#include <ECM.h>

Public Member Functions
void	import_config (vector< string > configlines)

void	export_for_resume (int MD_step)

void	export_for_resume (int MD_step, MyAtomInfo atoms[], int atom_count)

void	set_state (MyAtomInfo all_atoms[], int atom_count)
	Set the current state (OpenMM) of the class. More...

void	set_label (std::string lab)
	Assigns the label(pdb) used to write to the trajectory files. More...

std::string	get_label (void)
	return the label(pdb) used to write to the trajectory files. More...

void	set_file_time (char *buffer)

void	set_index (int ind)

double	get_spring_stiffness_coefficient (void)
	Return spring stiffness coefficient. More...

double	get_stiffness_gradient_x (void)
	Return spring stiffness gradient_x. More...

double	get_stiffness_gradient_y (void)
	Return spring stiffness gradient_y. More...

double	get_stiffness_gradient_z (void)
	Return spring stiffness gradient_z. More...

int	get_receptor_type (void)
	Return receptor type. More...

double	get_receptor_density (void)
	Return receptor density. More...

double	get_receptor_center_x (void)
	Return receptor center_x. More...

double	get_receptor_center_y (void)
	Return receptor center_y. More...

double	get_receptor_center_z (void)
	Return receptor center_z. More...

double	get_receptor_gradient_x (void)
	Return receptor density gradient_x. More...

double	get_receptor_gradient_y (void)
	Return receptor density gradient_y. More...

double	get_receptor_gradient_z (void)
	Return receptor density gradient_z. More...

int	get_num_of_nodes (void)
	public access to total number of ECM nodes. More...

int	get_num_of_triangles (void)
	public access to the total number of triangles in the ECM. More...

double	get_node_mass (void)
	Return the node mass. More...

int	get_num_of_node_pairs (void)
	Return the number of bonds between membrane nodes. More...

int	get_spring_model (void)
	Return input spring model, used to setup the openmm system for the bonds. More...

int	get_node_pair (int bond_num, int node_id)
	Return the id(int) of the nodes in the bonds. More...

double	get_avg_node_dist (void)
	Return the average distance of the nodes as calculated from the mesh. More...

double	get_sigma_LJ_12_6 (void)
	Return the Lenard Jones 12 6 sigma, used to setup the openmm system for the LJ interaction. More...

double	get_epsilon_LJ_12_6 (void)
	Return the Lenard Jones 12 6 sigma, used to setup the openmm system for the LJ interaction. More...

double	get_node_radius (void)

double	get_interaction_range (void)

void	set_interaction_range (double range)

double	get_epsilon (void)

double	get_sigma (void)

int	get_ext_force_model (void)
	Return external force model. More...

double	get_kx (void)

double	get_ky (void)

double	get_kz (void)

double	get_node_position (int node_number, int node_coordinate)

void	add_to_force (double force, int index, int coor)

void	shift_node_positions (void)

void	shift_velocity (double vx, double vy, double vz)

double	get_node_velocity (int node_number, int node_coordinate)
	Returns the x (0), y (1), and z (2) velocities of the node index (number). More...

void	update_COM_velocity (void)

void	update_COM_position (void)

void	set_FENE_param (double &le0, double &le1, double &lmin, double &lmax)
	Set FENE calculated parameters. More...

	ECM ()

std::map< string, vector< string > >	get_map ()

vector< string >	get_insertOrder ()

void	assign_key_value (string key, string value)

Public Attributes
std::string	output_file_neme

std::map< string, vector< string > >	Params

vector< string >	insertOrder

vector< string >	values

Private Member Functions
void	Node_Bond_identifier_2D (void)

void	Node_Bond_identifier_3D (void)

void	Node_Bond_identifier_3D_square (void)

void	initialise (int dimension)

void	Node_neighbour_list_constructor (void)

void	read_gmesh_file_2D (std::string gmesh_file)

void	read_gmesh_file_3D (std::string gmesh_file)

void	read_gmesh_file_3D_square (std::string gmesh_file)

void	normal_direction_Identifier (double x, double y, double z)

void	normal_direction_Identifier (void)

void	check (void)

