#include <Blob.h>

Public Member Functions
	Blob ()

	~Blob ()

int	config (const int blob_index, const int conformation_index, string node_filename, string topology_filename, string surface_filename, string material_params_filename, string stokes_filename, string ssint_filename, string pin_filename, string binding_filename, string beads_filename, scalar scale, scalar calc_compress, scalar compress, int linear_solver, int blob_state, SimulationParams params, PreComp_params pc_params, SSINT_matrix ssint_matrix, BindingSite_matrix binding_matrix, RngStream rng[])

int	init ()

int	update_internal_forces ()

int	check_inversion ()

int	update_positions ()

int	reset_solver ()

void	translate_linear (vector3 *vec)

void	rotate (float r11, float r12, float r13, float r21, float r22, float r23, float r31, float r32, float r33, bool beads=false)

void	rotate (float xang, float yang, float zang, bool beads=false)

vector3	position (scalar x, scalar y, scalar z)

void	position_beads (scalar x, scalar y, scalar z)

int	forget_beads ()
	num_beads = 0; delete bead_type; delete bead_position. More...

void	add_steric_nodes ()

void	move (scalar dx, scalar dy, scalar dz)

void	get_CoM (vector3 *com)

void	get_centroid (vector3 *com)

void	calc_and_store_centroid (vector3 &com)

vector3	calc_centroid ()

void	set_pos_0 ()

void	kinetically_set_faces (bool state)

int	create_viewer_node_file (const char *node_filename, scalar scale)

void	write_nodes_to_file (FILE *trajectory_out)

void	pre_print ()

void	write_pre_print_to_file (FILE *trajectory_out)

int	read_nodes_from_file (FILE *trajectory_out)

void	make_measurements ()

void	write_measurements_to_file (FILE *fout)

int	calculate_deformation ()

scalar	calc_volume ()

void	make_stress_measurements (FILE *stress_out, int blob_number)

void	calc_centroids_and_normals_of_all_faces ()

void	calc_all_centroids ()

int	get_num_faces ()

Face *	get_face (int i)

Face *	absolutely_get_face (int i)

tetra_element_linear *	get_element (int i)

void	get_bead_position (int i, arr3 &v)
	returns the position of bead i. More...

int *	get_bead_type_ptr ()
	returns the bead_type pointer. More...

int	get_bead_type (int i)
	returns the bead_type of bead i. More...

vector< int >	get_bead_assignment (int i)
	returns the list of nodes where bead i should be assigned to. More...

scalar	get_ssint_area ()

int	solve_poisson (scalar phi_gamma_IN, scalar J_Gamma_OUT)

int	apply_ctforces ()

void	zero_force ()

void	set_forces_to_zero ()

void	get_node (int index, arr3 &v)

void	get_node_0 (int index, arr3 &v)

void	copy_node_positions (vector3 *nodes)

vector3 **	get_actual_node_positions ()

void	set_node_positions (vector3 *node_pos)

void	add_force_to_node (vector3 f, int index)

void	velocity_all (scalar vel_x, scalar vel_y, scalar vel_z)

void	build_poisson_matrices ()

int	build_linear_node_viscosity_matrix (Eigen::SparseMatrix< scalar > *K)

int	build_linear_node_rp_diffusion_matrix (Eigen_MatrixX *D)

int	build_linear_node_elasticity_matrix (Eigen::SparseMatrix< scalar > *A)

int	build_linear_node_mass_matrix (Eigen::SparseMatrix< scalar > *M)

scalar	get_mass ()

void	enforce_box_boundaries (vector3 *box_dim)

void	linearise_elements ()

void	linearise_force ()

void	compress_blob (scalar compress)

int	get_num_nodes ()

int	get_num_elements ()

int	get_motion_state ()

scalar	get_scale ()

scalar	get_RandU01 ()

int	get_num_linear_nodes ()

int	get_num_beads ()

bool	is_using_beads ()

scalar	get_rmsd ()

int	get_linear_solver ()

void	get_stored_centroid (arr3 &cog)

int	get_conformation_index ()

int	get_previous_conformation_index ()

void	set_previous_conformation_index (int index)

int	get_state_index ()

void	set_state_index (int index)

int	get_previous_state_index ()

void	set_previous_state_index (int index)

BindingSite *	get_binding_site (int index)

scalar	calculate_strain_energy ()

void	get_min_max (vector3 blob_min, vector3 blob_max)

void	pin_binding_site (set< int > node_indices)

void	unpin_binding_site (set< int > node_indices)

void	print_node_positions ()

void	print_bead_positions ()

bool	there_is_mass ()

void	set_springs_on_blob (bool state)

bool	there_are_springs ()

bool	there_are_beads ()

bool	there_is_ssint ()

scalar	get_kinetic_energy ()

scalar	get_strain_energy ()

Data Fields
int	toBePrinted_conf [2]

int	toBePrinted_state [2]

int	blob_index

int	conformation_index

int	previous_conformation_index

int	state_index

int	previous_state_index

int	num_binding_sites

BindingSite *	binding_site

int	pbc_count [3]

Private Member Functions
int	load_nodes (const char *node_filename, scalar scale)

int	load_topology (const char *topology_filename)

int	load_surface (const char surface_filename, SimulationParams params)

int	load_surface_no_topology (const char surface_filename, SimulationParams params)

int	load_material_params (const char *material_params_filename)

int	load_stokes_params (const char *stokes_filename, scalar scale)

int	load_ssint (const char *ssint_filename, int num_ssint_face_types, string ssint_method)

int	load_beads (const char beads_filename, PreComp_params pc_params, scalar scale)
	Read the beads_filename, loading beads position and types. More...

