#include <World.h>

Public Member Functions
	World ()

	~World ()

int	init (string FFEA_script_filename, int frames_to_delete, int mode, bool writeEnergy)
	Reads the .ffea file and initialises the World. More...

int	get_smallest_time_constants ()
	Finds the largest allowed timesteps. More...

int	lem (set< int > blob_indices, int num_modes)
	Calculates an linear elastic model for a given blob. More...

int	dmm (set< int > blob_indices, int num_modes)
	Calculates an dynamic mode model for a given blob. More...

int	dmm_rp (set< int > blob_indices, int num_modes)
	Calculates an elastic network model for a given blob. More...

int	run ()

int	read_and_build_system (vector< string > script_vector)
	Parses <blobs>, <springs>, <rods> and <precomp>. More...

int	load_kinetic_maps (vector< string > map_fnames, vector< int > map_from, vector< int > map_to, int blob_index)
	Loads the maps from a given blob. More...

int	build_kinetic_identity_maps ()
	Builds additional maps for energy calculations. More...

int	load_kinetic_states (string states_fname, int blob_index)

int	load_kinetic_rates (string rates_fname, int blob_index)

void	print_kinetic_rates_to_screen (int type)

void	get_system_CoM (vector3 *system_CoM)

void	get_system_centroid (vector3 *centroid)

void	get_system_dimensions (vector3 *dimenstion_vector)

int	enm (int *blob_index, int num_modes)

int	get_num_blobs ()

Private Member Functions
int	load_springs (const char *fname)

rod::Rod_blob_interface *	rod_blob_interface_from_block (vector< string > block, int interface_id, FFEA_input_reader systemreader, rod::Rod rod_array, Blob *blob_array)

rod::Rod *	rod_from_block (vector< string > block, int block_id, FFEA_input_reader *systemreader)

void	activate_springs ()

int	apply_springs ()

scalar	get_spring_field_energy (int index0, int index1)

int	calculate_kinetic_rates ()
	calculates the kinetic rates as a function of the energy of the system More...

int	choose_new_kinetic_state (int blob_index, int *target)
	randomly chooses a new kinetic state based upon the kinetic rates / switching probabilitie More...

int	change_kinetic_state (int blob_index, int target_state)
	changes the kinetic state based upon the kinetic rates. Maps between conformations and adds/ removes bound sites More...

int	get_next_script_tag (FILE in, char buf)

void	apply_dense_matrix (scalar y, scalar M, scalar *x, int N)

void	do_es ()

void	make_trajectory_from_eigenvector (string traj_out_fname, int blob_index, int mode_index, Eigen_VectorX evec, scalar step)
	Calculates a pseudo-trajectory by varying an eigenvector by a constant factor. More...

void	print_evecs_to_file (string fname, Eigen_MatrixX ev, int num_rows, int num_modes)

void	print_evals_to_file (string fname, Eigen_VectorX ev, int num_modes, scalar scale)

void	write_eig_to_files (scalar evals_ordered, scalar *evecs_ordered, int num_modes, int num_nodes)
	Writes eigensystems to files in order. More...

void	write_output_header (FILE *fout, string fname)

void	print_trajectory_and_measurement_files (int step, scalar wtime)

void	print_checkpoints ()

void	write_pre_print_to_trajfile (int step)

void	do_nothing ()

int	prebuild_nearest_neighbour_lookup_wrapper (scalar cell_size)

void	make_measurements ()

void	write_measurements_to_file (FILE *fout, int step)

void	write_detailed_measurements_to_file (FILE *fout)

void	print_trajectory_conformation_changes (FILE fout, int step, int from_index, int *to_index)

void	print_kinetic_files (int step)

void	print_static_trajectory (int step, scalar wtime, int blob_index)

void	calc_blob_corr_matrix (int num_blobs, scalar *blob_corr)
	calculates the blob to blob corrections due to periodic boundary conditions More...

int	die_with_dignity (int step, scalar wtime)

Private Attributes
Blob **	blob_array
	2-D Array of Blob objects (blob i, conformation j) More...

Blob **	active_blob_array
	Which conformation is active in each blob. More...

rod::Rod **	rod_array
	1-D array containing pointers to all rod objects More...

rod::Rod_blob_interface **	rod_blob_interface_array
	1-D array containing pointers to all rod-blob interfaces More...

SparseMatrixFixedPattern ***	kinetic_map
	Maps for kinetic switching of conformations. More...

