The class 'Membrane' manages the required enviroment (system, forces, etc) of coordinates on a triangular mesh. More...

#include <Include/Membrane.h>

Public Member Functions
void	rotate_coordinates (double theta, double phi)

void	rotate_particle_to_axes (ArgStruct_Analysis args)

void	update_spherical_positions ()

void	convert_spherical_positions_to_cartisian ()

void	analysis_init (std::string Mesh_path)

void	get_ground_state_from_mesh (ArgStruct_Analysis args)

void	get_ground_state_from_frame (ArgStruct_Analysis args)

void	calculate_dOmega (void)

void	load_pdb_frame (int frame, ArgStruct_Analysis args)

void	import_pdb_frames (ArgStruct_Analysis args, int file_index)

void	generate_ulm_mode (int ell, int m, double ulm, double radius)

void	generate_ulm_mode_real (int Ell, int M, double uLM, double radius)

void	add_ulm_mode_real (int Ell, int M, double uLM, double radius)

void	myWritePDBFrame (int frameNum, std::string traj_name)

std::complex< double >	calc_vectorlist_vectorlist_surface_integral (vector< std::complex< double > > vectorlist1, vector< std::complex< double > > vectorlist2)

std::complex< double >	calc_vectorlist_vectorlist_surface_integral (vector< std::complex< double > > vectorlist1, vector< double > vectorlist2)

double	calc_vectorlist_vectorlist_surface_integral (vector< double > vectorlist1, vector< double > vectorlist2)

vector< std::complex< double > >	get_ylm_vectorlist_for_mesh (int ell, int m, bool complex_conjugate)

vector< double >	get_real_ylm_vectorlist_for_mesh (int ell, int m)

vector< double >	get_ulmYlm_vectorlist_for_mesh ()

vector< double >	get_ulmYlm_vectorlist_for_mesh (char Requiv)

void	get_ring (ArgStruct_Analysis args)

void	get_ring_from_projection (ArgStruct_Analysis args, int numpoints)

void	calculate_freqs (ArgStruct_Analysis args)

void	calculate_freqs_projection (ArgStruct_Analysis args)

void	calculate_2D_amplitudes_Alexandra (int q_max)

void	calculate_deltaphi (void)

void	calculate_deltaphi_Alexandra (void)

void	updatepos (double)

void	WriteMemPDBFrame (ArgStruct_Analysis args, vector< int > chainlist)

void	calculate_contourSegmentLength (void)

void	calculate_contourRadius (void)

void	calculate_modeAmplitudes2D (void)

std::complex< double >	calc_complex_ylm_surface_integral (int ell, int m, double radius)

std::complex< double >	calc_complex_ylmthetaphi (int l, int m, double theta, double phi)
	return the complex spherical harmonic for the provided parameters: Y_l,m (theta, phi). More...

double	calc_real_ylmthetaphi (int l, int m, double theta, double phi)

void	calculate_ulm (ArgStruct_Analysis args)

void	calculate_real_ulm (ArgStruct_Analysis args)

void	calculate_real_ulm (ArgStruct_Analysis args, char Requiv, bool clear)

void	calculate_ulm_radiustest (int ell_max, int analysis_averaging_option)

void	calculate_ulm_radiustest_real (int ell_max, int analysis_averaging_option)

void	calculate_ulm_sub_particles (int ell_max, int analysis_averaging_option)

void	write_ulm (ArgStruct_Analysis args, int file_index)

void	write_un_uq (ArgStruct_Analysis args, int file_index)

void	write_un_uq_projection (ArgStruct_Analysis args, int file_index)

void	write_uq_SH (ArgStruct_Analysis args, int file_index)

double	calc_assoc_legendre (int ell, int m, double x)

void	calculateH_2D_amplitudes (int q_max)

void	calculateH_2D_amplitudes_projection (int q_max, int numpoints)

void	calculate_2D_amplitudes_Alexandra_projection (int q_max, int numpoints)

void	set_com_to_zero ()

bool	get_GeometricProps_flag ()
	Return the geometrical properties write status. More...

void	write_geometrics ()

double	calculate_bending_energy (void)
	Returns the total bending energy of the membrane (indepentant of OpenMM calculations) More...

double	get_new_radius (void)
	Returns the node radius update value (set value in the configuration file). More...

bool	get_update_status (void)
	Returns whether the Membrane is setup for radius change (true) or not (false). More...

void	check (void)

void	get_bond_length_distribution (void)

void	set_bond_nominal_length (void)

void	set_node_radius (void)

void	set_bending_nominal_angle (void)

void	set_dihedral_atoms (void)

void	check_radius_update_values (void)

void	Triangle_Pair_and_Node_Bonds_Identifier ()

void	Elastic_Force_Calculator (double theta_0)

void	Mechanical_Energy_calculator ()

void	Export_Mechanical_Energy (string filename, int frame)

void	harmonic_potential_calculator (void)

void	Node_neighbour_list_constructor ()
	Construct a vector that lists all the neighbours of each node and their respective index in the 'Node_Bond_list'. More...

void	Bond_triangle_neighbour_list_constructor ()
	Construct a vector that lists the triangle neighbours of each node pair. More...

void	export_for_resume (int MD_step)

void	find_the_new_neighbour (int neighbour_id[6], int previous_dihedral_index, int initial_pair, bool A_or_B)

void	monte_carlo_flip (MyOpenMMData omm, Bonds bonds, Dihedrals *dihedrals, MyAtomInfo atoms[], double &localDeltaE, int &Accepted_Try_Counter, int &pyramid_counter, int &MC_total_tries, double &MC_Acceptance_Rate)

double	calculating_the_bond_energy (int index, bool initial_or_final, MyAtomInfo atoms[], int number_of_privious_mem_nodes)

double	calculating_the_bond_energy_check (int p1, int p2, MyAtomInfo atoms[])

double	calculating_the_bend_energy (int uncommn1, int common2, int common3, int uncommon4, bool initial_or_final, MyAtomInfo atoms[], int number_of_privious_mem_nodes)

double	calculating_the_bend_energy_2 (int uncommon1, int common2, int common3, int uncommon4, MyAtomInfo atoms[], int number_of_privious_mem_nodes)

double	calculating_the_bond_length_check (int p1, int p2, MyAtomInfo atoms[])

void	check_before_update (int triangle_A, int triangle_B, int new_neighbour_dihedrals[4][6], int &pyramid_counter, bool &accept)

void	update_Membrane_class_and_openmm (int initial_pair, int triangle_A, int triangle_B, int new_neighbour_dihedrals[4][6], MyOpenMMData omm, Bonds bonds, Dihedrals *dihedrals)

void	Update_Membrane (int initial_pair, int triangle_A, int triangle_B, int new_neighbour_dihedrals[4][6], int &bond_index)

bool	check_Pyramid (vector< int > A_neighbors, vector< int > B_neighbors)

bool	check_Pyramid_2 (int initial_pair, vector< int > A_neighbours_dihedral_index, vector< int > B_neighbours_dihedral_index)

void	check_the_flip (MyOpenMMData omm, Bonds bonds, Dihedrals *dihedrals)

