_mix = true

Whether to blend filtered and unfiltered data near the divertor plates

(set .false. for increasing stability in EM simulations)

double sml_mode_select_inpsi = -0.1

inner boundary for mode selection

bool sml_mode_select_keep_axisym = See Fortran description.

See Fortran description.

double sml_mode_select_max_kth_rho = 1.0

Max. k_theta*rhoi retained in poloidal Fourier filter

int sml_mode_select_mmax = 25

Highest pol. mode number for Fourier filter

int sml_mode_select_mmin = 0

Lowest pol. mode number for Fourier filter

int sml_mode_select_mode = 0

Fourier filter mode: 0) No filter,

1) single-n,

4) m_range (mmin..mmax)

2 or 5) n range + resonant m

3 or 6) n range + m range

int sml_mode_select_mres_q = 3

number of pol. mode numbers around the resonant mode divided by q;

–> |m/q - n| <= mres_q or |m -n*q| <= mres_q*q

int sml_mode_select_n = 1

Toroidal mode number for Fourier filter

int sml_mode_select_nmax = 1

Highest numerical tor. mode number for Fourier filter

(0,1,…,sml_nphi_total-1)

int sml_mode_select_nmax_real = 999

Highest real toroidal mode number for FFT filter

(n_real = (n_num+(i-1)*sml_nphi_total)*sml_wedge_n),

max. i depending on mesh resolution

int sml_mode_select_nmin = 1

Lowest numerical tor. mode number for Fourier filter

(0,1,…,sml_nphi_total-1)

int sml_mode_select_nmin_real = 0

Lowest real toroidal mode number for FFT filter

(n_real = (n_num+(i-1)*sml_nphi_total)*sml_wedge_n),

max. i depending on mesh resolution

bool sml_mode_select_no_m0 = See Fortran description.

See Fortran description.

int sml_mode_select_num_m_damp = See Fortran description.

See Fortran description.

double sml_mode_select_outpsi = 10.0

outer boundary for mode selection

double sml_mode_select_psitol = See Fortran description.

See Fortran description.

int sml_mode_select_sol_mode = 0

0: Retain sine and cosine modes in SOL but use a window function

1: Retain only sine modes in SOL and don’t use a window function

2: Retain sine and cosine modes and DO NOT use a window function

(Applies only to filter modes sml_mode_select_mode={5,6}!)

int sml_mode_select_use_minm = See Fortran description.

See Fortran description.

int sml_monte_num = monte_num_minimum

Number of Monte Carlo points to use in calculating various simulation volumes. The actual number of points used may depend on number of MPI ranks, OpenMP threads, and particles.

int sml_mstep = 3000

Number of time steps to run

bool sml_multirate_timestepping = false

Use multirate timestepping

int sml_ncycle_half = 30

Number of subcycles in electron push RK step 1. Total number of subcycles is twice this value.

bool sml_neutral = false

Switch for using the neutrals

bool sml_no_fp_in_f = false

If .true. the distribution function used for the source routines

will not include particle information (only for testing)

bool sml_no_turb = false

Set all non-axisymmetric field perturbations to zero (electromagnetic version only)

std::string sml_node_file = "example_file.node"

The grid file

int sml_node_file_spacing = 1

Option to take every nth grid file, starting from 0001

bool sml_node_vol_monte = node_vol_monte_default

Calculate node volume using Monte-Carlo method (true), or analytic method (false)

int sml_nphi_total = 16

Number of planes in the simulation

int sml_nsurf3 = See Fortran description.

See Fortran description.

int sml_nsurf3_2 = See Fortran description.

See Fortran description.

double sml_outpsi = 1.05

Outer psi boundary for the simulation

double sml_outpsi_priv1 = 0.97

Outer boundary (for Poisson solver), normalized poloidal flux

double sml_outpsi_priv2 = 2.0

Outer boundary (for Poisson solver, 2nd private region), normalized poloidal flux

bool sml_plane_major = See Fortran description.