SparseMatrixFixedPattern ****	kinetic_return_map

Spring *	spring_array
	An array of springs which connect nodes if necessary. More...

int	num_springs
	And how many springs are there? More...

int	num_binding_sites
	How many kinetic binding sites are there? More...

bool	mass_in_system
	Check whether mass is present anywhere, to determine whether or not to write kinetic energies to files. More...

int	num_threads
	How many threads are available for parallelisation. More...

RngStream *	rng
	An array of pointers to random number generators (for use in parallel) More...

unsigned long **	Seeds
	A pointer to an array of arrays, containing the seeds of the different RNGStreams. More...

int	num_seeds
	The number of seeds stored in Seeds. More...

RngStream *	kinetic_rng
	An array of pointers to random number generators for use in kinetics. More...

SimulationParams	params
	Parameters being used for this simulation. More...

NearestNeighbourLinkedListCube	lookup
	Data structure keeping track of which `cell' each face lies in (where the world has been discretised into a grid of cells of dimension 1.5 kappa) so that the BEM matrices may be constructed quickly and sparsely. More...

FILE *	trajectory_out
	Output trajectory file. More...

FILE *	kinetics_out
	Output kinetics file. More...

FILE *	measurement_out
	Output measurement file. More...

bool	writeDetailed
	Output detailed measurements file. May be unneccesary. More...

FILE *	detailed_meas_out

FILE *	trajbeads_out
	Output file for the trajectory beads. Completely optional. More...

FFEA_input_reader *	ffeareader

FFEA_input_reader *	systemreader

vector3	L

FILE *	checkpoint_out
	Output Checkpoint file More...

BEM_Poisson_Boltzmann	PB_solver
	BEM solver for the exterior electrostatics. More...

int	total_num_surface_faces
	Number of surface faces in entire system. More...

scalar *	phi_Gamma
	Vector of the electrostatic potential on each surface in entire system. More...

scalar *	J_Gamma

scalar *	work_vec

BiCGSTAB_solver	nonsymmetric_solver
	Biconjugate gradient stabilised solver for nonsymmetric matrices. More...

VdW_solver *	vdw_solver

SSINT_matrix	ssint_matrix
	LJ parameters matrix. More...

BindingSite_matrix	binding_matrix
	Binding Interactions matrix. More...

PreComp_params	pc_params
	stores info within the <precomp> block at the .ffea file. More...

PreComp_solver	pc_solver
	PreComputed potentials solver. More...

vector3	box_dim

long long	step_initial

scalar *	blob_corr


KineticState **	kinetic_state
	Kinetic State and Rate objects. More...

scalar ***	kinetic_rate

scalar ***	kinetic_base_rate


scalar	kineticenergy

scalar	strainenergy

scalar	springenergy

scalar **	springfieldenergy

scalar	ssintenergy

scalar	preCompenergy


vector3	CoM

vector3	CoG

scalar	rmsd

Friends
struct	ffea_test

Constructor & Destructor Documentation

◆ World()

World::World ( )

◆ ~World()

World::~World ( )

Member Function Documentation

◆ activate_springs()

void World::activate_springs ( )

private

Referenced by change_kinetic_state(), and load_springs().

◆ apply_dense_matrix()

void World::apply_dense_matrix	(	scalar *	y,
		scalar *	M,
		scalar *	x,
		int	N
	)

private

◆ apply_springs()

int World::apply_springs ( )

private

Referenced by run().

◆ build_kinetic_identity_maps()

int World::build_kinetic_identity_maps ( )

Builds additional maps for energy calculations.

This function uses the existing kinetic maps to build 'return_maps', which are used for energy calculations and comparisons

Referenced by read_and_build_system().

◆ calc_blob_corr_matrix()

void World::calc_blob_corr_matrix	(	int	num_blobs,
		scalar *	blob_corr
	)

private

calculates the blob to blob corrections due to periodic boundary conditions

Referenced by run().

◆ calculate_kinetic_rates()

int World::calculate_kinetic_rates ( )

private

calculates the kinetic rates as a function of the energy of the system

Calculates kinetic rates based upon the current state of the blob.

This function alters the given kinetic_rates using the energy of the system. The average rate throughout the simulation should still be the given values.

Referenced by run().

