#include <SimulationParams.h>

Public Member Functions
	SimulationParams ()

	~SimulationParams ()

int	validate (int sim_mode)

int	parse_param_assignment (char *str)
	DEPRECATED! Superseeded by: extract_params + assign. More...

int	extract_params (vector< string > script_vector)

int	assign (string lvalue, string rvalue)

int	get_max_num_states ()

void	write_to_file (FILE *fout, PreComp_params &pc_params)

Data Fields
scalar	dt
	time step More...

long long	num_steps
	Number of time steps to run simulation for. More...

int	check
	Every how many steps should the program 'check' the system i.e calculate energies, print snapshots etc. More...

int	num_blobs
	Number of blobs in the system. More...

int	num_rods
	Number of rods in the system. More...

int	num_interfaces
	Number of rod-blob or rod-rod interfaces. More...

int *	num_conformations
	Number of conformations for each blob. More...

int *	num_states
	Number of states for each blob. More...

int	state_array_size

int	conformation_array_size

int	rng_seed
	Seed for random number generator. More...

scalar	kT
	boltzmann's const times temperature More...

int	max_iterations_cg
	Max number of iterations when using conjugate gradient solver. More...

scalar	epsilon2
	The tolerance threshold for CG solver (squared) More...

int	es_update
	Every how many steps should the electrostatic potential be recalculated. More...

int	es_N_x
	X dimension of the 3D lookup grid (in number of cells) More...

int	es_N_y
	Y dimension of the 3D lookup grid (in number of cells) More...

int	es_N_z
	Z dimension of the 3D lookup grid (in number of cells) More...

int	move_into_box
	If box is set, do we move the world to it's center at the start of a simulation? Default is yes! More...

int	restrict_motion [3]
	[x,y,z] array defining whether motion in the given direction should be nullified More...

int	num_dimensions

scalar	es_h
	Number of active dimensions after restricted_motion is applied. More...

scalar	kappa
	Inverse Debye Screening length. More...

scalar	epsilon_0
	Permittivity of free space. More...

scalar	dielec_ext
	Exterior dielectric constant. More...

int	restart
	Whether or not to restart the simulation from the last available time step. More...

int	calc_ssint
	Whether or not to simulate surface-surface interactions between surfaces. More...

int	inc_self_ssint
	Whether or not to include surface-surface interactions derived from faces in the same blob. More...

string	ssint_type
	Current possible values: "lennard-jones" (default) or "steric". More...

int	calc_es
	Whether or not to simulate electrostatic interactions between proteins. More...

int	calc_noise
	Whether or noise to simulate thermal noise for the system. Kind of the entire point of this simulation technique. More...

int	calc_stokes
	Whether or not to include local action of the external fluid. More...

int	calc_kinetics
	Whether or not to calculate kinetic switching between different equilibrium states and binding sites. More...

int	calc_preComp
	Whether or not use preComputed potentials and forces. More...

int	calc_springs
	Whether or not to include the springs interactions defined in the springs block. More...

int	calc_ctforces
	Whether or not to include constant forces onto nodes defined in the ctforces block. More...

int	force_pbc
	Whether or not to apply pbc to surface insteractions. More...

int	kinetics_update
	How often to check for a state change. If rates are ~ >> dt then this can clearly be quite high. More...

int	wall_x_1

int	wall_x_2

int	wall_y_1

int	wall_y_2

int	wall_z_1

int	wall_z_2

int	sticky_wall_xz

scalar	stokes_visc

int	calc_steric
	Calculate steric interactions? More...

scalar	steric_factor
	Proportionality factor to the Steric repulsion. More...

scalar	ssint_cutoff
	Cutoff distance for the surface-surface interactions. More...

geoscalar	steric_dr
	used to calculate the numerical derivative. More...

string	FFEA_script_filename

b_fs::path	FFEA_script_path

b_fs::path	FFEA_script_basename

string	trajectory_out_fname

string	kinetics_out_fname

string	measurement_out_fname

string	detailed_meas_out_fname

string	ssint_in_fname

string	bsite_in_fname

string	icheckpoint_fname
	Input Checkpoint file name. More...