int	load_ctforces (string ctforces_fname)

int	load_binding_sites ()

int	load_pinned_nodes (const char *pin_filename)

int	create_pinned_nodes (set< int > list)

void	calc_rest_state_info ()

int	aggregate_forces_and_solve ()

void	euler_integrate ()

int	calculate_node_element_connectivity ()

int	build_mass_matrix ()

Private Attributes
int	num_nodes

int	num_elements

int	num_surface_elements

int	num_interior_elements

int	num_surface_faces

int	num_surface_nodes

int	num_interior_nodes

int	num_pinned_nodes

int	num_beads

int	num_l_ctf

int	num_r_ctf

int	num_sltotal_ctf

int	num_slsets_ctf
	number of surface sets, corresponding to the length of the ctf_sl_forces, num_slsurf_ctf array More...

int *	ctf_slsurf_ndx

int	blob_state

scalar	mass

scalar	ssint_bb_energy

mesh_node *	node

vector3 **	node_position

tetra_element_linear *	elem

Face *	surface

int *	pinned_nodes_list

set< int >	bsite_pinned_nodes_list

scalar *	bead_position

vector< vector< int > >	bead_assignment

int *	bead_type

int *	ctf_l_nodes

int *	ctf_r_nodes

int *	ctf_sl_faces

int *	ctf_sl_surfsize

scalar *	ctf_l_forces

scalar *	ctf_r_forces

scalar *	ctf_r_axis

char *	ctf_r_type

scalar *	ctf_sl_forces

string	s_node_filename

string	s_topology_filename

string	s_surface_filename

string	s_material_params_filename

string	s_stokes_filename

string	s_ssint_filename

string	s_pin_filename

string	s_binding_filename

string	s_beads_filename

scalar	scale

scalar	calc_compress

scalar	compress

SimulationParams *	params

PreComp_params *	pc_params

BindingSite_matrix *	binding_matrix

SSINT_matrix *	ssint_matrix

Solver *	solver

int	linear_solver

bool	mass_in_blob

bool	springs_on_blob

bool	ssint_on_blob

bool	beads_on_blob

vector3 *	force

RngStream *	rng

vector3	L

CG_solver *	poisson_solver

SparseMatrixFixedPattern *	poisson_surface_matrix

SparseMatrixFixedPattern *	poisson_interior_matrix

scalar *	phi_Omega

scalar *	phi_Gamma

scalar *	q

scalar *	nodal_q

scalar *	poisson_rhs

int *	num_contributing_faces

connectivity_entry *	element_connectivity_table

SparseMatrixFixedPattern *	M

scalar *	toBePrinted_nodes


scalar	kineticenergy

scalar	strainenergy


vector3	CoM

vector3	CoG

vector3	CoM_0

vector3	CoG_0

scalar	rmsd

Constructor & Destructor Documentation

◆ Blob()

Blob::Blob ( )

Blob constructor: Initialises all variables and pointers to 0 (or NULL). Does not perform any memory allocation. Actual Blob initialisation is carried out by the init() method.

◆ ~Blob()

Blob::~Blob ( )

Blob destructor: Closes all open files, deallocates memory held by arrays, solvers etc. and sets everything to zero (NULL)

Member Function Documentation

◆ absolutely_get_face()

Face * Blob::absolutely_get_face ( int i )

◆ add_force_to_node()

void Blob::add_force_to_node	(	vector3	f,
		int	index
	)

Referenced by World::apply_springs(), and rod::Rod_blob_interface::do_connection_timestep().

◆ add_steric_nodes()

void Blob::add_steric_nodes ( )

Add nodes to the face objects if and only if this blob is STATIC

Referenced by World::read_and_build_system().

◆ aggregate_forces_and_solve()

int Blob::aggregate_forces_and_solve ( )

private

Referenced by update_positions().

◆ apply_ctforces()

int Blob::apply_ctforces ( )

Apply the constant forces onto the corresponding nodes;

Referenced by update_internal_forces().

◆ build_linear_node_elasticity_matrix()

int Blob::build_linear_node_elasticity_matrix ( Eigen::SparseMatrix< scalar > * A )

Linearises the elasticity vector and build a global elasticity matrix for this blob

◆ build_linear_node_mass_matrix()

int Blob::build_linear_node_mass_matrix ( Eigen::SparseMatrix< scalar > * M )

Build the mass distribution matrix for this blob

◆ build_linear_node_rp_diffusion_matrix()

int Blob::build_linear_node_rp_diffusion_matrix ( Eigen_MatrixX * D )

Builds a global diffusion matrix for this blob based on the work of Rotne and Prager (1969)

◆ build_linear_node_viscosity_matrix()

int Blob::build_linear_node_viscosity_matrix ( Eigen::SparseMatrix< scalar > * K )

Builds a global viscosity matrix for this blob

◆ build_mass_matrix()

int Blob::build_mass_matrix ( )

private

Referenced by init().

◆ build_poisson_matrices()

void Blob::build_poisson_matrices ( )

Constructs the Poisson matrix for this Blob.

Referenced by World::do_es().

◆ calc_all_centroids()

void Blob::calc_all_centroids ( )

Get the centroid of all faces and elements in the blob

Referenced by World::init().

◆ calc_and_store_centroid()

void Blob::calc_and_store_centroid ( vector3 & com )

Referenced by World::run().

◆ calc_centroid()

vector3 Blob::calc_centroid ( )

◆ calc_centroids_and_normals_of_all_faces()

void Blob::calc_centroids_and_normals_of_all_faces ( )

Get the centroid of all faces on the blob surface

Referenced by World::run().

◆ calc_rest_state_info()

void Blob::calc_rest_state_info ( )

private

Calculate some quantities such as the rest jacobian, rest volume etc.

Referenced by init().