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

void	initialise (std::string Mesh_file_name)

void	import (std::string import_file_name)

void	import_config (vector< string > configlines)

void	write_pov_traj (std::string traj_name, std::string label, int currentstep)

vector< double >	get_gompper_params_lminlc1lc0lmax ()

double	get_volume (void)
	Returns the last saved volume. More...

vector< double >	get_voronoi_node_area ()
	Calculate the voronoi area of each node and return a list that indicated the voronoi area of each node. More...

void	calculate_volume_and_surface_area (void)
	Calculate the volume of a closed membrane by summing triangular pyramids. More...

void	calculate_surface_area_with_voronoi (void)
	Calculate the volume of a closed membrane by summing triangular pyramids. More...

double	get_surface_area (void)
	Returns the last saved surface area. More...

double	get_End_update_time_in_Ps (void)
	Return the new node radius 'end update time' in Ps. More...

double	get_Begin_update_time_in_Ps (void)
	Return the new node radius 'begin update time' in Ps. More...

vector< double >	get_node_normal_vec (int node)
	return normal vector of each node. More...

double	get_node_voronoi_area (int node)
	return the voronoi area associated with each node. More...

double	get_surface_area_voronoi ()
	Return the sum of the voronoi area of each node. More...

void	rescale_membrane (double factor)

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...

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

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

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

double	get_node_pair_Nominal_Length_in_Nm (int bond_num)
	Return the distance between node pair index. More...

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

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

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

double	get_damping_coefficient (void)
	Return damp coefficient. More...

double	get_bending_stiffness_coefficient (void)
	Return bending stiffness coefficient. More...

double	get_spontaneous_angle_in_Rad (int nodePairIndex)
	Return the spontaneous bending angle between triangle pairs in radians. More...

int	get_num_of_triangle_pairs ()
	Return the spontaneous bending angle between triangle pairs in radians. More...

vector< int >	get_traingle_pair_nodes_list (int triangle_pair)
	Return the node IDs of the dihedral angles. More...

vector< int >	get_dihedral_atoms_list (int index)
	Return the node IDs of the dihedral angles. More...

int	get_traingle_pair_node (int triangle_pair, int index)
	Return the node ID of the dihedral angles member. More...

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

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

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

double	get_kx (void)

double	get_ky (void)

double	get_kz (void)

void	set_FENE_param_2 (double &lmin, double &lmax, double &epsilon, double &k)

double	calc_theta_angle_ABC (int node_A, int node_B, int node_C)
	Calculate and return the cot of the angle between nodes A(middle of the angle), B, and C. More...

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

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

int	get_num_of_triangle ()
	Returns the calculated number of triangles in the imported mesh file. More...

double	get_spherical_position (int node_number, int node_coordinate)
	Returns the r (0), theta (1), and phi (2) spherical coordinate of the node index (number). More...

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

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

void	set_file_time (char *buffer)

void	set_index (int ind)

double	get_node_radius (int index)

double	get_membrane_weighted_radius (void)

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

void	update_COM_velocity (void)

void	update_COM_position (void)

void	shift_position (double x, double y, double z)
	This function shifts the whole membrane. More...

void	update_average_Membrane_radius (void)

double	get_average_Membrane_radius (void)

double	get_new_Membrane_radius (void)

void	ranfomundulationgenerator (void)

	Membrane ()

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

vector< string >	get_insertOrder ()

void	assign_parameters (void)

void	consistancy_check (void)

Public Attributes
bool	initial_random_rotation_coordinates = false

vector< double >	node_dOmega

vector< int >	ringNodeList

vector< double >	contourradii

vector< double >	contourSegmentLength

vector< vector< double > >	aq_alexandra

vector< vector< double > >	bq_alexandra

vector< vector< double > >	Aq_H

vector< vector< double > >	Bq_H

vector< vector< double > >	aq_alexandra_proj

vector< vector< double > >	bq_alexandra_proj

vector< vector< double > >	Aq_H_proj

vector< vector< double > >	Bq_H_proj

vector< double >	deltaphi

vector< int >	chainlist

vector< vector< double > >	ulm_avg

vector< vector< double > >	ulm_std

vector< vector< double > >	ulm_Mesh

vector< vector< double > >	ulm_temp_for_analysis

double	contourRadius

vector< double >	pdb_frames_time

vector< vector< vector< double > > >	pdb_frames

vector< vector< double > >	spherical_positions

std::string	output_file_neme

std::string	file_time

vector< vector< double > >	Node_Position

vector< vector< int > >	Triangle_list

vector< vector< int > >	Triangle_pair_list

vector< vector< int > >	Node_Bond_list

vector< double >	Node_Bond_Nominal_Length_in_Nm

string	Node_Bond_Nominal_Length_stat

double	Node_Bond_user_defined_Nominal_Length_in_Nm

vector< double >	Triangle_pair_angles_in_radians

string	Triangle_pair_angle_stat

double	Triangle_pair_Nominal_angle_in_degrees =-1

vector< vector< int > >	Triangle_Pair_Nodes

vector< vector< double > >	Node_Velocity

vector< vector< double > >	Node_Force

vector< vector< int > >	Node_neighbour_list
	This list is used to store all the neighbours of nodes: Example: If node i has 4 neighbours: m, n, o, p Then we find these neighbours in the 'Node_neighbour_list' as follows: Node_neighbour_list [ i ][0] = m Node_neighbour_list [ i ][1] = n Node_neighbour_list [ i ][2] = o Node_neighbour_list [ i ][3] = p. More...

vector< vector< int > >	Node_neighbour_list_respective_bond_index
	This list is used to cross reference the neighbouring nodes to their respective index in the 'Node_neighbour_list'. More...