Private Attributes
std::string	label

std::string	Mesh_file_name

std::string	file_time

int	index

std::map< std::string, double >	param_map

double	Node_Mass =1

double	Node_radius =1

int	spring_model =1

double	Spring_coefficient =10

double	stiffness_gradient_x =0

double	stiffness_gradient_y =0

double	stiffness_gradient_z =0

int	receptor_type = 1

double	receptor_density = 0.5

double	receptor_center_x = 0

double	receptor_center_y = 0

double	receptor_center_z = 0

double	receptor_gradient_x = 0

double	receptor_gradient_y = 0

double	receptor_gradient_z = 0

double	Shift_in_X_direction =0

double	Shift_in_Y_direction =0

double	Shift_in_Z_direction =0

int	Num_of_Nodes =0

int	Num_of_Triangle_Pairs =0

int	Num_of_Node_Pairs =0

int	Num_of_Triangles =0

double	x_speed =0.0

double	y_speed =0.0

double	z_speed =0.0

int	ext_force_model =0

double	kx =10

double	ky =10

double	kz =10

double	Kelvin_Damping_Coefficient =100

double	Dashpot_Viscosity =0.02

vector< vector< double > >	Node_Force

vector< vector< double > >	Node_Position

vector< vector< int > >	Triangle_List

vector< vector< int > >	Pyramid_Nodes

vector< vector< int > >	square_Nodes

double	interaction_range =1.0

double	epsilon =0.6

double	sigma =15.0

double	COM_velocity [3] ={0}

double	COM_position [3] ={0}

double	Min_node_pair_length

double	Max_node_pair_length

double	Average_node_pair_length

double	rescale_factor

double	sigma_LJ_12_6 =0

double	epsilon_LJ_12_6 =0

vector< vector< double > >	Node_Velocity

vector< vector< int > >	Node_Bond_list

vector< vector< int > >	Node_neighbour_list

Constructor & Destructor Documentation

◆ ECM()

ECM::ECM ( )

inline

Member Function Documentation

◆ add_to_force()

void ECM::add_to_force	(	double	force,
		int	index,
		int	coor
	)

inline

◆ assign_key_value()

void ECM::assign_key_value	(	string	key,
		string	value
	)

inline

◆ check()

void ECM::check ( void )

private

◆ export_for_resume() [1/2]

void ECM::export_for_resume ( int MD_step )

◆ export_for_resume() [2/2]

void ECM::export_for_resume	(	int	MD_step,
		MyAtomInfo	atoms[],
		int	atom_count
	)

◆ get_avg_node_dist()

double ECM::get_avg_node_dist ( void )

inline

Return the average distance of the nodes as calculated from the mesh.

◆ get_epsilon()

double ECM::get_epsilon ( void )

inline

◆ get_epsilon_LJ_12_6()

double ECM::get_epsilon_LJ_12_6 ( void )

inline

Return the Lenard Jones 12 6 sigma, used to setup the openmm system for the LJ interaction.

◆ get_ext_force_model()

int ECM::get_ext_force_model ( void )

inline

Return external force model.

◆ get_insertOrder()

vector<string > ECM::get_insertOrder ( )

inline

◆ get_interaction_range()

double ECM::get_interaction_range ( void )

inline

◆ get_kx()

double ECM::get_kx ( void )

inline

◆ get_ky()

double ECM::get_ky ( void )

inline

◆ get_kz()

double ECM::get_kz ( void )

inline

◆ get_label()

std::string ECM::get_label ( void )

inline

return the label(pdb) used to write to the trajectory files.

◆ get_map()

std::map<string, vector<string> > ECM::get_map ( )

inline

◆ get_node_mass()

double ECM::get_node_mass ( void )

inline

Return the node mass.

At the current stage of this code all membrane nodes have the same mass.

◆ get_node_pair()

int ECM::get_node_pair	(	int	bond_num,
		int	node_id
	)

inline

Return the id(int) of the nodes in the bonds.