◆ calc_volume()

scalar Blob::calc_volume ( )

Referenced by build_linear_node_elasticity_matrix().

◆ calculate_deformation()

int Blob::calculate_deformation ( )

Calculates the current jacobian and elasticity properties of the structure

Referenced by calculate_strain_energy().

◆ calculate_node_element_connectivity()

int Blob::calculate_node_element_connectivity ( )

private

Referenced by init().

◆ calculate_strain_energy()

scalar Blob::calculate_strain_energy ( )

◆ check_inversion()

int Blob::check_inversion ( )

Checks whether any of the elements have inverted or not

Referenced by World::change_kinetic_state().

◆ compress_blob()

void Blob::compress_blob ( scalar compress )

compresses blob by compression factor specified in input script

Referenced by init().

◆ config()

int Blob::config	(	const int	blob_index,
		const int	conformation_index,
		string	node_filename,
		string	topology_filename,
		string	surface_filename,
		string	material_params_filename,
		string	stokes_filename,
		string	ssint_filename,
		string	pin_filename,
		string	binding_filename,
		string	beads_filename,
		scalar	scale,
		scalar	calc_compress,
		scalar	compress,
		int	linear_solver,
		int	blob_state,
		SimulationParams *	params,
		PreComp_params *	pc_params,
		SSINT_matrix *	ssint_matrix,
		BindingSite_matrix *	binding_matrix,
		RngStream	rng[]
	)

Allocates the node, element and embedded charge arrays, initialised with the data read from the given node, element and embedded charge files. 'linear_solver' sets which type of linear solver is to be used: 0 for direct (forward/backward substitution) and 1 for iterative (preconditioned gonjugate gradient). Also takes the simulation parameters and the array of RNGs (for multiprocessor runs).

◆ copy_node_positions()

void Blob::copy_node_positions ( vector3 * nodes )

◆ create_pinned_nodes()

int Blob::create_pinned_nodes ( set< int > list )

private

Creates a new pinned nodes list from a given set

◆ create_viewer_node_file()

int Blob::create_viewer_node_file	(	const char *	node_filename,
		scalar	scale
	)

Writes a new node file for the case of an initially translated STATIC blob, so viewer doesn't read straight from node file

◆ enforce_box_boundaries()

void Blob::enforce_box_boundaries ( vector3 * box_dim )

Applies the WALL_TYPE_HARD boundary conditions simply by finding all nodes that have "passed through" the wall, then zeroing any component of those nodes' velocities that points into the wall. This allows the Blob to "wobble" its way back out of the wall (and effectively prevents any penetration larger than dt * largest velocity, generally very small for sensible dt).

Referenced by World::run().

◆ euler_integrate()

void Blob::euler_integrate ( )

private

Referenced by update_positions().

◆ get_actual_node_positions()

vector3 ** Blob::get_actual_node_positions ( )

Referenced by World::change_kinetic_state().

◆ get_binding_site()

BindingSite * Blob::get_binding_site ( int index )

Referenced by World::calculate_kinetic_rates().

◆ get_centroid()

void Blob::get_centroid ( vector3 * com )

Calculates and returns the centroid of this Blob

Referenced by calc_and_store_centroid(), compress_blob(), World::get_system_centroid(), and rotate().

◆ get_CoM()

void Blob::get_CoM ( vector3 * com )

Calculates and returns the centre of mass of this Blob

Referenced by World::get_system_CoM(), and make_measurements().

◆ get_conformation_index()

int Blob::get_conformation_index ( )

Referenced by World::change_kinetic_state().

◆ get_element()

tetra_element_linear * Blob::get_element ( int i )

Return pointer to the ith Element of this Blob's surface

Referenced by rod::Rod_blob_interface::get_element_id(), PreComp_solver::init(), and rod::Rod_blob_interface::Rod_blob_interface().

◆ get_face()

Face * Blob::get_face ( int i )

Return pointer to the ith Face of this Blob's surface

Referenced by World::init().

◆ get_kinetic_energy()

scalar Blob::get_kinetic_energy ( )

Referenced by World::make_measurements().

◆ get_linear_solver()

int Blob::get_linear_solver ( )

◆ get_mass()

scalar Blob::get_mass ( )

Returns the total mass of this Blob.

Referenced by World::get_system_CoM().

◆ get_min_max()

void Blob::get_min_max	(	vector3 *	blob_min,
		vector3 *	blob_max
	)

Referenced by World::dmm(), World::dmm_rp(), World::get_system_dimensions(), and World::lem().

◆ get_motion_state()

int Blob::get_motion_state ( )

Referenced by VdW_solver::consider_interaction(), move(), VdW_solver::solve(), and update_positions().

◆ get_node()

void Blob::get_node	(	int	index,
		arr3 &	v
	)

Referenced by World::apply_springs(), rod::Rod_blob_interface::get_element_id(), World::make_measurements(), and rod::Rod_blob_interface::select_face_nodes().

◆ get_node_0()

void Blob::get_node_0	(	int	index,
		arr3 &	v
	)

◆ get_num_beads()

int Blob::get_num_beads ( )

Referenced by PreComp_solver::init().

◆ get_num_elements()

int Blob::get_num_elements ( )

Referenced by rod::Rod_blob_interface::get_element_id(), and PreComp_solver::init().

◆ get_num_faces()

int Blob::get_num_faces ( )

Referenced by World::do_es(), get_ssint_area(), World::init(), and move().

◆ get_num_linear_nodes()

int Blob::get_num_linear_nodes ( )

Referenced by build_linear_node_mass_matrix(), build_linear_node_rp_diffusion_matrix(), build_linear_node_viscosity_matrix(), World::dmm(), World::dmm_rp(), World::get_smallest_time_constants(), World::lem(), World::make_trajectory_from_eigenvector(), and translate_linear().