vector< vector< double > >	node_voronoi_normal_vec

vector< double >	node_voronoi_area

double	surface_area_voronoi =0

vector< double >	GompperBondPotentialLminLc1Lc0Lmax

vector< int >	Bond_triangle_neighbour_indices

bool	check_monte_carlo =0

int	spring_model =0

int	bending_model =0

string	mesh_format

double	Spring_coefficient =0.

double	Bending_coefficient =0.

double	SpontaneousTriangleBendingInDegrees =0.

double	Damping_coefficient =0.0

vector< double >	Shift_position_xyzVector

vector< double >	Shift_velocities_xyzVector

int	ext_force_model =0

double	kx =10

double	ky =10

double	kz =10

double	Min_node_pair_length

double	Max_node_pair_length

double	Average_node_pair_length

double	rescale_factor =1

bool	AddRandomModes = false

int	NumberOfRandomModes

int	EllMaxOfRandomModes

double	UlmOfRandomModes

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

vector< string >	insertOrder

vector< string >	values

Protected Member Functions
double	Average_Node_Distance ()

void	read_gmesh_file (std::string gmesh_file)

void	read_ply_file (std::string ply_file)

void	Triangle_pair_counter ()

void	Normal_direction_Identifier ()

void	FENE_log (void)

void	custom (void)

void	Node_Bonds_identifier (void)

void	Triangle_pair_identifier (void)

void	Bending_potetial_2 (double theta_0)

void	calculating_dihedral_energy ()

Protected Attributes
std::string	label
	Store the label(pdb) used to write to the trajectory file. More...

int	index
	Store the mem index the instance of the class has in the vector of Membranes in the main programme. More...

double	volume
	Store the volume of the membrane. More...

double	surface_area
	Store the surface area of the membrane. More...

int	Num_of_Nodes =0
	Number of nodes in the membrane. More...

int	Num_of_Triangles
	This is the number of nodes on the membrane (Both the outer membrane and the Nucleus). This is the first number that appears in the 'membrane' file (once opend with a text editor) More...

std::map< std::string, double >	param_map
	This is the number of triangles on the membrane (Both the outer membrane and the Nucleus). This is the number that appears in the 'membrane' file after the node position list is finished and before Gmesh lists the nodes that make a triangle. More...

std::string	Mesh_file_name ="None"

std::string	resume_file_name ="None"

double	sigma_LJ_12_6 =0

double	epsilon_LJ_12_6 =0

double	Node_Mass =1.0

double	Total_Potential_Energy =0.0

double	Total_Bond_Energy =0.0

double	Total_Bending_Energy =0.0

double	Total_Kinetic_Energy

double	Radius =0

string	Node_radius_stat

vector< double >	Node_radius

double	New_Radius =-1

double	New_node_radius =-1

double	Begin_update_time_in_Ps =0

double	End_update_time_in_Ps =0

bool	update_radius_stat =false

double	COM_velocity [3] ={0}

double	COM_position [3] ={0}

double	FENE_min =0

double	FENE_max =0

double	FENE_epsilon =0

double	FENE_k =0

int	Num_of_Node_Pairs

int	Num_of_Triangle_Pairs

double	X_in =0

double	Y_in =0

double	Z_in =0

double	X_scale =0

double	Y_scale =0

double	Z_scale =0

vector< vector< int > >	dihedral_atoms

bool	WantGeometricProps =false
	write geometrical properties if it is true. More...

Detailed Description

The class 'Membrane' manages the required enviroment (system, forces, etc) of coordinates on a triangular mesh.

The Membrane class deciphers the mesh coordinates from the input mesh file provided in the configuration file. The bond information is also extracted from the mesh file and stored in the class. The various interactions of membrane nodes and all the membrane node info is also stored in this class.

Note: Work in progress.

Contact: a.far.nosp@m.nudi.nosp@m.@gmai.nosp@m.l.co.nosp@m.m

Constructor & Destructor Documentation

◆ Membrane()

Membrane::Membrane ( )

inline

Member Function Documentation

◆ add_to_force()

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

inline

◆ add_ulm_mode_real()

void Membrane::add_ulm_mode_real	(	int	Ell,
		int	M,
		double	uLM,
		double	radius
	)

◆ analysis_init()

void Membrane::analysis_init ( std::string Mesh_path )

◆ assign_parameters()

void Membrane::assign_parameters ( void )

◆ Average_Node_Distance()

double Membrane::Average_Node_Distance ( )

protected

◆ Bending_potetial_2()

void Membrane::Bending_potetial_2 ( double theta_0 )

protected

◆ Bond_triangle_neighbour_list_constructor()

void Membrane::Bond_triangle_neighbour_list_constructor ( )

Construct a vector that lists the triangle neighbours of each node pair.

◆ calc_assoc_legendre()

double Membrane::calc_assoc_legendre	(	int	ell,
		int	m,
		double	x
	)

◆ calc_complex_ylm_surface_integral()

std::complex<double> Membrane::calc_complex_ylm_surface_integral	(	int	ell,
		int	m,
		double	radius
	)

◆ calc_complex_ylmthetaphi()

std::complex<double> Membrane::calc_complex_ylmthetaphi	(	int	l,
		int	m,
		double	theta,
		double	phi
	)

return the complex spherical harmonic for the provided parameters: Y_l,m (theta, phi).

Where l is a positiv integer, m is defined -l <= m <= l, theta is 0 <= theta <= pi, and phi is defined 0 <= phi <= 2pi. s

◆ calc_real_ylmthetaphi()

double Membrane::calc_real_ylmthetaphi	(	int	l,
		int	m,
		double	theta,
		double	phi
	)

◆ calc_theta_angle_ABC()

double Membrane::calc_theta_angle_ABC	(	int	node_A,
		int	node_B,
		int	node_C
	)

Calculate and return the cot of the angle between nodes A(middle of the angle), B, and C.