string	ocheckpoint_fname
	Output Checkpoint file name. More...

string	ctforces_fname
	Input file containing constant forces onto a list of nodes. More...

string	springs_fname
	Input file containing the springs details. More...

string	trajectory_beads_fname
	Output optional file. More...

int	kinetics_out_fname_set

int	trajbeads_fname_set

Private Member Functions
int	checkFileName (string oFile)

string	RemoveFileExtension (const string &FileName)

Private Attributes
int	trajectory_out_fname_set

int	measurement_out_fname_set

int	icheckpoint_fname_set

int	ocheckpoint_fname_set

int	ssint_in_fname_set

int	bsite_in_fname_set

Constructor & Destructor Documentation

◆ SimulationParams()

SimulationParams::SimulationParams ( )

◆ ~SimulationParams()

SimulationParams::~SimulationParams ( )

Member Function Documentation

◆ assign()

int SimulationParams::assign	(	string	lvalue,
		string	rvalue
	)

Expects a parameter label and value, which will be assigned if valid and rejected if not

Referenced by extract_params().

◆ checkFileName()

int SimulationParams::checkFileName ( string oFile )

private

Check if the file oFile exists, and if so rename it to "__"+oFile+"__bckp.N", where N is an integer so that the resulting file is new.

Referenced by validate().

◆ extract_params()

int SimulationParams::extract_params ( vector< string > script_vector )

Expects a string of the form "<system>\n<>\n<>.....\n<system>" where parameter data can be extracted from.

Referenced by World::init().

◆ get_max_num_states()

int SimulationParams::get_max_num_states ( )

Returns maximum number of states on any blob

◆ parse_param_assignment()

int SimulationParams::parse_param_assignment ( char * str )

DEPRECATED! Superseeded by: extract_params + assign.

Expects a string of the form "lvalue = rvalue" where lvalue must be a recognised parameter name.

◆ RemoveFileExtension()

string SimulationParams::RemoveFileExtension ( const string & FileName )

private

Referenced by assign().

◆ validate()

int SimulationParams::validate ( int sim_mode )

Referenced by World::init().

◆ write_to_file()

void SimulationParams::write_to_file	(	FILE *	fout,
		PreComp_params &	pc_params
	)

Writes all params to fout (either a file or stdout) for user's info

Referenced by World::init(), and World::read_and_build_system().

Field Documentation

◆ bsite_in_fname

string SimulationParams::bsite_in_fname

Referenced by assign(), World::init(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ bsite_in_fname_set

int SimulationParams::bsite_in_fname_set

private

Referenced by assign(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ calc_ctforces

int SimulationParams::calc_ctforces

Whether or not to include constant forces onto nodes defined in the ctforces block.

Referenced by assign(), Blob::init(), World::read_and_build_system(), SimulationParams(), Blob::update_internal_forces(), validate(), write_to_file(), and ~SimulationParams().

◆ calc_es

int SimulationParams::calc_es

Whether or not to simulate electrostatic interactions between proteins.

Referenced by assign(), World::init(), Blob::init(), Blob::pre_print(), World::run(), SimulationParams(), Blob::update_internal_forces(), validate(), Blob::write_nodes_to_file(), Blob::write_pre_print_to_file(), write_to_file(), and ~SimulationParams().

◆ calc_kinetics

int SimulationParams::calc_kinetics

Whether or not to calculate kinetic switching between different equilibrium states and binding sites.

Referenced by assign(), World::init(), World::print_checkpoints(), World::print_kinetic_files(), World::print_trajectory_and_measurement_files(), World::print_trajectory_conformation_changes(), World::read_and_build_system(), World::run(), SimulationParams(), validate(), World::write_pre_print_to_trajfile(), write_to_file(), ~SimulationParams(), and World::~World().