◆ get_num_nodes()

int Blob::get_num_nodes ( )

Referenced by World::get_system_centroid(), World::load_kinetic_maps(), and World::make_measurements().

◆ get_previous_conformation_index()

int Blob::get_previous_conformation_index ( )

◆ get_previous_state_index()

int Blob::get_previous_state_index ( )

Referenced by World::print_trajectory_and_measurement_files().

◆ get_RandU01()

scalar Blob::get_RandU01 ( )

◆ get_rmsd()

scalar Blob::get_rmsd ( )

Referenced by World::make_measurements().

◆ get_scale()

scalar Blob::get_scale ( )

Referenced by World::read_and_build_system().

◆ get_ssint_area()

scalar Blob::get_ssint_area ( )

◆ get_state_index()

int Blob::get_state_index ( )

Referenced by World::calculate_kinetic_rates(), World::change_kinetic_state(), World::choose_new_kinetic_state(), World::print_trajectory_and_measurement_files(), and World::run().

◆ get_stored_centroid()

void Blob::get_stored_centroid ( arr3 & cog )

Referenced by World::calc_blob_corr_matrix(), and World::make_measurements().

◆ get_strain_energy()

scalar Blob::get_strain_energy ( )

Referenced by World::make_measurements().

◆ init()

int Blob::init ( )

◆ is_using_beads()

bool Blob::is_using_beads ( )

◆ kinetically_set_faces()

void Blob::kinetically_set_faces ( bool state )

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

◆ linearise_elements()

void Blob::linearise_elements ( )

Referenced by translate_linear().

◆ linearise_force()

void Blob::linearise_force ( )

Referenced by aggregate_forces_and_solve().

◆ load_binding_sites()

int Blob::load_binding_sites ( )

private

Opens and reads the given 'ffea binding site file', extracting all the kinetic binding sites (types and face lists) for this Blob.

Referenced by init().

◆ load_ctforces()

int Blob::load_ctforces ( string ctforces_fname )

private

Opens and reads the given 'ffea ctforces file', and assigns the constant forces onto nodes for this Blob.

Referenced by init().

◆ load_material_params()

int Blob::load_material_params ( const char * material_params_filename )

private

Opens and reads the given 'ffea material params file', extracting the material parameters for each element.

Referenced by init().

◆ load_nodes()

int Blob::load_nodes	(	const char *	node_filename,
		scalar	scale
	)

private

Opens and reads the given 'ffea node file', extracting all the nodes for this Blob. Records how many of these are surface nodes and how many are interior nodes.

Referenced by init().

◆ load_pinned_nodes()

int Blob::load_pinned_nodes ( const char * pin_filename )

private

Opens and reads the given 'ffea pinned nodes file', extracting all the faces for this Blob.

Referenced by init().

◆ load_ssint()

int Blob::load_ssint	(	const char *	ssint_filename,
		int	num_ssint_face_types,
		string	ssint_method
	)

private

Opens and reads the given 'ffea ssint file', extracting all the van der waals species for each face of this Blob.

Referenced by init().

◆ load_stokes_params()

int Blob::load_stokes_params	(	const char *	stokes_filename,
		scalar	scale
	)

private

Opens and reads the given 'ffea stokes params file', extracting the stokes radii for each node in the Blob.

Referenced by init().

◆ load_surface()

int Blob::load_surface	(	const char *	surface_filename,
		SimulationParams *	params
	)

private

Opens and reads the given 'ffea surface file', extracting all the faces for this Blob.

Referenced by init().

◆ load_surface_no_topology()

int Blob::load_surface_no_topology	(	const char *	surface_filename,
		SimulationParams *	params
	)

private

Opens and reads the given 'ffea surface file', extracting all the faces for this Blob, ignoring topology.

Referenced by init().

◆ load_topology()

int Blob::load_topology ( const char * topology_filename )

private

Opens and reads the given 'ffea topology file', extracting all the elements for this Blob. Records how many of these are surface elements and how many are interior elements.

Referenced by init().

◆ make_measurements()

void Blob::make_measurements ( )

Takes measurements of system properties: KE, PE, Centre of Mass and Angular momentum etc

Referenced by World::print_trajectory_and_measurement_files().

◆ make_stress_measurements()

void Blob::make_stress_measurements	(	FILE *	stress_out,
		int	blob_number
	)

◆ move()

void Blob::move	(	scalar	dx,
		scalar	dy,
		scalar	dz
	)

Translate the Blob by the given vector

Referenced by World::init(), ffea_test::lower_sphere(), rod::Rod_blob_interface::position_blob_from_rod(), and World::run().

◆ pin_binding_site()

void Blob::pin_binding_site ( set< int > node_indices )

Activates binding sites by adding nodes to the list

Referenced by World::change_kinetic_state().

◆ position()

vector3 Blob::position	(	scalar	x,
		scalar	y,
		scalar	z
	)

Calculates the centroid of this Blob, then translates all nodes in the Blob so that the new centroid position is at the given (x,y,z) position, while returning a vector with the displacement (dx, dy, dz) applied to every node.

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

◆ position_beads()

void Blob::position_beads	(	scalar	x,
		scalar	y,
		scalar	z
	)

Moves the beads according to (dx, dy, dz). The name is to be related to "vector3 position(scalar x, scalar y, scalar z).

Referenced by World::read_and_build_system().

◆ pre_print()

void Blob::pre_print ( )

Dumps all the node positions (in order) from the node array to the given file stream in two steps.

Referenced by World::print_trajectory_and_measurement_files().