◆ calc_vectorlist_vectorlist_surface_integral() [1/3]

double Membrane::calc_vectorlist_vectorlist_surface_integral	(	vector< double >	vectorlist1,
		vector< double >	vectorlist2
	)

◆ calc_vectorlist_vectorlist_surface_integral() [2/3]

std::complex<double> Membrane::calc_vectorlist_vectorlist_surface_integral	(	vector< std::complex< double > >	vectorlist1,
		vector< double >	vectorlist2
	)

◆ calc_vectorlist_vectorlist_surface_integral() [3/3]

std::complex<double> Membrane::calc_vectorlist_vectorlist_surface_integral	(	vector< std::complex< double > >	vectorlist1,
		vector< std::complex< double > >	vectorlist2
	)

◆ calculate_2D_amplitudes_Alexandra()

void Membrane::calculate_2D_amplitudes_Alexandra ( int q_max )

◆ calculate_2D_amplitudes_Alexandra_projection()

void Membrane::calculate_2D_amplitudes_Alexandra_projection	(	int	q_max,
		int	numpoints
	)

◆ calculate_bending_energy()

double Membrane::calculate_bending_energy ( void )

Returns the total bending energy of the membrane (indepentant of OpenMM calculations)

◆ calculate_contourRadius()

void Membrane::calculate_contourRadius ( void )

◆ calculate_contourSegmentLength()

void Membrane::calculate_contourSegmentLength ( void )

◆ calculate_deltaphi()

void Membrane::calculate_deltaphi ( void )

◆ calculate_deltaphi_Alexandra()

void Membrane::calculate_deltaphi_Alexandra ( void )

◆ calculate_dOmega()

void Membrane::calculate_dOmega ( void )

◆ calculate_freqs()

void Membrane::calculate_freqs ( ArgStruct_Analysis args )

◆ calculate_freqs_projection()

void Membrane::calculate_freqs_projection ( ArgStruct_Analysis args )

◆ calculate_modeAmplitudes2D()

void Membrane::calculate_modeAmplitudes2D ( void )

◆ calculate_real_ulm() [1/2]

void Membrane::calculate_real_ulm ( ArgStruct_Analysis args )

◆ calculate_real_ulm() [2/2]

void Membrane::calculate_real_ulm	(	ArgStruct_Analysis	args,
		char	Requiv,
		bool	clear
	)

◆ calculate_surface_area_with_voronoi()

void Membrane::calculate_surface_area_with_voronoi ( void )

Calculate the volume of a closed membrane by summing triangular pyramids.

◆ calculate_ulm()

void Membrane::calculate_ulm ( ArgStruct_Analysis args )

◆ calculate_ulm_radiustest()

void Membrane::calculate_ulm_radiustest	(	int	ell_max,
		int	analysis_averaging_option
	)

◆ calculate_ulm_radiustest_real()

void Membrane::calculate_ulm_radiustest_real	(	int	ell_max,
		int	analysis_averaging_option
	)

◆ calculate_ulm_sub_particles()

void Membrane::calculate_ulm_sub_particles	(	int	ell_max,
		int	analysis_averaging_option
	)

◆ calculate_volume_and_surface_area()

void Membrane::calculate_volume_and_surface_area ( void )

Calculate the volume of a closed membrane by summing triangular pyramids.

◆ calculateH_2D_amplitudes()

void Membrane::calculateH_2D_amplitudes ( int q_max )

◆ calculateH_2D_amplitudes_projection()

void Membrane::calculateH_2D_amplitudes_projection	(	int	q_max,
		int	numpoints
	)

◆ calculating_dihedral_energy()

void Membrane::calculating_dihedral_energy ( )

protected

◆ calculating_the_bend_energy()

double Membrane::calculating_the_bend_energy	(	int	uncommn1,
		int	common2,
		int	common3,
		int	uncommon4,
		bool	initial_or_final,
		MyAtomInfo	atoms[],
		int	number_of_privious_mem_nodes
	)

◆ calculating_the_bend_energy_2()

double Membrane::calculating_the_bend_energy_2	(	int	uncommon1,
		int	common2,
		int	common3,
		int	uncommon4,
		MyAtomInfo	atoms[],
		int	number_of_privious_mem_nodes
	)

◆ calculating_the_bond_energy()

double Membrane::calculating_the_bond_energy	(	int	index,
		bool	initial_or_final,
		MyAtomInfo	atoms[],
		int	number_of_privious_mem_nodes
	)

◆ calculating_the_bond_energy_check()

double Membrane::calculating_the_bond_energy_check	(	int	p1,
		int	p2,
		MyAtomInfo	atoms[]
	)

◆ calculating_the_bond_length_check()

double Membrane::calculating_the_bond_length_check	(	int	p1,
		int	p2,
		MyAtomInfo	atoms[]
	)

◆ check()

void Membrane::check ( void )

◆ check_before_update()

void Membrane::check_before_update	(	int	triangle_A,
		int	triangle_B,
		int	new_neighbour_dihedrals[4][6],
		int &	pyramid_counter,
		bool &	accept
	)

◆ check_Pyramid()

bool Membrane::check_Pyramid	(	vector< int >	A_neighbors,
		vector< int >	B_neighbors
	)

◆ check_Pyramid_2()

bool Membrane::check_Pyramid_2	(	int	initial_pair,
		vector< int >	A_neighbours_dihedral_index,
		vector< int >	B_neighbours_dihedral_index
	)

◆ check_radius_update_values()

void Membrane::check_radius_update_values ( void )

◆ check_the_flip()

void Membrane::check_the_flip	(	MyOpenMMData *	omm,
		Bonds *	bonds,
		Dihedrals *	dihedrals
	)

◆ consistancy_check()

void Membrane::consistancy_check ( void )

◆ convert_spherical_positions_to_cartisian()

void Membrane::convert_spherical_positions_to_cartisian ( )

◆ custom()

void Membrane::custom ( void )

protected

◆ Elastic_Force_Calculator()

void Membrane::Elastic_Force_Calculator ( double theta_0 )

◆ export_for_resume() [1/2]

void Membrane::export_for_resume ( int MD_step )

◆ export_for_resume() [2/2]

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

◆ Export_Mechanical_Energy()

void Membrane::Export_Mechanical_Energy	(	string	filename,
		int	frame
	)

◆ FENE_log()

void Membrane::FENE_log ( void )

protected

◆ find_the_new_neighbour()

void Membrane::find_the_new_neighbour	(	int	neighbour_id[6],
		int	previous_dihedral_index,
		int	initial_pair,
		bool	A_or_B
	)

◆ generate_ulm_mode()

void Membrane::generate_ulm_mode	(	int	ell,
		int	m,
		double	ulm,
		double	radius
	)

◆ generate_ulm_mode_real()

void Membrane::generate_ulm_mode_real	(	int	Ell,
		int	M,
		double	uLM,
		double	radius
	)

◆ get_average_Membrane_radius()

double Membrane::get_average_Membrane_radius ( void )

inline

◆ get_avg_node_dist()

double Membrane::get_avg_node_dist ( void )

inline

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

◆ get_Begin_update_time_in_Ps()

double Membrane::get_Begin_update_time_in_Ps ( void )

inline

Return the new node radius 'begin update time' in Ps.