See Fortran description.

bool sml_poisson_0m_full_geo = false

Whether to use full toroidal geometry in the axisymmetric Poisson solver

(w/o approximation B_R<<B, and B_Z<<B)

bool sml_poisson_adia_wall = false

EXPERIMENTAL! DON’T USE UNLESS ADVISED BY AN EXPERT

If true, an adiabatic wall condition is used (no polarization, n_i=0, n_e!=0)

in the axisymmetric solver; this is an experimental option and should

be used together with sml_sheath_mode=1 and sml_sheath_init_pot_factor=0.

bool sml_poisson_bias = false

Add bias potential

double sml_poisson_bias_amp = 10.0

Ampltude of the bias potential in Volt

double sml_poisson_bias_amp2 = 10.0

Additional Ampltude of the bias potential in Volt for the kick drive

int sml_poisson_bias_freq = 10000

Frequency in Hz of the bias potential

bool sml_poisson_bias_kick = false

If true, a periodic kick drive instead of a continuous sinusoidal drive is used

double sml_poisson_bias_psic = 0.5

Center position of bias potential phi_bia ~ exp(-(psi-psi0)^2), psi_normalized

double sml_poisson_bias_psiw = 0.02

Decay length of the radial envelope of the bias potential

int sml_poisson_bias_start = 1

Time step in which the bias potential is started

bool sml_poisson_natural_boundary = false

Set the potential on the solver boundary equal to the flux-surface

averaged potential (implies \(\delta\phi_wall=0\)).

This is supposed to prevent a sheath-like potential drop at the mesh

boundary and make sure that the logical sheath model takes care of

the sheath physics. Also, it should prevent \(\delta\phi/\phi\sim1\).

bool sml_poisson_use_bc = false

(XGCa only) False: 00-bc is phi=0 everywhere; true: 00-boundary

bool sml_pol_decomp = true

Switch to use poloidal domain decomposition

bool sml_positive_phi00_sol = false

If .true., it is made sure that the flux-surface averaged potential in the scrape-off layer is positive by adding a global constant to the result of the field solver.

double sml_ptl_imbal_ion = See Fortran description.

See Fortran description.

bool sml_radiation = false

Switch for a simple radiation module using part of the ADAS

data base (must be configured with the rad_param namelist)

bool sml_read_eq = true

Read magnetic equilibrium from a .eqd file

bool sml_read_eq_m3dc1 = false

Read magnetic equilbrium from an m3dc1 result

Ignore read_eqd if read_m3dc1 is true

bool sml_reduce_core_ptl = See Fortran description.

See Fortran description.

bool sml_replace_pot0 = See Fortran description.

See Fortran description.

bool sml_resamp_on = false

Switch to use particle resampling

bool sml_restart = false

Whether to restart if possible

int sml_restart_write_period = 10000000

Number of time steps between each simulation checkpoint. A checkpoint file is also written after the final time step of the simulation.

bool sml_rgn1_pot0_only = false

If .true., the axisymmetric Poisson equation is solved only inside the separatrix.

double sml_rhomax = 1.0e-2

Upper cutoff of the gyroradius grid (should be the gyroradius of the fastest ions of interest)

int sml_sep2_surf_index = See Fortran description.

See Fortran description.

int sml_sep_surf_index = See Fortran description.

See Fortran description.

bool sml_separate_n0 = default_separate_n0

Use separate n0 poisson solver. True by default if total-f, false if reduced-deltaf. Must be true for total-f.

double sml_sheath_adjust_factor = See Fortran description.

See Fortran description.

bool sml_sheath_global_balance = false

Whether to use the global loss balance functionality in sheath_mode=2

bool sml_sheath_init_pot_auto = See Fortran description.

See Fortran description.

double sml_sheath_init_pot_factor = See Fortran description.

See Fortran description.

int sml_sheath_mode = 0

Type of sheath (0 is none)

bool sml_sheath_adjust = false

Whether to adjust the sheath

bool sml_source = false

Switch for using the heat source

std::string sml_surf_file = "example_file.flx.aif"

The flux surface file

bool sml_symmetric_f = is_XGCa ? true : false

Enforce axisymmetry of the total distribution function on the grid

bool sml_symmetric_f0g = See Fortran description.

See Fortran description.

bool sml_thermal_bath_on = false

Switch for thermal bath

double sml_tri_psi_weighting = See Fortran description.