◆ change_kinetic_state()

int World::change_kinetic_state	(	int	blob_index,
		int	target_state
	)

private

changes the kinetic state based upon the kinetic rates. Maps between conformations and adds/ removes bound sites

Changes the active kinetic state for a given blob.

Parameters

[in]	int	blob_index Index of the blob to be changed
[in]	int	target_state State the blob should be changed to

This function changes the kinetic state of the blob. For a conformational change, the current structure is mapped to the target and the active_blob_array[i] pointer is updated. For a binding / unbinding event, the binding sites are activated.

Referenced by run().

◆ choose_new_kinetic_state()

int World::choose_new_kinetic_state	(	int	blob_index,
		int *	target
	)

private

randomly chooses a new kinetic state based upon the kinetic rates / switching probabilitie

Selects a new states based on the current kinetic rates.

Parameters

[in]	int	blob_index Which blob wants to switch
[in]	int	*target A list of potential states

This function randomly chooses a state to switch to out of the given allowed taget states based upon the current kinetic rates.

Referenced by run().

◆ die_with_dignity()

int World::die_with_dignity	(	int	step,
		scalar	wtime
	)

private

Referenced by run().

◆ dmm()

int World::dmm	(	set< int >	blob_indices,
		int	num_modes
	)

Calculates an dynamic mode model for a given blob.

Parameters

[in]	set<int>	List of blobs to get Dynamic Mode Model
[in]	int	num_modes The number of modes / eigenvalues to be calculated

By linearising the elasticity vector around the initial position, this function performs matrix algebra using the Eigen libraries to diagonalise the coupling between the elasticity and viscosity matrices, and outputs pseudo-trajectories based upon these eigenvectors

Referenced by main().

◆ dmm_rp()

int World::dmm_rp	(	set< int >	blob_indices,
		int	num_modes
	)

Calculates an elastic network model for a given blob.

Parameters

[in]	set<int>	List of blobs to get Elastic Network Model
[in]	int	num_modes The number of modes / eigenvalues to be calculated

By linearising the elasticity vector around the initial position, this function performs matrix algebra using the Eigen libraries to diagonalise the coupling between the elasticity and rotne-praga viscosity matrices, and outputs pseudo-trajectories based upon these eigenvectors

Referenced by main().

◆ do_es()

void World::do_es ( )

private

Referenced by run().

◆ do_nothing()

void World::do_nothing ( )

private

Referenced by init().

◆ enm()

int World::enm	(	int *	blob_index,
		int	num_modes
	)

◆ get_next_script_tag()

int World::get_next_script_tag	(	FILE *	in,
		char *	buf
	)

private

◆ get_num_blobs()

int World::get_num_blobs ( )

Referenced by main().

◆ get_smallest_time_constants()

int World::get_smallest_time_constants ( )

Finds the largest allowed timesteps.

By linearising the equation of motion, this function performs matrix algebra using the Eigen libraries to find the largest allowed timestep for ffea numerical integration.

Referenced by main().

◆ get_spring_field_energy()

scalar World::get_spring_field_energy	(	int	index0,
		int	index1
	)

private

Referenced by make_measurements(), and write_detailed_measurements_to_file().

◆ get_system_centroid()

void World::get_system_centroid ( vector3 * centroid )

Blob centroid

Rod centroid

I'm leaving it like this and there's nothing you can do about it

Referenced by init().

◆ get_system_CoM()

void World::get_system_CoM ( vector3 * system_CoM )

◆ get_system_dimensions()

void World::get_system_dimensions ( vector3 * dimenstion_vector )

Referenced by init().

◆ init()

int World::init	(	string	FFEA_script_filename,
		int	frames_to_delete,
		int	mode,
		bool	writeDetail
	)

Reads the .ffea file and initialises the World.

Parameters

[in] string FFEA_script_filename

Open and read .ffea file, parse the block through SimulationParams::extract_params in the "SimulationParams params" private attribute, parse the <blobs> and <springs> blocks through World::read_and_build_system initialise a number of RNG, prepare output files, initialise VdW solver, initialise BEM PBE solver

Referenced by ffea_test::connection_energy(), ffea_test::connection_energy_2(), ffea_test::connection_energy_3(), ffea_test::connection_orientation_test(), ffea_test::connection_propagation(), ffea_test::connection_test(), ffea_test::identify_face(), load_kinetic_states(), ffea_test::lower_sphere(), main(), read_and_build_system(), and ffea_test::recover_normal().