◆ print_bead_positions()

void Blob::print_bead_positions ( )

◆ print_node_positions()

void Blob::print_node_positions ( )

◆ read_nodes_from_file()

int Blob::read_nodes_from_file ( FILE * trajectory_out )

Reads the node positions from the given trajectory file stream. This is useful for restarting simulations from trajectory files.

◆ reset_solver()

int Blob::reset_solver ( )

If the system changes mid run (binding event, say) we may need to reinitialise the solver

Referenced by World::change_kinetic_state().

◆ rotate() [1/2]

void Blob::rotate	(	float	r11,
		float	r12,
		float	r13,
		float	r21,
		float	r22,
		float	r23,
		float	r31,
		float	r32,
		float	r33,
		bool	beads = `false`
	)

Calculates the centroid of this Blob, then brings the Blob to the origin, rotates all nodes in the Blob, and brings back the Blob to the initial position. If beads = 1, then it rotates its own "bead_positions" too.

Referenced by rod::Rod_blob_interface::position_blob_from_rod(), World::read_and_build_system(), and rotate().

◆ rotate() [2/2]

void Blob::rotate	(	float	xang,
		float	yang,
		float	zang,
		bool	beads = `false`
	)

Performs rotation about x axis, then y axis, then z axis

◆ set_forces_to_zero()

void Blob::set_forces_to_zero ( )

Referenced by World::run().

◆ set_node_positions()

void Blob::set_node_positions ( vector3 * node_pos )

◆ set_pos_0()

void Blob::set_pos_0 ( )

Referenced by World::init().

◆ set_previous_conformation_index()

void Blob::set_previous_conformation_index ( int index )

Referenced by World::change_kinetic_state(), and World::print_kinetic_files().

◆ set_previous_state_index()

void Blob::set_previous_state_index ( int index )

Referenced by World::change_kinetic_state(), and World::print_kinetic_files().

◆ set_springs_on_blob()

void Blob::set_springs_on_blob ( bool state )

Referenced by World::load_springs().

◆ set_state_index()

void Blob::set_state_index ( int index )

Referenced by World::change_kinetic_state().

◆ solve_poisson()

int Blob::solve_poisson	(	scalar *	phi_gamma_IN,
		scalar *	J_Gamma_OUT
	)

Solves the poisson equation inside this Blob for a given fixed surface potential, and calculates the surface flux out of the protein

Referenced by World::do_es().

◆ there_are_beads()

bool Blob::there_are_beads ( )

◆ there_are_springs()

bool Blob::there_are_springs ( )

Referenced by World::write_detailed_measurements_to_file().

◆ there_is_mass()

bool Blob::there_is_mass ( )

Referenced by write_measurements_to_file().

◆ there_is_ssint()

bool Blob::there_is_ssint ( )

◆ translate_linear()

void Blob::translate_linear ( vector3 * vec )

Translates the linear nodes, then linearises the secondary nodes

◆ unpin_binding_site()

void Blob::unpin_binding_site ( set< int > node_indices )

Deactivates binding sites by removing nodes to the list

Referenced by World::change_kinetic_state().

◆ update_internal_forces()

int Blob::update_internal_forces ( )

Calculates all internal forces on the finite element mesh, storing them on the elements This requires the jacobian for each element, so if the mesh has inverted anywhere we will find out within this function

◆ update_positions()

int Blob::update_positions ( )

Solves the EOM on the finite element mesh, updating the node positions and velocities by one time step

Referenced by World::run().

◆ velocity_all()

void Blob::velocity_all	(	scalar	vel_x,
		scalar	vel_y,
		scalar	vel_z
	)

Set all nodes on the Blob to the given velocity vector

Referenced by World::read_and_build_system().

◆ write_measurements_to_file()

void Blob::write_measurements_to_file ( FILE * fout )

Writes only the detailed measurements local to this blob to file!

Referenced by World::print_trajectory_and_measurement_files().

◆ write_nodes_to_file()

void Blob::write_nodes_to_file ( FILE * trajectory_out )

Dumps all the node positions (in order) from the node array to the given file stream.

Referenced by World::print_static_trajectory(), and World::print_trajectory_and_measurement_files().

◆ write_pre_print_to_file()

void Blob::write_pre_print_to_file ( FILE * trajectory_out )

Referenced by World::write_pre_print_to_trajfile().

◆ zero_force()

void Blob::zero_force ( )

Set all forces on the blob to zero

Referenced by World::run().

Field Documentation

◆ bead_assignment

vector<vector<int> > Blob::bead_assignment

private

2D vector with the set of nodes where every bead should be assigned to. It will be removed after PreComp_solver is initialised [precomp]

Referenced by get_bead_assignment(), and load_beads().

◆ bead_position

scalar* Blob::bead_position

private

Array with bead positions xyzxyzxyz.... [precomp] will be NULL after info is loaded into PreComp_solver

Referenced by forget_beads(), get_bead_position(), load_beads(), position_beads(), print_bead_positions(), rotate(), and ~Blob().

◆ bead_type

int* Blob::bead_type

private

Array with bead types [precomp] will be NULL after info is loaded into PreComp_solver

Referenced by forget_beads(), get_bead_type(), get_bead_type_ptr(), load_beads(), and ~Blob().

◆ beads_on_blob

bool Blob::beads_on_blob

private

Are the preComp beads on this blob?

Referenced by Blob(), load_beads(), there_are_beads(), and ~Blob().

◆ binding_matrix

BindingSite_matrix* Blob::binding_matrix

private

A pointer to the same binding matrix configured in World

Referenced by config(), and load_binding_sites().

◆ binding_site

BindingSite* Blob::binding_site

Referenced by Blob(), get_binding_site(), load_binding_sites(), and ~Blob().