◆ get_bending_model()

int Membrane::get_bending_model ( void )

inline

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

◆ get_bending_stiffness_coefficient()

double Membrane::get_bending_stiffness_coefficient ( void )

inline

Return bending stiffness coefficient.

◆ get_bond_length_distribution()

void Membrane::get_bond_length_distribution ( void )

◆ get_damping_coefficient()

double Membrane::get_damping_coefficient ( void )

inline

Return damp coefficient.

◆ get_dihedral_atoms_list()

vector<int> Membrane::get_dihedral_atoms_list ( int index )

inline

Return the node IDs of the dihedral angles.

◆ get_End_update_time_in_Ps()

double Membrane::get_End_update_time_in_Ps ( void )

inline

Return the new node radius 'end update time' in Ps.

◆ get_epsilon_LJ_12_6()

double Membrane::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 Membrane::get_ext_force_model ( void )

inline

Return external force model.

◆ get_GeometricProps_flag()

bool Membrane::get_GeometricProps_flag ( )

inline

Return the geometrical properties write status.

◆ get_gompper_params_lminlc1lc0lmax()

vector<double > Membrane::get_gompper_params_lminlc1lc0lmax ( )

inline

◆ get_ground_state_from_frame()

void Membrane::get_ground_state_from_frame ( ArgStruct_Analysis args )

◆ get_ground_state_from_mesh()

void Membrane::get_ground_state_from_mesh ( ArgStruct_Analysis args )

◆ get_insertOrder()

vector<string > Membrane::get_insertOrder ( )

inline

◆ get_kx()

double Membrane::get_kx ( void )

inline

◆ get_ky()

double Membrane::get_ky ( void )

inline

◆ get_kz()

double Membrane::get_kz ( void )

inline

◆ get_label()

std::string Membrane::get_label ( void )

inline

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

◆ get_map()

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

inline

◆ get_membrane_weighted_radius()

double Membrane::get_membrane_weighted_radius ( void )

inline

◆ get_new_Membrane_radius()

double Membrane::get_new_Membrane_radius ( void )

inline

◆ get_new_radius()

double Membrane::get_new_radius ( void )

inline

Returns the node radius update value (set value in the configuration file).

◆ get_node_mass()

double Membrane::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_normal_vec()

vector<double> Membrane::get_node_normal_vec ( int node )

inline

return normal vector of each node.

The normal vector of node N is the average of vectors normal to triangles that have node N as one of their vertices. It is garanteed that the vector will point away from the Membrane centre of mass.

◆ get_node_pair()

int Membrane::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_pair_Nominal_Length_in_Nm()

double Membrane::get_node_pair_Nominal_Length_in_Nm ( int bond_num )

inline

Return the distance between node pair index.

This list is initiated at the begining of the simulation.

◆ get_node_position()

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

inline

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

◆ get_node_radius()

double Membrane::get_node_radius ( int index )

inline

◆ get_node_velocity()

double Membrane::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_node_voronoi_area()

double Membrane::get_node_voronoi_area ( int node )

inline

return the voronoi area associated with each node.

◆ get_num_of_node_pairs()

int Membrane::get_num_of_node_pairs ( void )

inline

Return the number of bonds between membrane nodes.

◆ get_num_of_nodes()

int Membrane::get_num_of_nodes ( void )

inline

public access to total number of membrane nodes.

Returns: integer number of nodes in the membrane

◆ get_num_of_triangle()

int Membrane::get_num_of_triangle ( )

inline

Returns the calculated number of triangles in the imported mesh file.

◆ get_num_of_triangle_pairs()

int Membrane::get_num_of_triangle_pairs ( )

inline

Return the spontaneous bending angle between triangle pairs in radians.

Returns the calculated number of triangles in the imported mesh file.

◆ get_real_ylm_vectorlist_for_mesh()

vector<double> Membrane::get_real_ylm_vectorlist_for_mesh	(	int	ell,
		int	m
	)

◆ get_ring()

void Membrane::get_ring ( ArgStruct_Analysis args )

◆ get_ring_from_projection()

void Membrane::get_ring_from_projection	(	ArgStruct_Analysis	args,
		int	numpoints
	)

◆ get_sigma_LJ_12_6()

double Membrane::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_spherical_position()

double Membrane::get_spherical_position	(	int	node_number,
		int	node_coordinate
	)

inline

Returns the r (0), theta (1), and phi (2) spherical coordinate of the node index (number).

Note: update_spherical_positions(); should be called to upddate the values.

◆ get_spontaneous_angle_in_Rad()

double Membrane::get_spontaneous_angle_in_Rad ( int nodePairIndex )

inline

Return the spontaneous bending angle between triangle pairs in radians.

◆ get_spring_model()

int Membrane::get_spring_model ( void )

inline

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

◆ get_spring_stiffness_coefficient()

double Membrane::get_spring_stiffness_coefficient ( void )

inline

Return spring stiffness coefficient.

◆ get_surface_area()

double Membrane::get_surface_area ( void )

inline

Returns the last saved surface area.

◆ get_surface_area_voronoi()

double Membrane::get_surface_area_voronoi ( )

inline

Return the sum of the voronoi area of each node.

◆ get_traingle_pair_node()

int Membrane::get_traingle_pair_node	(	int	triangle_pair,
		int	index
	)

inline

Return the node ID of the dihedral angles member.

◆ get_traingle_pair_nodes_list()

vector<int> Membrane::get_traingle_pair_nodes_list ( int triangle_pair )

inline

Return the node IDs of the dihedral angles.

◆ get_ulmYlm_vectorlist_for_mesh() [1/2]

vector<double> Membrane::get_ulmYlm_vectorlist_for_mesh ( )

◆ get_ulmYlm_vectorlist_for_mesh() [2/2]

vector<double> Membrane::get_ulmYlm_vectorlist_for_mesh ( char Requiv )

◆ get_update_status()

bool Membrane::get_update_status ( void )

inline

Returns whether the Membrane is setup for radius change (true) or not (false).

◆ get_volume()

double Membrane::get_volume ( void )

inline

Returns the last saved volume.

◆ get_voronoi_node_area()

vector<double> Membrane::get_voronoi_node_area ( )

inline

Calculate the voronoi area of each node and return a list that indicated the voronoi area of each node.