The id of each node in the bond list is stored in the first (0) and the second (1) id slot.

◆ get_node_position()

double ECM::get_node_position	(	int	node_number,
		int	node_coordinate
	)

inline

◆ get_node_radius()

double ECM::get_node_radius ( void )

inline

◆ get_node_velocity()

double ECM::get_node_velocity	(	int	node_number,
		int	node_coordinate
	)

inline

Returns the x (0), y (1), and z (2) velocities of the node index (number).

◆ get_num_of_node_pairs()

int ECM::get_num_of_node_pairs ( void )

inline

Return the number of bonds between membrane nodes.

◆ get_num_of_nodes()

int ECM::get_num_of_nodes ( void )

inline

public access to total number of ECM nodes.

Returns: integer number of nodes in the ECM.

◆ get_num_of_triangles()

int ECM::get_num_of_triangles ( void )

inline

public access to the total number of triangles in the ECM.

◆ get_receptor_center_x()

double ECM::get_receptor_center_x ( void )

inline

Return receptor center_x.

◆ get_receptor_center_y()

double ECM::get_receptor_center_y ( void )

inline

Return receptor center_y.

◆ get_receptor_center_z()

double ECM::get_receptor_center_z ( void )

inline

Return receptor center_z.

◆ get_receptor_density()

double ECM::get_receptor_density ( void )

inline

Return receptor density.

◆ get_receptor_gradient_x()

double ECM::get_receptor_gradient_x ( void )

inline

Return receptor density gradient_x.

◆ get_receptor_gradient_y()

double ECM::get_receptor_gradient_y ( void )

inline

Return receptor density gradient_y.

◆ get_receptor_gradient_z()

double ECM::get_receptor_gradient_z ( void )

inline

Return receptor density gradient_z.

◆ get_receptor_type()

int ECM::get_receptor_type ( void )

inline

Return receptor type.

◆ get_sigma()

double ECM::get_sigma ( void )

inline

◆ get_sigma_LJ_12_6()

double ECM::get_sigma_LJ_12_6 ( void )

inline

Return the Lenard Jones 12 6 sigma, used to setup the openmm system for the LJ interaction.

◆ get_spring_model()

int ECM::get_spring_model ( void )

inline

Return input spring model, used to setup the openmm system for the bonds.

◆ get_spring_stiffness_coefficient()

double ECM::get_spring_stiffness_coefficient ( void )

inline

Return spring stiffness coefficient.

◆ get_stiffness_gradient_x()

double ECM::get_stiffness_gradient_x ( void )

inline

Return spring stiffness gradient_x.

◆ get_stiffness_gradient_y()

double ECM::get_stiffness_gradient_y ( void )

inline

Return spring stiffness gradient_y.

◆ get_stiffness_gradient_z()

double ECM::get_stiffness_gradient_z ( void )

inline

Return spring stiffness gradient_z.

◆ import_config()

void ECM::import_config ( vector< string > configlines )

◆ initialise()

void ECM::initialise ( int dimension )

private

◆ Node_Bond_identifier_2D()

void ECM::Node_Bond_identifier_2D ( void )

private

◆ Node_Bond_identifier_3D()

void ECM::Node_Bond_identifier_3D ( void )

private

◆ Node_Bond_identifier_3D_square()

void ECM::Node_Bond_identifier_3D_square ( void )

private

◆ Node_neighbour_list_constructor()

void ECM::Node_neighbour_list_constructor ( void )

private

◆ normal_direction_Identifier() [1/2]

void ECM::normal_direction_Identifier	(	double	x,
		double	y,
		double	z
	)

private

◆ normal_direction_Identifier() [2/2]

void ECM::normal_direction_Identifier ( void )

private

◆ read_gmesh_file_2D()

void ECM::read_gmesh_file_2D ( std::string gmesh_file )

private

◆ read_gmesh_file_3D()

void ECM::read_gmesh_file_3D ( std::string gmesh_file )

private

◆ read_gmesh_file_3D_square()

void ECM::read_gmesh_file_3D_square ( std::string gmesh_file )

private

◆ set_FENE_param()

void ECM::set_FENE_param	(	double &	le0,
		double &	le1,
		double &	lmin,
		double &	lmax
	)

inline

Set FENE calculated parameters.