◆ calc_noise

int SimulationParams::calc_noise

Whether or noise to simulate thermal noise for the system. Kind of the entire point of this simulation technique.

Referenced by Blob::aggregate_forces_and_solve(), assign(), Blob::init(), Blob::reset_solver(), SimulationParams(), Blob::update_internal_forces(), validate(), write_to_file(), and ~SimulationParams().

◆ calc_preComp

int SimulationParams::calc_preComp

Whether or not use preComputed potentials and forces.

Referenced by assign(), World::init(), Blob::init(), World::make_measurements(), World::read_and_build_system(), World::run(), SimulationParams(), validate(), World::write_measurements_to_file(), write_to_file(), and ~SimulationParams().

◆ calc_springs

int SimulationParams::calc_springs

Whether or not to include the springs interactions defined in the springs block.

Referenced by assign(), World::init(), Blob::init(), World::make_measurements(), World::read_and_build_system(), SimulationParams(), validate(), World::write_measurements_to_file(), write_to_file(), and ~SimulationParams().

◆ calc_ssint

int SimulationParams::calc_ssint

Whether or not to simulate surface-surface interactions between surfaces.

Referenced by assign(), World::init(), Blob::init(), Blob::load_ssint(), World::make_measurements(), World::run(), SimulationParams(), validate(), World::write_measurements_to_file(), write_to_file(), and ~SimulationParams().

◆ calc_steric

int SimulationParams::calc_steric

Calculate steric interactions?

Referenced by assign(), World::init(), Blob::init(), World::make_measurements(), World::read_and_build_system(), World::run(), SimulationParams(), validate(), World::write_measurements_to_file(), write_to_file(), and ~SimulationParams().

◆ calc_stokes

int SimulationParams::calc_stokes

Whether or not to include local action of the external fluid.

Referenced by Blob::aggregate_forces_and_solve(), assign(), Blob::build_linear_node_viscosity_matrix(), NoMassCGSolver::init(), Blob::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ check

int SimulationParams::check

Every how many steps should the program 'check' the system i.e calculate energies, print snapshots etc.

Referenced by assign(), ffea_test::lower_sphere(), World::print_trajectory_and_measurement_files(), World::run(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ conformation_array_size

int SimulationParams::conformation_array_size

Referenced by assign(), SimulationParams(), validate(), and ~SimulationParams().

◆ ctforces_fname

string SimulationParams::ctforces_fname

Input file containing constant forces onto a list of nodes.

Referenced by Blob::init(), World::read_and_build_system(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ detailed_meas_out_fname

string SimulationParams::detailed_meas_out_fname

Referenced by assign(), World::init(), SimulationParams(), validate(), and ~SimulationParams().

◆ dielec_ext

scalar SimulationParams::dielec_ext

Exterior dielectric constant.

Referenced by assign(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ dt

scalar SimulationParams::dt

time step

Referenced by tetra_element_linear::add_fluctuating_stress(), Blob::aggregate_forces_and_solve(), assign(), Blob::euler_integrate(), World::load_kinetic_rates(), World::print_trajectory_and_measurement_files(), World::read_and_build_system(), SimulationParams(), World::write_measurements_to_file(), write_to_file(), and ~SimulationParams().

◆ epsilon2

scalar SimulationParams::epsilon2

The tolerance threshold for CG solver (squared)

Referenced by assign(), ConjugateGradientSolver::init(), NoMassCGSolver::init(), World::init(), Blob::init(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ epsilon_0

scalar SimulationParams::epsilon_0

Permittivity of free space.

Referenced by assign(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ es_h

scalar SimulationParams::es_h

Number of active dimensions after restricted_motion is applied.

Dimension of each cell in the lookup grid (in multiples of inverse kappa)

Referenced by assign(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ es_N_x

int SimulationParams::es_N_x

X dimension of the 3D lookup grid (in number of cells)

Referenced by assign(), PreComp_solver::init(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ es_N_y

int SimulationParams::es_N_y

Y dimension of the 3D lookup grid (in number of cells)

Referenced by assign(), PreComp_solver::init(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ es_N_z

int SimulationParams::es_N_z

Z dimension of the 3D lookup grid (in number of cells)

Referenced by assign(), PreComp_solver::init(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ es_update

int SimulationParams::es_update

Every how many steps should the electrostatic potential be recalculated.