◆ get_ylm_vectorlist_for_mesh()

vector<std::complex<double> > Membrane::get_ylm_vectorlist_for_mesh	(	int	ell,
		int	m,
		bool	complex_conjugate
	)

◆ harmonic_potential_calculator()

void Membrane::harmonic_potential_calculator ( void )

◆ import()

void Membrane::import ( std::string import_file_name )

◆ import_config()

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

◆ import_pdb_frames()

void Membrane::import_pdb_frames	(	ArgStruct_Analysis	args,
		int	file_index
	)

◆ initialise()

void Membrane::initialise ( std::string Mesh_file_name )

◆ load_pdb_frame()

void Membrane::load_pdb_frame	(	int	frame,
		ArgStruct_Analysis	args
	)

◆ Mechanical_Energy_calculator()

void Membrane::Mechanical_Energy_calculator ( )

◆ monte_carlo_flip()

void Membrane::monte_carlo_flip	(	MyOpenMMData *	omm,
		Bonds *	bonds,
		Dihedrals *	dihedrals,
		MyAtomInfo	atoms[],
		double &	localDeltaE,
		int &	Accepted_Try_Counter,
		int &	pyramid_counter,
		int &	MC_total_tries,
		double &	MC_Acceptance_Rate
	)

◆ myWritePDBFrame()

void Membrane::myWritePDBFrame	(	int	frameNum,
		std::string	traj_name
	)

◆ Node_Bonds_identifier()

void Membrane::Node_Bonds_identifier ( void )

protected

◆ Node_neighbour_list_constructor()

void Membrane::Node_neighbour_list_constructor ( )

Construct a vector that lists all the neighbours of each node and their respective index in the 'Node_Bond_list'.

◆ Normal_direction_Identifier()

void Membrane::Normal_direction_Identifier ( )

protected

◆ ranfomundulationgenerator()

void Membrane::ranfomundulationgenerator ( void )

◆ read_gmesh_file()

void Membrane::read_gmesh_file ( std::string gmesh_file )

protected

◆ read_ply_file()

void Membrane::read_ply_file ( std::string ply_file )

protected

◆ rescale_membrane()

void Membrane::rescale_membrane ( double factor )

inline

◆ rotate_coordinates()

void Membrane::rotate_coordinates	(	double	theta,
		double	phi
	)

◆ rotate_particle_to_axes()

void Membrane::rotate_particle_to_axes ( ArgStruct_Analysis args )

◆ set_bending_nominal_angle()

void Membrane::set_bending_nominal_angle ( void )

◆ set_bond_nominal_length()

void Membrane::set_bond_nominal_length ( void )

◆ set_com_to_zero()

void Membrane::set_com_to_zero ( )

inline

◆ set_dihedral_atoms()

void Membrane::set_dihedral_atoms ( void )

◆ set_FENE_param()

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

inline

Set FENE calculated parameters.

◆ set_FENE_param_2()

void Membrane::set_FENE_param_2	(	double &	lmin,
		double &	lmax,
		double &	epsilon,
		double &	k
	)

inline

◆ set_file_time()

void Membrane::set_file_time ( char * buffer )

inline

◆ set_index()

void Membrane::set_index ( int ind )

inline

◆ set_label()

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

inline

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

◆ set_node_radius()

void Membrane::set_node_radius ( void )

◆ set_state()

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

Set the current state (OpenMM) of the class.

◆ shift_position()

void Membrane::shift_position	(	double	x,
		double	y,
		double	z
	)

inline

This function shifts the whole membrane.

◆ shift_velocity()

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

inline

◆ Triangle_Pair_and_Node_Bonds_Identifier()

void Membrane::Triangle_Pair_and_Node_Bonds_Identifier ( )

◆ Triangle_pair_counter()

void Membrane::Triangle_pair_counter ( )

protected

◆ Triangle_pair_identifier()

void Membrane::Triangle_pair_identifier ( void )

protected

◆ update_average_Membrane_radius()

void Membrane::update_average_Membrane_radius ( void )

inline

◆ update_COM_position()

void Membrane::update_COM_position ( void )

inline

◆ update_COM_velocity()

void Membrane::update_COM_velocity ( void )

inline

◆ Update_Membrane()

void Membrane::Update_Membrane	(	int	initial_pair,
		int	triangle_A,
		int	triangle_B,
		int	new_neighbour_dihedrals[4][6],
		int &	bond_index
	)

◆ update_Membrane_class_and_openmm()

void Membrane::update_Membrane_class_and_openmm	(	int	initial_pair,
		int	triangle_A,
		int	triangle_B,
		int	new_neighbour_dihedrals[4][6],
		MyOpenMMData *	omm,
		Bonds *	bonds,
		Dihedrals *	dihedrals
	)

◆ update_spherical_positions()

void Membrane::update_spherical_positions ( )

◆ updatepos()

void Membrane::updatepos ( double )

◆ write_geometrics()

void Membrane::write_geometrics ( )

◆ write_pov_traj()

void Membrane::write_pov_traj	(	std::string	traj_name,
		std::string	label,
		int	currentstep
	)

◆ write_ulm()

void Membrane::write_ulm	(	ArgStruct_Analysis	args,
		int	file_index
	)

◆ write_un_uq()

void Membrane::write_un_uq	(	ArgStruct_Analysis	args,
		int	file_index
	)

◆ write_un_uq_projection()

void Membrane::write_un_uq_projection	(	ArgStruct_Analysis	args,
		int	file_index
	)

◆ write_uq_SH()

void Membrane::write_uq_SH	(	ArgStruct_Analysis	args,
		int	file_index
	)

◆ WriteMemPDBFrame()

void Membrane::WriteMemPDBFrame	(	ArgStruct_Analysis	args,
		vector< int >	chainlist
	)

Member Data Documentation

◆ AddRandomModes

bool Membrane::AddRandomModes = false

◆ aq_alexandra

vector<vector<double> > Membrane::aq_alexandra

◆ aq_alexandra_proj

vector<vector<double> > Membrane::aq_alexandra_proj

◆ Aq_H

vector<vector<double> > Membrane::Aq_H

◆ Aq_H_proj

vector<vector<double> > Membrane::Aq_H_proj

◆ Average_node_pair_length

double Membrane::Average_node_pair_length

◆ Begin_update_time_in_Ps

double Membrane::Begin_update_time_in_Ps =0

protected

◆ Bending_coefficient

double Membrane::Bending_coefficient =0.