◆ set_file_time()

void ECM::set_file_time ( char * buffer )

inline

◆ set_index()

void ECM::set_index ( int ind )

inline

◆ set_interaction_range()

void ECM::set_interaction_range ( double range )

inline

◆ set_label()

void ECM::set_label ( std::string lab )

inline

Assigns the label(pdb) used to write to the trajectory files.

◆ set_state()

void ECM::set_state	(	MyAtomInfo	all_atoms[],
		int	atom_count
	)

Set the current state (OpenMM) of the class.

◆ shift_node_positions()

void ECM::shift_node_positions ( void )

inline

◆ shift_velocity()

void ECM::shift_velocity	(	double	vx,
		double	vy,
		double	vz
	)

inline

◆ update_COM_position()

void ECM::update_COM_position ( void )

inline

◆ update_COM_velocity()

void ECM::update_COM_velocity ( void )

inline

Member Data Documentation

◆ Average_node_pair_length

double ECM::Average_node_pair_length

private

◆ COM_position

double ECM::COM_position[3] ={0}

private

◆ COM_velocity

double ECM::COM_velocity[3] ={0}

private

◆ Dashpot_Viscosity

double ECM::Dashpot_Viscosity =0.02

private

◆ epsilon

double ECM::epsilon =0.6

private

◆ epsilon_LJ_12_6

double ECM::epsilon_LJ_12_6 =0

private

◆ ext_force_model

int ECM::ext_force_model =0

private

◆ file_time

std::string ECM::file_time

private

◆ index

int ECM::index

private

◆ insertOrder

vector<string> ECM::insertOrder

◆ interaction_range

double ECM::interaction_range =1.0

private

◆ Kelvin_Damping_Coefficient

double ECM::Kelvin_Damping_Coefficient =100

private

◆ kx

double ECM::kx =10

private

◆ ky

double ECM::ky =10

private

◆ kz

double ECM::kz =10

private

◆ label

std::string ECM::label

private

◆ Max_node_pair_length

double ECM::Max_node_pair_length

private

◆ Mesh_file_name

std::string ECM::Mesh_file_name

private

◆ Min_node_pair_length

double ECM::Min_node_pair_length

private

◆ Node_Bond_list

vector<vector<int> > ECM::Node_Bond_list

private

◆ Node_Force

vector<vector<double> > ECM::Node_Force

private

◆ Node_Mass

double ECM::Node_Mass =1

private

◆ Node_neighbour_list

vector<vector<int> > ECM::Node_neighbour_list

private

◆ Node_Position

vector<vector<double> > ECM::Node_Position

private

◆ Node_radius

double ECM::Node_radius =1

private

◆ Node_Velocity

vector<vector<double> > ECM::Node_Velocity

private

◆ Num_of_Node_Pairs

int ECM::Num_of_Node_Pairs =0

private

◆ Num_of_Nodes

int ECM::Num_of_Nodes =0

private

◆ Num_of_Triangle_Pairs

int ECM::Num_of_Triangle_Pairs =0

private

◆ Num_of_Triangles

int ECM::Num_of_Triangles =0

private

◆ output_file_neme

std::string ECM::output_file_neme

◆ param_map

std::map<std::string, double> ECM::param_map

private

◆ Params

std::map<string, vector<string> > ECM::Params

◆ Pyramid_Nodes

vector<vector<int> > ECM::Pyramid_Nodes

private

◆ receptor_center_x

double ECM::receptor_center_x = 0

private

◆ receptor_center_y

double ECM::receptor_center_y = 0

private

◆ receptor_center_z

double ECM::receptor_center_z = 0

private

◆ receptor_density

double ECM::receptor_density = 0.5

private

◆ receptor_gradient_x

double ECM::receptor_gradient_x = 0