◆ lem()

int World::lem	(	set< int >	blob_indices,
		int	num_modes
	)

Calculates an linear elastic model for a given blob.

Parameters

[in]	set<int>	List of blobs to get Linear Elastic Model
[in]	int	num_modes The number of modes / eigenvalues to be calculated

By linearising the elasticity vector around the initial position, this function performs matrix algebra using the Eigen libraries to diagonalise elasticity matrix and output pseudo-trajectories based upon these eigenvectors

Referenced by main().

◆ load_kinetic_maps()

int World::load_kinetic_maps	(	vector< string >	map_fnames,
		vector< int >	map_from,
		vector< int >	map_to,
		int	blob_index
	)

Loads the maps from a given blob.

Parameters

[in]	vector<string>	map_fnames A vector of maps to load
[in]	vector<int>	map_from Which conformation the maps are from
[in]	vector<int>	map_to Which conformation the maps go to
[in]	int	blob_index Which blob the maps belong to

This function reads in the maps required for kinetic switching between conformations. Does no error checking for correct number of maps

Referenced by read_and_build_system().

◆ load_kinetic_rates()

int World::load_kinetic_rates	(	string	rates_fname,
		int	blob_index
	)

Referenced by read_and_build_system().

◆ load_kinetic_states()

int World::load_kinetic_states	(	string	states_fname,
		int	blob_index
	)

Referenced by read_and_build_system().

◆ load_springs()

int World::load_springs ( const char * fname )

private

Referenced by read_and_build_system().

◆ make_measurements()

void World::make_measurements ( )

private

Referenced by print_trajectory_and_measurement_files().

◆ make_trajectory_from_eigenvector()

void World::make_trajectory_from_eigenvector	(	string	traj_out_fname,
		int	blob_index,
		int	mode_index,
		Eigen_VectorX	evec,
		scalar	step
	)

private

Calculates a pseudo-trajectory by varying an eigenvector by a constant factor.

This function takes an Eigen::VectorXd and applies it as a series of translations to the given blob.

Referenced by dmm(), dmm_rp(), and lem().

◆ prebuild_nearest_neighbour_lookup_wrapper()

int World::prebuild_nearest_neighbour_lookup_wrapper ( scalar cell_size )

private

Referenced by die_with_dignity(), init(), and run().

◆ print_checkpoints()

void World::print_checkpoints ( )

private

Print the RNG values responsible for the current state of the system i.e. do this before all forces are calculated, which advances the system

Referenced by run().

◆ print_evals_to_file()

void World::print_evals_to_file	(	string	fname,
		Eigen_VectorX	ev,
		int	num_modes,
		scalar	scale
	)

private

Referenced by dmm(), dmm_rp(), and lem().

◆ print_evecs_to_file()

void World::print_evecs_to_file	(	string	fname,
		Eigen_MatrixX	ev,
		int	num_rows,
		int	num_modes
	)

private

Referenced by dmm(), dmm_rp(), and lem().

◆ print_kinetic_files()

void World::print_kinetic_files ( int step )

private

Referenced by die_with_dignity(), and run().

◆ print_kinetic_rates_to_screen()

void World::print_kinetic_rates_to_screen ( int type )

◆ print_static_trajectory()

void World::print_static_trajectory	(	int	step,
		scalar	wtime,
		int	blob_index
	)

private

◆ print_trajectory_and_measurement_files()

void World::print_trajectory_and_measurement_files	(	int	step,
		scalar	wtime
	)

private

Write trajectory for each blob, then do blob specific measurements (which are needed for globals, but only explicitly printed if "-d" was used)

Referenced by ffea_test::connection_energy(), ffea_test::connection_orientation_test(), die_with_dignity(), ffea_test::identify_face(), and run().

◆ print_trajectory_conformation_changes()

void World::print_trajectory_conformation_changes	(	FILE *	fout,
		int	step,
		int *	from_index,
		int *	to_index
	)

private

Referenced by make_trajectory_from_eigenvector().

◆ read_and_build_system()

int World::read_and_build_system ( vector< string > script_vector )

Parses <blobs>, <springs>, <rods> and <precomp>.

Parameters

[in] vector<string> script_vector, which is essentially the FFEA input file, line by line, as it comes out of FFEA_input_reader::file_to_lines

Referenced by init().

