#include <iostream>
#include <cmath>
#include <cstdlib>
#include <math.h>
#include <random>
#include <time.h>
#include <vector>
#include <unistd.h>
#include <algorithm>
#include <ctime>
#include <chrono>
#include <fstream>
#include <sstream>
#include <string>
#include <cstring>
#include <stddef.h>
#include "vel.h"
#include "params.h"

Include dependency graph for helper_funcs.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions
int	get_num_vertices (int elem_type)

bool	contains (vector< int > &vec, int elem)

float	getnorm (const float *vec, const int dim=DIM)

void	mapping (int &edge_counter, int elem_type, int n_vertices, stringstream &input, int *edges)
	Converts mesh elements from GMSH file to edges and nodes. Only implemented elements of <element-id> = 2 or 3. Need to extend for 3D. More...

string	read_dump (int &n_nodes, int &n_elems, string &fname)
	Reads the number of nodes and poly chains left at the end of previous simulation. The code does not take care of parameters. Assumes user will change params.h file while restarting the previous simulation. More...

void	mapping (int &edge_counter, int elem_type)
	Reads the number of edges in elements. Only implemented elements of <element-id> = 2 or 3. More...

void	read_n (int &n_nodes, int &n_elems, string &fname)
	Reads the number of nodes and edges according to the .msh file. Useful for allocating memory in the class' constructors. More...

void	take_input (float R, int edges, int n_nodes, int n_elems, string &fname)
	Reads the input and converts to appropriate network data. More...

void	__init__ (float L, float damage, bool *PBC, int n_elems)
	Initializes various properties for each edge in the graph. More...

int	filename (const string &)
	Gives an integer value to be appended to the network dump filename. More...

void	normalize_vector (float result, const float vec)

bool	does_file_exist (string &fname)

void	normalize_vector (float *vec)

void	unitvector (float result, float r1, float *r2)

float	force_wlc (float x, float L)

void	convert_to_vector (float result, const float mag, const float direction)

float	dist (const float r1, const float r2)

void	forcevector (float result, float r1, float *r2, float L)
	Gives a force vector given the nodes and the contour length of the polymer connecting these. More...

bool	ismember (int item, int *array, size_t size)

float	getabsmax (float *arr, size_t sizeofarr)
	Gets the absolute maximum of an array. More...

template<typename t >
void	write_to_file (string &fname, t *arr, int rows, int cols)

float	kf (float force)

float	kfe (float force_mag)

void	__init__ (float L, int m, float damage, float sacdamage, bool *PBC, int n_elems)
	Overrides init for sacNetworks. More...

Function Documentation

void __init__	(	float *	L,
		float *	damage,
		bool *	PBC,
		int	n_elems
	)

Initializes various properties for each edge in the graph.

void __init__	(	float *	L,
		int *	m,
		float *	damage,
		float *	sacdamage,
		bool *	PBC,
		int	n_elems
	)

Overrides init for sacNetworks.

bool contains	(	vector< int > &	vec,
		int	elem
	)

inline

void convert_to_vector	(	float *	result,
		const float	mag,
		const float *	direction
	)

inline

float dist	(	const float *	r1,
		const float *	r2
	)

inline

bool does_file_exist ( string & fname )

inline

int filename ( const string & )

Gives an integer value to be appended to the network dump filename.

float force_wlc	(	float	x,
		float	L
	)

inline

void forcevector	(	float *	result,
		float *	r1,
		float *	r2,
		float	L
	)

Gives a force vector given the nodes and the contour length of the polymer connecting these.

int get_num_vertices ( int elem_type )

inline

float getabsmax	(	float *	arr,
		size_t	sizeofarr
	)

Gets the absolute maximum of an array.

float getnorm	(	const float *	vec,
		const int	dim = `DIM`
	)

inline

bool ismember	(	int	item,
		int *	array,
		size_t	size
	)

inline

float kf ( float force )

inline

float kfe ( float force_mag )

inline

void mapping	(	int &	edge_counter,
		int	elem_type,
		int	n_vertices,
		stringstream &	input,
		int *	edges
	)

Converts mesh elements from GMSH file to edges and nodes. Only implemented elements of <element-id> = 2 or 3. Need to extend for 3D.

void mapping	(	int &	edge_counter,
		int	elem_type
	)

Reads the number of edges in elements. Only implemented elements of <element-id> = 2 or 3.

void normalize_vector	(	float *	result,
		const float *	vec
	)

inline

void normalize_vector ( float * vec )

inline

string read_dump	(	int &	n_nodes,
		int &	n_elems,
		string &	fname
	)

Reads the number of nodes and poly chains left at the end of previous simulation. The code does not take care of parameters. Assumes user will change params.h file while restarting the previous simulation.

void read_n	(	int &	n_nodes,
		int &	n_elems,
		string &	fname
	)

Reads the number of nodes and edges according to the .msh file. Useful for allocating memory in the class' constructors.

void take_input	(	float *	R,
		int *	edges,
		int	n_nodes,
		int	n_elems,
		string &	fname
	)

Reads the input and converts to appropriate network data.

void unitvector	(	float *	result,
		float *	r1,
		float *	r2
	)

inline

template<typename t >

void write_to_file	(	string &	fname,
		t *	arr,
		int	rows,
		int	cols
	)

Functions

Function Documentation