Referenced by assign(), World::run(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ FFEA_script_basename

b_fs::path SimulationParams::FFEA_script_basename

Referenced by assign(), and validate().

◆ FFEA_script_filename

string SimulationParams::FFEA_script_filename

Referenced by assign(), World::init(), and validate().

◆ FFEA_script_path

b_fs::path SimulationParams::FFEA_script_path

Referenced by assign(), World::read_and_build_system(), and validate().

◆ force_pbc

int SimulationParams::force_pbc

Whether or not to apply pbc to surface insteractions.

Referenced by assign(), World::read_and_build_system(), World::run(), SimulationParams(), and write_to_file().

◆ icheckpoint_fname

string SimulationParams::icheckpoint_fname

Input Checkpoint file name.

Referenced by assign(), World::init(), SimulationParams(), validate(), and ~SimulationParams().

◆ icheckpoint_fname_set

int SimulationParams::icheckpoint_fname_set

private

Referenced by assign(), SimulationParams(), validate(), and ~SimulationParams().

◆ inc_self_ssint

int SimulationParams::inc_self_ssint

Whether or not to include surface-surface interactions derived from faces in the same blob.

Referenced by assign(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ kappa

scalar SimulationParams::kappa

Inverse Debye Screening length.

Referenced by assign(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ kinetics_out_fname

string SimulationParams::kinetics_out_fname

Referenced by assign(), World::init(), SimulationParams(), validate(), and ~SimulationParams().

◆ kinetics_out_fname_set

int SimulationParams::kinetics_out_fname_set

These set parameters are not private because the World needs them!!

Referenced by assign(), World::init(), SimulationParams(), and ~SimulationParams().

◆ kinetics_update

int SimulationParams::kinetics_update

How often to check for a state change. If rates are ~ >> dt then this can clearly be quite high.

Referenced by assign(), World::load_kinetic_rates(), World::print_trajectory_conformation_changes(), World::run(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ kT

scalar SimulationParams::kT

boltzmann's const times temperature

Referenced by tetra_element_linear::add_fluctuating_stress(), Blob::aggregate_forces_and_solve(), assign(), Blob::build_linear_node_rp_diffusion_matrix(), World::read_and_build_system(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ max_iterations_cg

int SimulationParams::max_iterations_cg

Max number of iterations when using conjugate gradient solver.

Referenced by assign(), ConjugateGradientSolver::init(), NoMassCGSolver::init(), World::init(), Blob::init(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ measurement_out_fname

string SimulationParams::measurement_out_fname

Referenced by assign(), World::init(), SimulationParams(), validate(), and ~SimulationParams().

◆ measurement_out_fname_set

int SimulationParams::measurement_out_fname_set

private

Referenced by assign(), SimulationParams(), validate(), and ~SimulationParams().

◆ move_into_box

int SimulationParams::move_into_box

If box is set, do we move the world to it's center at the start of a simulation? Default is yes!

Referenced by assign(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ num_blobs

int SimulationParams::num_blobs

Number of blobs in the system.

Referenced by assign(), World::build_kinetic_identity_maps(), World::calculate_kinetic_rates(), World::do_es(), get_max_num_states(), World::get_num_blobs(), World::get_smallest_time_constants(), World::get_spring_field_energy(), World::get_system_centroid(), World::get_system_CoM(), World::get_system_dimensions(), PreComp_solver::init(), World::init(), Face::init(), World::load_springs(), World::make_measurements(), World::print_kinetic_files(), World::print_kinetic_rates_to_screen(), World::print_trajectory_and_measurement_files(), World::print_trajectory_conformation_changes(), World::read_and_build_system(), World::run(), SimulationParams(), validate(), World::write_detailed_measurements_to_file(), World::write_pre_print_to_trajfile(), write_to_file(), ~SimulationParams(), and World::~World().