◆ rod_blob_interface_from_block()

rod::Rod_blob_interface * World::rod_blob_interface_from_block	(	vector< string >	block,
		int	interface_id,
		FFEA_input_reader *	systemreader,
		rod::Rod **	rod_array,
		Blob **	blob_array
	)

private

Referenced by read_and_build_system().

◆ rod_from_block()

rod::Rod * World::rod_from_block	(	vector< string >	block,
		int	block_id,
		FFEA_input_reader *	systemreader
	)

private

Referenced by read_and_build_system().

◆ run()

int World::run ( )

Update entire World for num_steps time steps

Referenced by ffea_test::connection_energy_3(), ffea_test::connection_propagation(), ffea_test::lower_sphere(), and main().

◆ write_detailed_measurements_to_file()

void World::write_detailed_measurements_to_file ( FILE * fout )

private

Referenced by print_trajectory_and_measurement_files().

◆ write_eig_to_files()

void World::write_eig_to_files	(	scalar *	evals_ordered,
		scalar **	evecs_ordered,
		int	num_modes,
		int	num_nodes
	)

private

Writes eigensystems to files in order.

This function writes the eigenvalues calculated for enms and dmms to files

◆ write_measurements_to_file()

void World::write_measurements_to_file	(	FILE *	fout,
		int	step
	)

private

Referenced by print_trajectory_and_measurement_files().

◆ write_output_header()

void World::write_output_header	(	FILE *	fout,
		string	fname
	)

private

Referenced by init().

◆ write_pre_print_to_trajfile()

void World::write_pre_print_to_trajfile ( int step )

private

Referenced by print_trajectory_and_measurement_files().

Friends And Related Function Documentation

◆ ffea_test

friend struct ffea_test

friend

Field Documentation

◆ active_blob_array

Blob** World::active_blob_array

private

◆ binding_matrix

BindingSite_matrix World::binding_matrix

private

Binding Interactions matrix.

Referenced by init(), load_kinetic_states(), and read_and_build_system().

◆ blob_array

Blob** World::blob_array

private

2-D Array of Blob objects (blob i, conformation j)

Referenced by change_kinetic_state(), init(), load_kinetic_maps(), load_springs(), ffea_test::lower_sphere(), read_and_build_system(), World(), and ~World().

◆ blob_corr

scalar* World::blob_corr

private

Referenced by read_and_build_system(), run(), World(), and ~World().

◆ box_dim

vector3 World::box_dim

private

Referenced by calc_blob_corr_matrix(), init(), run(), World(), and ~World().

◆ checkpoint_out

FILE* World::checkpoint_out

private

Output Checkpoint file

Referenced by init(), print_checkpoints(), World(), and ~World().

◆ CoG

vector3 World::CoG

private

Referenced by make_measurements(), World(), write_measurements_to_file(), and ~World().

◆ CoM

vector3 World::CoM

private

Geometries

Referenced by World(), and ~World().

◆ detailed_meas_out

FILE* World::detailed_meas_out

private

Referenced by init(), print_trajectory_and_measurement_files(), World(), write_detailed_measurements_to_file(), and ~World().

◆ ffeareader

FFEA_input_reader* World::ffeareader

private

Reader objects

Referenced by init(), World(), and ~World().

◆ J_Gamma

scalar* World::J_Gamma

private

Referenced by do_es(), and init().

◆ kinetic_base_rate

scalar*** World::kinetic_base_rate

private

Referenced by calculate_kinetic_rates(), init(), load_kinetic_rates(), print_kinetic_rates_to_screen(), World(), and ~World().

◆ kinetic_map

SparseMatrixFixedPattern*** World::kinetic_map

private

Maps for kinetic switching of conformations.

Referenced by build_kinetic_identity_maps(), change_kinetic_state(), init(), load_kinetic_maps(), World(), and ~World().

◆ kinetic_rate

scalar*** World::kinetic_rate

private

Referenced by calculate_kinetic_rates(), choose_new_kinetic_state(), init(), load_kinetic_rates(), print_kinetic_rates_to_screen(), World(), and ~World().

◆ kinetic_return_map

SparseMatrixFixedPattern**** World::kinetic_return_map

private

Referenced by build_kinetic_identity_maps(), init(), World(), and ~World().

◆ kinetic_rng

RngStream* World::kinetic_rng

private

An array of pointers to random number generators for use in kinetics.

Referenced by choose_new_kinetic_state(), init(), and print_checkpoints().