private

◆ receptor_gradient_y

double ECM::receptor_gradient_y = 0

private

◆ receptor_gradient_z

double ECM::receptor_gradient_z = 0

private

◆ receptor_type

int ECM::receptor_type = 1

private

◆ rescale_factor

double ECM::rescale_factor

private

◆ Shift_in_X_direction

double ECM::Shift_in_X_direction =0

private

◆ Shift_in_Y_direction

double ECM::Shift_in_Y_direction =0

private

◆ Shift_in_Z_direction

double ECM::Shift_in_Z_direction =0

private

◆ sigma

double ECM::sigma =15.0

private

◆ sigma_LJ_12_6

double ECM::sigma_LJ_12_6 =0

private

◆ Spring_coefficient

double ECM::Spring_coefficient =10

private

◆ spring_model

int ECM::spring_model =1

private

◆ square_Nodes

vector<vector<int> > ECM::square_Nodes

private

◆ stiffness_gradient_x

double ECM::stiffness_gradient_x =0

private

◆ stiffness_gradient_y

double ECM::stiffness_gradient_y =0

private

◆ stiffness_gradient_z

double ECM::stiffness_gradient_z =0

private

◆ Triangle_List

vector<vector<int> > ECM::Triangle_List

private

◆ values

vector<string> ECM::values

◆ x_speed

double ECM::x_speed =0.0

private

◆ y_speed

double ECM::y_speed =0.0

private

◆ z_speed

double ECM::z_speed =0.0

private

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

/Users/ali/Documents/Dr Ejtehadi/Programming/Latest Tiam/Ali/Membrane_OBJ/include/ECM.h

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ ECM()

Member Function Documentation

◆ add_to_force()

◆ assign_key_value()

◆ check()

◆ export_for_resume() [1/2]

◆ export_for_resume() [2/2]

◆ get_avg_node_dist()

◆ get_epsilon()

◆ get_epsilon_LJ_12_6()

◆ get_ext_force_model()

◆ get_insertOrder()

◆ get_interaction_range()

◆ get_kx()

◆ get_ky()

◆ get_kz()

◆ get_label()

◆ get_map()

◆ get_node_mass()

◆ get_node_pair()

◆ get_node_position()

◆ get_node_radius()

◆ get_node_velocity()

◆ get_num_of_node_pairs()

◆ get_num_of_nodes()

◆ get_num_of_triangles()

◆ get_receptor_center_x()

◆ get_receptor_center_y()

◆ get_receptor_center_z()

◆ get_receptor_density()

◆ get_receptor_gradient_x()

◆ get_receptor_gradient_y()

◆ get_receptor_gradient_z()

◆ get_receptor_type()

◆ get_sigma()

◆ get_sigma_LJ_12_6()

◆ get_spring_model()

◆ get_spring_stiffness_coefficient()

◆ get_stiffness_gradient_x()

◆ get_stiffness_gradient_y()

◆ get_stiffness_gradient_z()

◆ import_config()

◆ initialise()

◆ Node_Bond_identifier_2D()

◆ Node_Bond_identifier_3D()

◆ Node_Bond_identifier_3D_square()

◆ Node_neighbour_list_constructor()

◆ normal_direction_Identifier() [1/2]

◆ normal_direction_Identifier() [2/2]

◆ read_gmesh_file_2D()

◆ read_gmesh_file_3D()

◆ read_gmesh_file_3D_square()

◆ set_FENE_param()

◆ set_file_time()

◆ set_index()

◆ set_interaction_range()

◆ set_label()

◆ set_state()

◆ shift_node_positions()

◆ shift_velocity()

◆ update_COM_position()

◆ update_COM_velocity()

Member Data Documentation

◆ Average_node_pair_length

◆ COM_position

◆ COM_velocity

◆ Dashpot_Viscosity

◆ epsilon

◆ epsilon_LJ_12_6

◆ ext_force_model

◆ file_time

◆ index

◆ insertOrder

◆ interaction_range

◆ Kelvin_Damping_Coefficient