◆ blob_index

int Blob::blob_index

Referenced by Blob(), config(), ffea_test::connection_test(), VdW_solver::consider_interaction(), VdW_solver::do_gensoft_interaction(), LJSteric_solver::do_interaction(), Steric_solver::do_interaction(), GenSoftSSINT_solver::do_interaction(), VdW_solver::do_lj_interaction(), VdW_solver::do_steric_interaction(), PreComp_solver::init(), init(), load_ctforces(), PreComp_solver::solve(), and PreComp_solver::solve_using_neighbours().

◆ blob_state

int Blob::blob_state

private

Whether this Blob is DYNAMIC (movable; dynamics simulated) or STATIC (fixed; no simulation of dynamics; Blob is a perfectly solid object fixed in space)

Referenced by Blob(), calc_rest_state_info(), config(), get_motion_state(), init(), pre_print(), read_nodes_from_file(), update_internal_forces(), write_nodes_to_file(), write_pre_print_to_file(), and ~Blob().

◆ bsite_pinned_nodes_list

set<int> Blob::bsite_pinned_nodes_list

private

Additional pinned node list for binding processes

Referenced by aggregate_forces_and_solve(), Blob(), init(), pin_binding_site(), reset_solver(), unpin_binding_site(), and ~Blob().

◆ calc_compress

scalar Blob::calc_compress

private

Compression stuff:

Referenced by config(), and init().

◆ CoG

vector3 Blob::CoG

private

Referenced by calc_and_store_centroid(), get_stored_centroid(), make_measurements(), and write_measurements_to_file().

◆ CoG_0

vector3 Blob::CoG_0

private

Referenced by make_measurements(), and set_pos_0().

◆ CoM

vector3 Blob::CoM

private

Geometries

Referenced by make_measurements().

◆ CoM_0

vector3 Blob::CoM_0

private

◆ compress

scalar Blob::compress

private

Referenced by compress_blob(), config(), and init().

◆ conformation_index

int Blob::conformation_index

Referenced by Blob(), config(), get_conformation_index(), init(), load_ctforces(), pre_print(), World::print_trajectory_conformation_changes(), and ~Blob().

◆ ctf_l_forces

scalar* Blob::ctf_l_forces

private

Array with the linear ctforces: FxFyFzFxFyFz..., being Fx, Fy, Fz the components of the force

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_l_nodes

int* Blob::ctf_l_nodes

private

Array with the nodes having linear ctforces assigned

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_r_axis

scalar* Blob::ctf_r_axis

private

Array with the rotational axis (given with point + unit vector) for ctforces: XYZxyzXYZxyzFxFyFz..., or BlobConfNodeBlobConfNode,BlobConfNodeBlobConfNode,... if using two nodes to define the axis.

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_r_forces

scalar* Blob::ctf_r_forces

private

Array with the magnitude of the rotational ctforces: FFF...,

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_r_nodes

int* Blob::ctf_r_nodes

private

Array with the nodes having rotational ctforces assigned

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_r_type

char* Blob::ctf_r_type

private

Array with the type of rotation force, 2 chars per node: where the first one can be n or p, depending of the axis defined by nodes or points and the second one can be f or t, depending on applying ctforce or cttorque.

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_sl_faces

int* Blob::ctf_sl_faces

private

Array with the faces having linear ctforces assigned

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_sl_forces

scalar* Blob::ctf_sl_forces

private

Array with the linear surface ctforces: FxFyFzFxFyFz..., being Fx, Fy, Fz the components of the force

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_sl_surfsize

int* Blob::ctf_sl_surfsize

private

array with the number of faces in every surface set.

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ ctf_slsurf_ndx

int* Blob::ctf_slsurf_ndx

private

Number of faces in every surface set:

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

◆ elem

◆ element_connectivity_table

connectivity_entry* Blob::element_connectivity_table

private

◆ force

vector3* Blob::force

private

The Blob force vector (an array of the force on every node)

Referenced by add_force_to_node(), aggregate_forces_and_solve(), apply_ctforces(), Blob(), euler_integrate(), init(), linearise_force(), pre_print(), read_nodes_from_file(), set_forces_to_zero(), write_nodes_to_file(), and ~Blob().

◆ kineticenergy

scalar Blob::kineticenergy

private

Energies

Referenced by get_kinetic_energy(), make_measurements(), and write_measurements_to_file().

◆ L

vector3 Blob::L

private

Momenta

Referenced by make_measurements().

◆ linear_solver

int Blob::linear_solver

private

Remember what type of solver we are using

Referenced by aggregate_forces_and_solve(), Blob(), config(), euler_integrate(), get_linear_solver(), init(), make_measurements(), pre_print(), update_internal_forces(), write_nodes_to_file(), write_pre_print_to_file(), and ~Blob().

◆ M

SparseMatrixFixedPattern* Blob::M

private

Referenced by build_mass_matrix().

◆ mass

scalar Blob::mass

private

Total mass of Blob

Referenced by Blob(), calc_rest_state_info(), get_mass(), and ~Blob().

◆ mass_in_blob

bool Blob::mass_in_blob

private

And whether or not there is mass in this system

Referenced by Blob(), init(), there_is_mass(), and ~Blob().

◆ nodal_q

scalar* Blob::nodal_q

private

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

◆ node

mesh_node* Blob::node

private

◆ node_position

vector3** Blob::node_position

private

Array of node positions only

Referenced by Blob(), get_actual_node_positions(), load_nodes(), and ~Blob().

◆ num_beads

int Blob::num_beads

private

Amount of interacting beads within this Blob will be zero after info is loaded into PreComp_solver

Referenced by Blob(), forget_beads(), get_num_beads(), is_using_beads(), load_beads(), position_beads(), print_bead_positions(), rotate(), and ~Blob().