◆ num_conformations

int* SimulationParams::num_conformations

Number of conformations for each blob.

Referenced by assign(), World::build_kinetic_identity_maps(), PreComp_solver::init(), World::init(), World::load_kinetic_states(), World::load_springs(), World::read_and_build_system(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ num_dimensions

int SimulationParams::num_dimensions

◆ num_interfaces

int SimulationParams::num_interfaces

Number of rod-blob or rod-rod interfaces.

Referenced by assign(), World::init(), World::read_and_build_system(), World::run(), SimulationParams(), and ~SimulationParams().

◆ num_rods

int SimulationParams::num_rods

Number of rods in the system.

Referenced by assign(), World::get_system_centroid(), World::get_system_dimensions(), World::init(), World::print_trajectory_and_measurement_files(), World::read_and_build_system(), World::run(), SimulationParams(), validate(), and ~SimulationParams().

◆ num_states

int* SimulationParams::num_states

Number of states for each blob.

Referenced by assign(), World::calculate_kinetic_rates(), World::choose_new_kinetic_state(), get_max_num_states(), World::load_kinetic_rates(), World::load_kinetic_states(), World::print_kinetic_rates_to_screen(), World::read_and_build_system(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ num_steps

long long SimulationParams::num_steps

Number of time steps to run simulation for.

Referenced by assign(), ffea_test::lower_sphere(), World::run(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ ocheckpoint_fname

string SimulationParams::ocheckpoint_fname

Output Checkpoint file name.

Referenced by assign(), World::init(), SimulationParams(), validate(), and ~SimulationParams().

◆ ocheckpoint_fname_set

int SimulationParams::ocheckpoint_fname_set

private

Referenced by assign(), SimulationParams(), validate(), and ~SimulationParams().

◆ restart

int SimulationParams::restart

Whether or not to restart the simulation from the last available time step.

Referenced by assign(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ restrict_motion

int SimulationParams::restrict_motion[3]

[x,y,z] array defining whether motion in the given direction should be nullified

◆ rng_seed

int SimulationParams::rng_seed

Seed for random number generator.

Referenced by assign(), World::init(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ springs_fname

string SimulationParams::springs_fname

Input file containing the springs details.

Referenced by World::read_and_build_system(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ ssint_cutoff

scalar SimulationParams::ssint_cutoff

Cutoff distance for the surface-surface interactions.

Referenced by assign(), PreComp_solver::init(), World::init(), World::run(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ ssint_in_fname

string SimulationParams::ssint_in_fname

Referenced by assign(), World::init(), SimulationParams(), write_to_file(), and ~SimulationParams().

◆ ssint_in_fname_set

int SimulationParams::ssint_in_fname_set

private

Referenced by assign(), SimulationParams(), validate(), and ~SimulationParams().

◆ ssint_type

string SimulationParams::ssint_type

Current possible values: "lennard-jones" (default) or "steric".

Referenced by assign(), World::init(), Blob::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ state_array_size

int SimulationParams::state_array_size

Referenced by assign(), SimulationParams(), and ~SimulationParams().

◆ steric_dr

geoscalar SimulationParams::steric_dr

used to calculate the numerical derivative.

Referenced by assign(), World::init(), SimulationParams(), validate(), and ~SimulationParams().

◆ steric_factor

scalar SimulationParams::steric_factor

Proportionality factor to the Steric repulsion.

Referenced by assign(), World::init(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ sticky_wall_xz

int SimulationParams::sticky_wall_xz

Referenced by assign(), World::run(), SimulationParams(), and ~SimulationParams().

◆ stokes_visc

scalar SimulationParams::stokes_visc

Referenced by assign(), Blob::build_linear_node_rp_diffusion_matrix(), Blob::init(), World::read_and_build_system(), SimulationParams(), validate(), write_to_file(), and ~SimulationParams().