◆ kinetic_state

KineticState** World::kinetic_state

private

Kinetic State and Rate objects.

Referenced by calculate_kinetic_rates(), change_kinetic_state(), init(), load_kinetic_states(), World(), and ~World().

◆ kineticenergy

scalar World::kineticenergy

private

Energies

Referenced by make_measurements(), World(), write_measurements_to_file(), and ~World().

◆ kinetics_out

FILE* World::kinetics_out

private

Output kinetics file.

Referenced by init(), print_kinetic_files(), World(), and ~World().

◆ L

vector3 World::L

private

Momenta

Referenced by World(), and ~World().

◆ lookup

NearestNeighbourLinkedListCube World::lookup

private

Data structure keeping track of which `cell' each face lies in (where the world has been discretised into a grid of cells of dimension 1.5 kappa) so that the BEM matrices may be constructed quickly and sparsely.

Referenced by die_with_dignity(), init(), and run().

◆ mass_in_system

bool World::mass_in_system

private

Check whether mass is present anywhere, to determine whether or not to write kinetic energies to files.

Referenced by init(), read_and_build_system(), World(), write_measurements_to_file(), and ~World().

◆ measurement_out

FILE* World::measurement_out

private

Output measurement file.

Referenced by init(), print_trajectory_and_measurement_files(), World(), write_output_header(), and ~World().

◆ nonsymmetric_solver

BiCGSTAB_solver World::nonsymmetric_solver

private

Biconjugate gradient stabilised solver for nonsymmetric matrices.

Referenced by do_es(), and init().

◆ num_binding_sites

int World::num_binding_sites

private

How many kinetic binding sites are there?

◆ num_seeds

int World::num_seeds

private

The number of seeds stored in Seeds.

Referenced by init(), print_checkpoints(), World(), and ~World().

◆ num_springs

int World::num_springs

private

And how many springs are there?

Referenced by activate_springs(), apply_springs(), load_springs(), make_measurements(), World(), and ~World().

◆ num_threads

int World::num_threads

private

How many threads are available for parallelisation.

Referenced by init(), print_checkpoints(), World(), and ~World().

◆ params

SimulationParams World::params

private

◆ PB_solver

BEM_Poisson_Boltzmann World::PB_solver

private

BEM solver for the exterior electrostatics.

Referenced by do_es(), and init().

◆ pc_params

PreComp_params World::pc_params

private

stores info within the <precomp> block at the .ffea file.

Referenced by init(), and read_and_build_system().

◆ pc_solver

PreComp_solver World::pc_solver

private

PreComputed potentials solver.

Referenced by die_with_dignity(), init(), make_measurements(), print_trajectory_and_measurement_files(), run(), and write_detailed_measurements_to_file().

◆ phi_Gamma

scalar* World::phi_Gamma

private

Vector of the electrostatic potential on each surface in entire system.

Referenced by do_es(), init(), World(), and ~World().

◆ preCompenergy

scalar World::preCompenergy

private

Referenced by make_measurements(), World(), write_measurements_to_file(), and ~World().

◆ rmsd

scalar World::rmsd

private

Referenced by make_measurements(), World(), write_measurements_to_file(), and ~World().

◆ rng

RngStream* World::rng

private

An array of pointers to random number generators (for use in parallel)

Referenced by ffea_test::connection_propagation(), init(), print_checkpoints(), read_and_build_system(), run(), World(), and ~World().

◆ rod_array

rod::Rod** World::rod_array

private

1-D array containing pointers to all rod objects

Referenced by ffea_test::connection_propagation(), get_system_centroid(), get_system_dimensions(), init(), print_trajectory_and_measurement_files(), read_and_build_system(), run(), World(), and ~World().

◆ rod_blob_interface_array

rod::Rod_blob_interface** World::rod_blob_interface_array

private

1-D array containing pointers to all rod-blob interfaces

Referenced by ffea_test::connection_energy(), ffea_test::connection_energy_2(), ffea_test::connection_energy_3(), ffea_test::connection_orientation_test(), ffea_test::connection_propagation(), ffea_test::connection_test(), ffea_test::identify_face(), init(), read_and_build_system(), ffea_test::recover_normal(), and run().

◆ Seeds

unsigned long** World::Seeds

private

A pointer to an array of arrays, containing the seeds of the different RNGStreams.

Referenced by init(), print_checkpoints(), World(), and ~World().