See Fortran description.

bool sml_turb_efield = true

E-field calculated only with \(<\phi>\) if .false.

psn%dpot will still contain all (n=0,|m|>0) and (|n|>0,m) modes

bool sml_update_ampere_solver = false

If .true. density and temperature in the Ampere’s

law solver operators will be updated every

sml_update_ampere_solver_nstep time steps

int sml_update_ampere_solver_nstep = 1

Number of time steps between subsequent updates of the Ampere’s law solver operators

double sml_update_g_alpha = 0.0

Fraction of the numerical marker particle density that is transferred to the g2

bool sml_update_poisson_solver = false

Whether poisson solver is updated

int sml_update_poisson_solver_nstep = 1

Number of time steps between subsequent updates of the Poisson solver operators

bool sml_update_poisson_turb = false

Update the n != 0 Poisson solver, too (energy conservation?)

bool sml_use_loading_factor = false

Marker particle distribution taking into account the local

(configuration space) node volume, i.e. aim for uniform

number of ptl/mesh vertex. Set .true. when using a

mesh with very non-uniform resolution

bool sml_use_pade = false

Use Pade approximation for short wavelengths

int sml_wedge_n = 1

Simulate a wedge of 2pi/sml_wedge_n of the full torus

bool sml_zero_inner_bd = false

If .true., use Dirichlet boundary condition \(\phi=0\)

bool sml_zero_inner_bd_turb = true

If .true., use Dirichlet boundary condition \(\delta\phi=0\),

!! if .false., set the magnetic axis to the flux-surface average of the

!! first flux-surface (provides continuity of the m=0 mode).

!! (requires the inner boundaries be set to <0)

smooth_param

double smooth_fourier_filt_bd_width = 0.02

Boundary width (tanh) for Fourier filter

double smooth_fourier_filt_inpsi = -0.1

Inner boundary for Fourier filter (outside of boundary will be zero!)

int smooth_fourier_filt_maxm = 30

Maximal poloidal mode number for SOL Fourier filter

int smooth_fourier_filt_minm = 0

Minimal poloidal mode number for SOL Fourier filter

bool smooth_fourier_filt_on = false

Switch for additional SOL Fourier filter

double smooth_fourier_filt_outpsi = 10.0

Outer boundary for Fourier filter (outside of boundary will be zero!)

bool smooth_hyp_vis_parallel_on = false

Switch for 2nd order accurate 4th derivative field-aligned hyperviscosity

double smooth_hyp_vis_parallel = 1.0

Strength of the parallel hyperviscosity; sml_dt/smooth_hyp_vis_parallel corresponds

to the decay time of a mode with k_x=pi/dx, where dx is the local mesh size

bool smooth_hyp_vis_rad_on = false

Switch for 2nd order accurate 4th derivative radial (grad(psi)) hyperviscosity

double smooth_hyp_vis_rad = 0.1

Strength of the radial hyperviscosity; sml_dt/smooth_hyp_vis_rad corresponds

to the decay time of a mode with k_x=pi/dx, where dx is the local mesh size

[Also used when sml_param:sml_em_dasdt_hypvis=true]

double smooth_hyp_vis_rad_priv = 1.0

Strength of the radial hyperviscosity in the private region; sml_dt/smooth_hyp_vis_rad corresponds

to the decay time of a mode with k_x=pi/dx, where dx is the local mesh size

[Also used when sml_param:sml_em_dasdt_hypvis=true]

double smooth_pol_d0 = 0.1

Smoothing length for poloidal smoothing

bool smooth_pol_efield = false

Smoothing of poloidal potential before computing the poloidal field

int smooth_pol_width = 3

Width for poloidal smoothing

double smooth_sol_filt_lp0 = See Fortran description.

See Fortran description.

double smooth_sol_filt_width = See Fortran description.

See Fortran description.

src_param

double src_current_drive_d = 1.0

Current drive PID controller: factor for derivative controller (\(D\))

double src_current_drive_i = 0.01

Current drive PID controller: factor for integral controller (\(I\))

double src_current_drive_p = 0.4

Current drive PID controller: factor for proportional controller (\(P\))

int src_current_drive_start_time = 1

Time step at which current drive turns on

double src_decay_width1 = See Fortran description.

See Fortran description.

double src_decay_width2 = See Fortran description.

See Fortran description.

double src_decay_width3 = See Fortran description.

See Fortran description.

double src_decay_width4 = See Fortran description.

See Fortran description.

double src_heat_power1 = See Fortran description.

See Fortran description.

double src_heat_power2 = See Fortran description.