◆ bending_model

int Membrane::bending_model =0

◆ Bond_triangle_neighbour_indices

vector<int> Membrane::Bond_triangle_neighbour_indices

◆ bq_alexandra

vector<vector<double> > Membrane::bq_alexandra

◆ bq_alexandra_proj

vector<vector<double> > Membrane::bq_alexandra_proj

◆ Bq_H

vector<vector<double> > Membrane::Bq_H

◆ Bq_H_proj

vector<vector<double> > Membrane::Bq_H_proj

◆ chainlist

vector<int> Membrane::chainlist

◆ check_monte_carlo

bool Membrane::check_monte_carlo =0

◆ COM_position

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

protected

◆ COM_velocity

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

protected

◆ contourradii

vector<double> Membrane::contourradii

◆ contourRadius

double Membrane::contourRadius

◆ contourSegmentLength

vector<double> Membrane::contourSegmentLength

◆ Damping_coefficient

double Membrane::Damping_coefficient =0.0

◆ deltaphi

vector<double> Membrane::deltaphi

◆ dihedral_atoms

vector<vector< int > > Membrane::dihedral_atoms

protected

◆ EllMaxOfRandomModes

int Membrane::EllMaxOfRandomModes

◆ End_update_time_in_Ps

double Membrane::End_update_time_in_Ps =0

protected

◆ epsilon_LJ_12_6

double Membrane::epsilon_LJ_12_6 =0

protected

◆ ext_force_model

int Membrane::ext_force_model =0

◆ FENE_epsilon

double Membrane::FENE_epsilon =0

protected

◆ FENE_k

double Membrane::FENE_k =0

protected

◆ FENE_max

double Membrane::FENE_max =0

protected

◆ FENE_min

double Membrane::FENE_min =0

protected

◆ file_time

std::string Membrane::file_time

◆ GompperBondPotentialLminLc1Lc0Lmax

vector<double> Membrane::GompperBondPotentialLminLc1Lc0Lmax

◆ index

int Membrane::index

protected

Store the mem index the instance of the class has in the vector of Membranes in the main programme.

◆ initial_random_rotation_coordinates

bool Membrane::initial_random_rotation_coordinates = false

◆ insertOrder

vector<string> Membrane::insertOrder

◆ kx

double Membrane::kx =10

◆ ky

double Membrane::ky =10

◆ kz

double Membrane::kz =10

◆ label

std::string Membrane::label

protected

Store the label(pdb) used to write to the trajectory file.

◆ Max_node_pair_length

double Membrane::Max_node_pair_length

◆ Mesh_file_name

std::string Membrane::Mesh_file_name ="None"

protected

◆ mesh_format

string Membrane::mesh_format

◆ Min_node_pair_length

double Membrane::Min_node_pair_length

◆ New_node_radius

double Membrane::New_node_radius =-1

protected

◆ New_Radius

double Membrane::New_Radius =-1

protected

◆ Node_Bond_list

vector<vector<int> > Membrane::Node_Bond_list

◆ Node_Bond_Nominal_Length_in_Nm

vector<double> Membrane::Node_Bond_Nominal_Length_in_Nm

◆ Node_Bond_Nominal_Length_stat

string Membrane::Node_Bond_Nominal_Length_stat

◆ Node_Bond_user_defined_Nominal_Length_in_Nm

double Membrane::Node_Bond_user_defined_Nominal_Length_in_Nm

◆ node_dOmega

vector<double> Membrane::node_dOmega

◆ Node_Force

vector<vector<double> > Membrane::Node_Force

◆ Node_Mass

double Membrane::Node_Mass =1.0

protected

◆ Node_neighbour_list

vector<vector<int> > Membrane::Node_neighbour_list

This list is used to store all the neighbours of nodes: Example: If node i has 4 neighbours: m, n, o, p Then we find these neighbours in the 'Node_neighbour_list' as follows: Node_neighbour_list [ i ][0] = m Node_neighbour_list [ i ][1] = n Node_neighbour_list [ i ][2] = o Node_neighbour_list [ i ][3] = p.

◆ Node_neighbour_list_respective_bond_index

vector<vector<int> > Membrane::Node_neighbour_list_respective_bond_index

This list is used to cross reference the neighbouring nodes to their respective index in the 'Node_neighbour_list'.

Example: Suppose node i has 4 neighbours: m, n, o, p Then we find these neighbours in the 'Node_neighbour_list' as follows: Node_neighbour_list [ i ][0] = m Node_neighbour_list [ i ][1] = n Node_neighbour_list [ i ][2] = o Node_neighbour_list [ i ][3] = p

Then the i'th index of the 'Node_neighbour_list_respective_bond_index' will also contain 4 elements: Node_neighbour_list_respective_bond_index [ i ][0] = index_1 Node_neighbour_list_respective_bond_index [ i ][1] = index_2 Node_neighbour_list_respective_bond_index [ i ][2] = index_3 Node_neighbour_list_respective_bond_index [ i ][3] = index_4

The index_::s will point to the index in the 'Node_Bond_list' that has stored the respective nodes as pairs: Node_Bond_list [ index_1 ][ 0 ] and Node_Bond_list [ index_1 ][ 1 ] = i, m Node_Bond_list [ index_2 ][ 0 ] and Node_Bond_list [ index_2 ][ 1 ] = i, n Node_Bond_list [ index_3 ][ 0 ] and Node_Bond_list [ index_3 ][ 1 ] = i, o Node_Bond_list [ index_4 ][ 0 ] and Node_Bond_list [ index_4 ][ 1 ] = i, p

◆ Node_Position

vector<vector<double> > Membrane::Node_Position

◆ Node_radius

vector<double> Membrane::Node_radius

protected

◆ Node_radius_stat

string Membrane::Node_radius_stat

protected

◆ Node_Velocity

vector<vector<double> > Membrane::Node_Velocity

◆ node_voronoi_area

vector<double> Membrane::node_voronoi_area

◆ node_voronoi_normal_vec

vector<vector<double> > Membrane::node_voronoi_normal_vec

◆ Num_of_Node_Pairs

int Membrane::Num_of_Node_Pairs

protected

◆ Num_of_Nodes

int Membrane::Num_of_Nodes =0

protected

Number of nodes in the membrane.

◆ Num_of_Triangle_Pairs

int Membrane::Num_of_Triangle_Pairs

protected

◆ Num_of_Triangles

int Membrane::Num_of_Triangles

protected

This is the number of nodes on the membrane (Both the outer membrane and the Nucleus). This is the first number that appears in the 'membrane' file (once opend with a text editor)

◆ NumberOfRandomModes

int Membrane::NumberOfRandomModes

◆ output_file_neme

std::string Membrane::output_file_neme

◆ param_map

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

protected

This is the number of triangles on the membrane (Both the outer membrane and the Nucleus). This is the number that appears in the 'membrane' file after the node position list is finished and before Gmesh lists the nodes that make a triangle.