◆ trajbeads_fname_set

int SimulationParams::trajbeads_fname_set

Referenced by assign(), PreComp_solver::init(), World::init(), World::print_trajectory_and_measurement_files(), SimulationParams(), and validate().

◆ trajectory_beads_fname

string SimulationParams::trajectory_beads_fname

Output optional file.

Referenced by assign(), World::init(), SimulationParams(), validate(), and ~SimulationParams().

◆ trajectory_out_fname

string SimulationParams::trajectory_out_fname

Referenced by assign(), World::dmm(), World::dmm_rp(), World::init(), World::lem(), SimulationParams(), validate(), World::write_eig_to_files(), and ~SimulationParams().

◆ trajectory_out_fname_set

int SimulationParams::trajectory_out_fname_set

private

Referenced by assign(), SimulationParams(), validate(), and ~SimulationParams().

◆ wall_x_1

int SimulationParams::wall_x_1

Referenced by assign(), Blob::enforce_box_boundaries(), World::run(), SimulationParams(), and ~SimulationParams().

◆ wall_x_2

int SimulationParams::wall_x_2

Referenced by assign(), Blob::enforce_box_boundaries(), World::run(), SimulationParams(), and ~SimulationParams().

◆ wall_y_1

int SimulationParams::wall_y_1

Referenced by assign(), Blob::enforce_box_boundaries(), World::run(), SimulationParams(), and ~SimulationParams().

◆ wall_y_2

int SimulationParams::wall_y_2

Referenced by assign(), Blob::enforce_box_boundaries(), World::run(), SimulationParams(), and ~SimulationParams().

◆ wall_z_1

int SimulationParams::wall_z_1

Referenced by assign(), Blob::enforce_box_boundaries(), World::run(), SimulationParams(), and ~SimulationParams().

◆ wall_z_2

int SimulationParams::wall_z_2

Referenced by assign(), Blob::enforce_box_boundaries(), World::run(), SimulationParams(), and ~SimulationParams().

The documentation for this class was generated from the following files:

FFEA

Public Member Functions

Data Fields

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ SimulationParams()

◆ ~SimulationParams()

Member Function Documentation

◆ assign()

◆ checkFileName()

◆ extract_params()

◆ get_max_num_states()

◆ parse_param_assignment()

◆ RemoveFileExtension()

◆ validate()

◆ write_to_file()

Field Documentation

◆ bsite_in_fname

◆ bsite_in_fname_set

◆ calc_ctforces

◆ calc_es

◆ calc_kinetics

◆ calc_noise

◆ calc_preComp

◆ calc_springs

◆ calc_ssint

◆ calc_steric

◆ calc_stokes

◆ check

◆ conformation_array_size

◆ ctforces_fname

◆ detailed_meas_out_fname

◆ dielec_ext

◆ dt

◆ epsilon2

◆ epsilon_0

◆ es_h

◆ es_N_x

◆ es_N_y

◆ es_N_z

◆ es_update

◆ FFEA_script_basename

◆ FFEA_script_filename

◆ FFEA_script_path

◆ force_pbc

◆ icheckpoint_fname

◆ icheckpoint_fname_set

◆ inc_self_ssint

◆ kappa

◆ kinetics_out_fname

◆ kinetics_out_fname_set

◆ kinetics_update

◆ kT

◆ max_iterations_cg

◆ measurement_out_fname

◆ measurement_out_fname_set

◆ move_into_box

◆ num_blobs

◆ num_conformations

◆ num_dimensions

◆ num_interfaces

◆ num_rods

◆ num_states

◆ num_steps

◆ ocheckpoint_fname

◆ ocheckpoint_fname_set

◆ restart

◆ restrict_motion

◆ rng_seed

◆ springs_fname

◆ ssint_cutoff

◆ ssint_in_fname

◆ ssint_in_fname_set

◆ ssint_type

◆ state_array_size

◆ steric_dr

◆ steric_factor

◆ sticky_wall_xz

◆ stokes_visc