See Fortran description.

double src_heat_power3 = See Fortran description.

See Fortran description.

double src_heat_power4 = See Fortran description.

See Fortran description.

int src_ishape1 = See Fortran description.

See Fortran description.

int src_ishape2 = See Fortran description.

See Fortran description.

int src_ishape3 = See Fortran description.

See Fortran description.

int src_ishape4 = See Fortran description.

See Fortran description.

double src_loop_voltage = 0.0

Initial value for loop voltage

double src_loop_voltage_psimax = 1.0

Inductive current drive: outer boundary (in pol. flux) of the loop voltage

int src_narea = See Fortran description.

See Fortran description.

int src_niter = See Fortran description.

See Fortran description.

int src_nsubsection = See Fortran description.

See Fortran description.

double src_pellet_cloud_a = 0.1

Semi-major axis of the neutral gas cloud around the pellet in m

double src_pellet_cloud_angle = 0.0

Angle of the semi-major axis wrt the horizontal plane

double src_pellet_cloud_b = 0.1

Semi-minor axis of the neutral gas cloud around the pellet in m

double src_pellet_etemp = 5.0

Electron temperature of the pellet cloud in eV

int src_pellet_ion_species = MAIN_ION

Index of the ion species in the pellet; default is a main ion pellet

double src_pellet_itemp = 5.0

Ion temperature of the pellet cloud in eV

double src_pellet_n_atoms = 1.0e21

Total number of atoms in the pellet; ablation stops after the pellet is spent

bool src_pellet_on = false

On/off switch for pellet ablation

double src_pellet_r = 1.0

Position of the pellet, R-coordinate in m

double src_pellet_rad = 1.0e-3

Radius of the pellet in m

int src_pellet_start_time = 1

Start time step of the pellet ablation

int src_pellet_stop_time = -1

End time step of the pellet ablation; if <0, no stop time

double src_pellet_z = 0.0

Position of the pellet, Z-coordinate in m

int src_period = See Fortran description.

See Fortran description.

double src_pin1 = See Fortran description.

See Fortran description.

double src_pin2 = See Fortran description.

See Fortran description.

double src_pin3 = See Fortran description.

See Fortran description.

double src_pin4 = See Fortran description.

See Fortran description.

double src_pout1 = See Fortran description.

See Fortran description.

double src_pout2 = See Fortran description.

See Fortran description.

double src_pout3 = See Fortran description.

See Fortran description.

double src_pout4 = See Fortran description.

See Fortran description.

double src_r_begin1 = See Fortran description.

See Fortran description.

double src_r_begin2 = See Fortran description.

See Fortran description.

double src_r_begin3 = See Fortran description.

See Fortran description.

double src_r_begin4 = See Fortran description.

See Fortran description.

double src_radius1 = See Fortran description.

See Fortran description.

double src_radius2 = See Fortran description.

See Fortran description.

double src_radius3 = See Fortran description.

See Fortran description.

double src_radius4 = See Fortran description.

See Fortran description.

int src_special_mode1 = See Fortran description.

See Fortran description.

int src_special_mode2 = See Fortran description.

See Fortran description.

int src_special_mode3 = See Fortran description.

See Fortran description.

int src_special_mode4 = See Fortran description.

See Fortran description.

int src_start_time = 1

Start time of source in ion time steps

double src_torque1 = See Fortran description.

See Fortran description.

double src_torque2 = See Fortran description.

See Fortran description.

double src_torque3 = See Fortran description.

See Fortran description.

double src_torque4 = See Fortran description.

See Fortran description.

double src_z_begin1 = See Fortran description.

See Fortran description.

double src_z_begin2 = See Fortran description.

See Fortran description.

double src_z_begin3 = See Fortran description.

See Fortran description.

double src_z_begin4 = See Fortran description.

See Fortran description.

thermal_bath_param

double gamma = 5000.0

gamma_k

double gamma_coarse_graining = 5000.0

Coarse-graining gamma_cg

double inpsi = 1.05

Overlap region inner boundary

int n_diag_bins = 1

Number of bins for diagnostic

int n_energy_bins = 1

Number of energy bins

double outpsi = 1.05

Overlap region outer boundary

double vmax = 5.0

Maximum velocity for energy bins (normalized to thermal velocity)