◆ Params

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

◆ pdb_frames

vector<vector<vector<double> > > Membrane::pdb_frames

◆ pdb_frames_time

vector<double> Membrane::pdb_frames_time

◆ Radius

double Membrane::Radius =0

protected

◆ rescale_factor

double Membrane::rescale_factor =1

◆ resume_file_name

std::string Membrane::resume_file_name ="None"

protected

◆ ringNodeList

vector<int> Membrane::ringNodeList

◆ Shift_position_xyzVector

vector<double> Membrane::Shift_position_xyzVector

◆ Shift_velocities_xyzVector

vector<double> Membrane::Shift_velocities_xyzVector

◆ sigma_LJ_12_6

double Membrane::sigma_LJ_12_6 =0

protected

◆ spherical_positions

vector<vector<double> > Membrane::spherical_positions

◆ SpontaneousTriangleBendingInDegrees

double Membrane::SpontaneousTriangleBendingInDegrees =0.

◆ Spring_coefficient

double Membrane::Spring_coefficient =0.

◆ spring_model

int Membrane::spring_model =0

◆ surface_area

double Membrane::surface_area

protected

Store the surface area of the membrane.

◆ surface_area_voronoi

double Membrane::surface_area_voronoi =0

◆ Total_Bending_Energy

double Membrane::Total_Bending_Energy =0.0

protected

◆ Total_Bond_Energy

double Membrane::Total_Bond_Energy =0.0

protected

◆ Total_Kinetic_Energy

double Membrane::Total_Kinetic_Energy

protected

◆ Total_Potential_Energy

double Membrane::Total_Potential_Energy =0.0

protected

◆ Triangle_list

vector<vector<int> > Membrane::Triangle_list

◆ Triangle_pair_angle_stat

string Membrane::Triangle_pair_angle_stat

◆ Triangle_pair_angles_in_radians

vector<double> Membrane::Triangle_pair_angles_in_radians

◆ Triangle_pair_list

vector<vector<int> > Membrane::Triangle_pair_list

◆ Triangle_Pair_Nodes

vector<vector<int> > Membrane::Triangle_Pair_Nodes

◆ Triangle_pair_Nominal_angle_in_degrees

double Membrane::Triangle_pair_Nominal_angle_in_degrees =-1

◆ ulm_avg

vector<vector<double> > Membrane::ulm_avg

◆ ulm_Mesh

vector<vector<double> > Membrane::ulm_Mesh

◆ ulm_std

vector<vector<double> > Membrane::ulm_std

◆ ulm_temp_for_analysis

vector<vector<double> > Membrane::ulm_temp_for_analysis

◆ UlmOfRandomModes

double Membrane::UlmOfRandomModes

◆ update_radius_stat

bool Membrane::update_radius_stat =false

protected

◆ values

vector<string> Membrane::values

◆ volume

double Membrane::volume

protected

Store the volume of the membrane.

◆ WantGeometricProps

bool Membrane::WantGeometricProps =false

protected

write geometrical properties if it is true.

◆ X_in

double Membrane::X_in =0

protected

◆ X_scale

double Membrane::X_scale =0

protected

◆ Y_in

double Membrane::Y_in =0

protected

◆ Y_scale

double Membrane::Y_scale =0

protected

◆ Z_in

double Membrane::Z_in =0

protected

◆ Z_scale

double Membrane::Z_scale =0

protected

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

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

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Membrane()

Member Function Documentation

◆ add_to_force()

◆ add_ulm_mode_real()

◆ analysis_init()

◆ assign_parameters()

◆ Average_Node_Distance()

◆ Bending_potetial_2()

◆ Bond_triangle_neighbour_list_constructor()

◆ calc_assoc_legendre()

◆ calc_complex_ylm_surface_integral()

◆ calc_complex_ylmthetaphi()

◆ calc_real_ylmthetaphi()

◆ calc_theta_angle_ABC()

◆ calc_vectorlist_vectorlist_surface_integral() [1/3]

◆ calc_vectorlist_vectorlist_surface_integral() [2/3]

◆ calc_vectorlist_vectorlist_surface_integral() [3/3]

◆ calculate_2D_amplitudes_Alexandra()

◆ calculate_2D_amplitudes_Alexandra_projection()

◆ calculate_bending_energy()

◆ calculate_contourRadius()

◆ calculate_contourSegmentLength()

◆ calculate_deltaphi()

◆ calculate_deltaphi_Alexandra()

◆ calculate_dOmega()

◆ calculate_freqs()

◆ calculate_freqs_projection()

◆ calculate_modeAmplitudes2D()

◆ calculate_real_ulm() [1/2]

◆ calculate_real_ulm() [2/2]

◆ calculate_surface_area_with_voronoi()

◆ calculate_ulm()

◆ calculate_ulm_radiustest()

◆ calculate_ulm_radiustest_real()

◆ calculate_ulm_sub_particles()

◆ calculate_volume_and_surface_area()

◆ calculateH_2D_amplitudes()

◆ calculateH_2D_amplitudes_projection()

◆ calculating_dihedral_energy()

◆ calculating_the_bend_energy()

◆ calculating_the_bend_energy_2()

◆ calculating_the_bond_energy()

◆ calculating_the_bond_energy_check()

◆ calculating_the_bond_length_check()

◆ check()

◆ check_before_update()

◆ check_Pyramid()

◆ check_Pyramid_2()

◆ check_radius_update_values()

◆ check_the_flip()

◆ consistancy_check()

◆ convert_spherical_positions_to_cartisian()

◆ custom()

◆ Elastic_Force_Calculator()

◆ export_for_resume() [1/2]

◆ export_for_resume() [2/2]

◆ Export_Mechanical_Energy()

◆ FENE_log()

◆ find_the_new_neighbour()

◆ generate_ulm_mode()

◆ generate_ulm_mode_real()

◆ get_average_Membrane_radius()

◆ get_avg_node_dist()

◆ get_Begin_update_time_in_Ps()

◆ get_bending_model()

◆ get_bending_stiffness_coefficient()

◆ get_bond_length_distribution()

◆ get_damping_coefficient()

◆ get_dihedral_atoms_list()

◆ get_End_update_time_in_Ps()

◆ get_epsilon_LJ_12_6()

◆ get_ext_force_model()

◆ get_GeometricProps_flag()

◆ get_gompper_params_lminlc1lc0lmax()