◆ spring_array

Spring* World::spring_array

private

An array of springs which connect nodes if necessary.

Referenced by activate_springs(), apply_springs(), load_springs(), make_measurements(), World(), and ~World().

◆ springenergy

scalar World::springenergy

private

Referenced by make_measurements(), World(), write_measurements_to_file(), and ~World().

◆ springfieldenergy

scalar ** World::springfieldenergy

private

Referenced by get_spring_field_energy(), load_springs(), make_measurements(), World(), and ~World().

◆ ssint_matrix

SSINT_matrix World::ssint_matrix

private

LJ parameters matrix.

Referenced by init(), and read_and_build_system().

◆ ssintenergy

scalar World::ssintenergy

private

Referenced by make_measurements(), World(), write_measurements_to_file(), and ~World().

◆ step_initial

long long World::step_initial

private

Referenced by die_with_dignity(), init(), run(), World(), and ~World().

◆ strainenergy

scalar World::strainenergy

private

Referenced by make_measurements(), World(), write_measurements_to_file(), and ~World().

◆ systemreader

FFEA_input_reader* World::systemreader

private

Referenced by read_and_build_system(), World(), and ~World().

◆ total_num_surface_faces

int World::total_num_surface_faces

private

Number of surface faces in entire system.

Referenced by do_es(), init(), World(), and ~World().

◆ trajbeads_out

FILE* World::trajbeads_out

private

Output file for the trajectory beads. Completely optional.

Referenced by init(), and print_trajectory_and_measurement_files().

◆ trajectory_out

FILE* World::trajectory_out

private

Output trajectory file.

Referenced by init(), print_static_trajectory(), print_trajectory_and_measurement_files(), World(), write_pre_print_to_trajfile(), and ~World().

◆ vdw_solver

VdW_solver* World::vdw_solver

private

Van der Waals solver

Referenced by init(), make_measurements(), run(), World(), write_detailed_measurements_to_file(), and ~World().

◆ work_vec

scalar* World::work_vec

private

Referenced by do_es(), and init().

◆ writeDetailed

bool World::writeDetailed

private

Output detailed measurements file. May be unneccesary.

Referenced by init(), World(), and ~World().

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

FFEA

Public Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

◆ World()

◆ ~World()

Member Function Documentation

◆ activate_springs()

◆ apply_dense_matrix()

◆ apply_springs()

◆ build_kinetic_identity_maps()

◆ calc_blob_corr_matrix()

◆ calculate_kinetic_rates()

◆ change_kinetic_state()

◆ choose_new_kinetic_state()

◆ die_with_dignity()

◆ dmm()

◆ dmm_rp()

◆ do_es()

◆ do_nothing()

◆ enm()

◆ get_next_script_tag()

◆ get_num_blobs()

◆ get_smallest_time_constants()

◆ get_spring_field_energy()

◆ get_system_centroid()

◆ get_system_CoM()

◆ get_system_dimensions()

◆ init()

◆ lem()

◆ load_kinetic_maps()

◆ load_kinetic_rates()

◆ load_kinetic_states()

◆ load_springs()

◆ make_measurements()

◆ make_trajectory_from_eigenvector()

◆ prebuild_nearest_neighbour_lookup_wrapper()

◆ print_checkpoints()

◆ print_evals_to_file()

◆ print_evecs_to_file()

◆ print_kinetic_files()

◆ print_kinetic_rates_to_screen()

◆ print_static_trajectory()

◆ print_trajectory_and_measurement_files()

◆ print_trajectory_conformation_changes()

◆ read_and_build_system()

◆ rod_blob_interface_from_block()

◆ rod_from_block()

◆ run()

◆ write_detailed_measurements_to_file()

◆ write_eig_to_files()

◆ write_measurements_to_file()

◆ write_output_header()

◆ write_pre_print_to_trajfile()

Friends And Related Function Documentation

◆ ffea_test

Field Documentation

◆ active_blob_array

◆ binding_matrix

◆ blob_array

◆ blob_corr

◆ box_dim

◆ checkpoint_out

◆ CoG

◆ CoM

◆ detailed_meas_out

◆ ffeareader

◆ J_Gamma

◆ kinetic_base_rate

◆ kinetic_map

◆ kinetic_rate

◆ kinetic_return_map

◆ kinetic_rng

◆ kinetic_state

◆ kineticenergy

◆ kinetics_out

◆ L

◆ lookup