◆ num_binding_sites

int Blob::num_binding_sites

Binding sites must be known publicly

Referenced by Blob(), World::calculate_kinetic_rates(), load_binding_sites(), and ~Blob().

◆ num_contributing_faces

int* Blob::num_contributing_faces

private

Referenced by Blob(), init(), solve_poisson(), and ~Blob().

◆ num_elements

◆ num_interior_elements

int Blob::num_interior_elements

private

Total number of interior elements in Blob

Referenced by Blob(), load_topology(), and ~Blob().

◆ num_interior_nodes

int Blob::num_interior_nodes

private

Total number of nodes on Blob interior

Referenced by Blob(), build_poisson_matrices(), create_viewer_node_file(), init(), load_nodes(), solve_poisson(), and ~Blob().

◆ num_l_ctf

int Blob::num_l_ctf

private

Number of ctforces to be applied to this Blob

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ num_nodes

int Blob::num_nodes

private

Total number of nodes in Blob

Referenced by aggregate_forces_and_solve(), Blob(), build_linear_node_elasticity_matrix(), build_linear_node_mass_matrix(), build_linear_node_rp_diffusion_matrix(), build_linear_node_viscosity_matrix(), build_mass_matrix(), calc_centroid(), calculate_node_element_connectivity(), compress_blob(), copy_node_positions(), create_viewer_node_file(), euler_integrate(), get_centroid(), get_min_max(), get_num_nodes(), init(), load_ctforces(), load_nodes(), load_pinned_nodes(), load_stokes_params(), load_surface(), load_surface_no_topology(), load_topology(), make_measurements(), move(), position(), pre_print(), print_node_positions(), read_nodes_from_file(), reset_solver(), rotate(), set_forces_to_zero(), set_node_positions(), set_pos_0(), translate_linear(), update_internal_forces(), velocity_all(), write_nodes_to_file(), write_pre_print_to_file(), and ~Blob().

◆ num_pinned_nodes

int Blob::num_pinned_nodes

private

Number of 'pinned' nodes (nodes which are not able to move, removing degrees of freedom from system)

Referenced by aggregate_forces_and_solve(), Blob(), init(), load_pinned_nodes(), reset_solver(), update_internal_forces(), and ~Blob().

◆ num_r_ctf

int Blob::num_r_ctf

private

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ num_slsets_ctf

int Blob::num_slsets_ctf

private

number of surface sets, corresponding to the length of the ctf_sl_forces, num_slsurf_ctf array

Referenced by apply_ctforces(), Blob(), load_ctforces(), and ~Blob().

◆ num_sltotal_ctf

int Blob::num_sltotal_ctf

private

Referenced by Blob(), load_ctforces(), and ~Blob().

◆ num_surface_elements

int Blob::num_surface_elements

private

Total number of surface elements in Blob

Referenced by Blob(), load_topology(), and ~Blob().

◆ num_surface_faces

int Blob::num_surface_faces

private

Total number of faces on Blob surface

Referenced by add_steric_nodes(), aggregate_forces_and_solve(), Blob(), calc_all_centroids(), calc_centroids_and_normals_of_all_faces(), calc_rest_state_info(), get_num_faces(), init(), kinetically_set_faces(), load_binding_sites(), load_ctforces(), load_ssint(), load_surface(), load_surface_no_topology(), solve_poisson(), zero_force(), and ~Blob().

◆ num_surface_nodes

int Blob::num_surface_nodes

private

Total number of nodes on Blob surface

Referenced by Blob(), create_viewer_node_file(), enforce_box_boundaries(), init(), load_nodes(), solve_poisson(), and ~Blob().

◆ params

SimulationParams* Blob::params

private

A pointer to a class containing simulation parameters, such as the time step, dt

Referenced by aggregate_forces_and_solve(), build_linear_node_rp_diffusion_matrix(), build_linear_node_viscosity_matrix(), config(), enforce_box_boundaries(), euler_integrate(), init(), load_ssint(), pre_print(), reset_solver(), update_internal_forces(), write_nodes_to_file(), and write_pre_print_to_file().

◆ pbc_count

int Blob::pbc_count[3]

Referenced by Blob(), and World::run().

◆ pc_params

PreComp_params* Blob::pc_params

private

Referenced by config(), and init().

◆ phi_Gamma

scalar* Blob::phi_Gamma

private

Referenced by Blob(), init(), solve_poisson(), and ~Blob().

◆ phi_Omega

scalar* Blob::phi_Omega

private

Referenced by Blob(), init(), solve_poisson(), and ~Blob().

◆ pinned_nodes_list

int* Blob::pinned_nodes_list

private

List of fixed ('pinned') nodes

Referenced by aggregate_forces_and_solve(), Blob(), create_pinned_nodes(), init(), load_pinned_nodes(), reset_solver(), and ~Blob().

◆ poisson_interior_matrix

SparseMatrixFixedPattern* Blob::poisson_interior_matrix

private

Referenced by Blob(), build_poisson_matrices(), init(), solve_poisson(), and ~Blob().

◆ poisson_rhs

scalar* Blob::poisson_rhs

private

Referenced by Blob(), init(), solve_poisson(), and ~Blob().

◆ poisson_solver

CG_solver* Blob::poisson_solver

private

Referenced by Blob(), init(), solve_poisson(), and ~Blob().

◆ poisson_surface_matrix

SparseMatrixFixedPattern* Blob::poisson_surface_matrix

private

Referenced by Blob(), build_poisson_matrices(), init(), solve_poisson(), and ~Blob().

◆ previous_conformation_index

int Blob::previous_conformation_index

Referenced by Blob(), get_previous_conformation_index(), pre_print(), set_previous_conformation_index(), and ~Blob().

◆ previous_state_index

int Blob::previous_state_index

Referenced by Blob(), get_previous_state_index(), pre_print(), set_previous_state_index(), and ~Blob().

◆ q

scalar* Blob::q

private

Referenced by Blob(), init(), solve_poisson(), and ~Blob().

◆ rmsd

scalar Blob::rmsd

private

Referenced by get_rmsd(), make_measurements(), and write_measurements_to_file().

◆ rng

RngStream* Blob::rng

private

The array of random number generators (needed for parallel runs)

Referenced by Blob(), config(), get_RandU01(), update_internal_forces(), and ~Blob().

◆ s_beads_filename

string Blob::s_beads_filename

private

Referenced by config(), and init().

◆ s_binding_filename

string Blob::s_binding_filename

private

Referenced by config(), and load_binding_sites().

◆ s_material_params_filename

string Blob::s_material_params_filename

private

Referenced by config(), and init().

◆ s_node_filename

string Blob::s_node_filename

private

Strings of all the files that contain input data:

Referenced by config(), and init().

◆ s_pin_filename

string Blob::s_pin_filename

private

Referenced by config(), and init().

◆ s_ssint_filename

string Blob::s_ssint_filename

private

Referenced by config(), and init().

◆ s_stokes_filename

string Blob::s_stokes_filename

private

Referenced by config(), and init().

◆ s_surface_filename

string Blob::s_surface_filename

private

Referenced by config(), and init().

◆ s_topology_filename

string Blob::s_topology_filename

private

Referenced by config(), and init().

◆ scale

scalar Blob::scale

private

Scale of the input coordinates to m:

Referenced by config(), get_scale(), init(), and load_stokes_params().

◆ solver

Solver* Blob::solver

private

A pointer to whatever Solver is being used for this Blob (eg SparseSubstitutionSolver or ConjugateGradientSolver). The Solver solves the equation Mx = f where M is the mass matrix of this Blob and f is the force vector.

Referenced by aggregate_forces_and_solve(), Blob(), init(), reset_solver(), and ~Blob().

◆ springs_on_blob

bool Blob::springs_on_blob

private

Are there springs on this blob?

Referenced by Blob(), set_springs_on_blob(), there_are_springs(), and ~Blob().

◆ ssint_bb_energy

scalar Blob::ssint_bb_energy

private

Total ssint energy between blobs

◆ ssint_matrix

SSINT_matrix* Blob::ssint_matrix

private

pointer to the ssint forcefield parameters (for some energy calcs)

Referenced by config(), and init().

◆ ssint_on_blob

bool Blob::ssint_on_blob

private

Are there ssint on this blob?

Referenced by Blob(), load_ssint(), there_is_ssint(), and ~Blob().

◆ state_index

int Blob::state_index

Referenced by Blob(), get_state_index(), pre_print(), set_state_index(), and ~Blob().

◆ strainenergy

scalar Blob::strainenergy

private

Referenced by get_strain_energy(), make_measurements(), and write_measurements_to_file().

◆ surface

Face* Blob::surface

private

◆ toBePrinted_conf

int Blob::toBePrinted_conf[2]

Referenced by pre_print().

◆ toBePrinted_nodes

scalar* Blob::toBePrinted_nodes

private

Referenced by Blob(), init(), pre_print(), write_pre_print_to_file(), and ~Blob().

◆ toBePrinted_state

int Blob::toBePrinted_state[2]

Referenced by pre_print(), and World::write_pre_print_to_trajfile().

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

◆ Blob()

◆ ~Blob()

Member Function Documentation

◆ absolutely_get_face()

◆ add_force_to_node()

◆ add_steric_nodes()

◆ aggregate_forces_and_solve()

◆ apply_ctforces()

◆ build_linear_node_elasticity_matrix()

◆ build_linear_node_mass_matrix()

◆ build_linear_node_rp_diffusion_matrix()

◆ build_linear_node_viscosity_matrix()

◆ build_mass_matrix()

◆ build_poisson_matrices()

◆ calc_all_centroids()

◆ calc_and_store_centroid()

◆ calc_centroid()

◆ calc_centroids_and_normals_of_all_faces()

◆ calc_rest_state_info()

◆ calc_volume()

◆ calculate_deformation()

◆ calculate_node_element_connectivity()

◆ calculate_strain_energy()

◆ check_inversion()

◆ compress_blob()

◆ config()

◆ copy_node_positions()

◆ create_pinned_nodes()

◆ create_viewer_node_file()

◆ enforce_box_boundaries()

◆ euler_integrate()

◆ get_actual_node_positions()

◆ get_binding_site()

◆ get_centroid()

◆ get_CoM()

◆ get_conformation_index()

◆ get_element()

◆ get_face()

◆ get_kinetic_energy()

◆ get_linear_solver()

◆ get_mass()

◆ get_min_max()

◆ get_motion_state()

◆ get_node()

◆ get_node_0()

◆ get_num_beads()

◆ get_num_elements()

◆ get_num_faces()

◆ get_num_linear_nodes()

◆ get_num_nodes()

◆ get_previous_conformation_index()

◆ get_previous_state_index()

◆ get_RandU01()

◆ get_rmsd()

◆ get_scale()

◆ get_ssint_area()

◆ get_state_index()

◆ get_stored_centroid()

◆ get_strain_energy()

◆ init()

◆ is_using_beads()

◆ kinetically_set_faces()

◆ linearise_elements()

◆ linearise_force()

◆ load_binding_sites()

◆ load_ctforces()

◆ load_material_params()

◆ load_nodes()

◆ load_pinned_nodes()

◆ load_ssint()

◆ load_stokes_params()

◆ load_surface()

◆ load_surface_no_topology()

◆ load_topology()