/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/utils.h File Reference

#include <iostream>
#include <iomanip>
#include <fstream>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <cstdlib>
#include <ctime>
#include <sys/time.h>
#include "constants.h"

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Namespaces
namespace	Utils
Functions
void	trans (double *A, double *B, int m, int n)
int	Diagonalize (double *A, double *eigen, int size)
int	SVD (double *A, double *Ut, double *eigen, int size1, int size2)
int	Invert (double *A, int m)
int	mat_root (double *A, int size)
int	mat_root_inv (double *A, int size)
int	mat_times_mat (double *C, double *A, double *B, int size)
int	mat_times_mat_bt (double *C, double *A, double *B, int size)
int	mat_times_mat_at_bt (double *C, double *A, double *B, int size)
int	mat_times_mat (double *C, double *A, double *B, int N, int M, int K)
int	mat_times_mat_bt (double *C, double *A, double *B, int N, int M, int K)
int	sign (double x)
void	cross (double *x, double *r1, double *r2)
int	close_val (double x1, double x2, double diff)
int	check_array (int size, double *A)
void	Utils::normalize_string_step_direc (double **a, int nstring, int LEN)
double	Utils::step_direc_overlap (double **a, double **b, int nstring, int LEN)
void	Utils::display_matrix (double **a, int LEN)
void	Utils::eigen_decomp (double **mat, double **evecs, double *evals, int n)
void	Utils::matrix_times_matrix (double **A, double **B, double **C, int LEN)
void	Utils::display_structure_nonames (double *a, int natoms)
void	Utils::display_structure (double *a, int natoms, string *anames)
void	Utils::jacobi (float **a, int n, float d[], float **v, int *nrot)
void	Utils::eigsrt (float d[], float **v, int n)
void	Utils::S_straight_line_in_angs (double **string_angs, double *S, int nstring, int natoms)
void	Utils::subtract_arrays (double *a, double *b, double *diff, int LEN)
void	Utils::vector_outer_prod (double *vec1, double *vec2, int LEN, double **output)
void	Utils::copy_2D_array (double **pointer1, double **pointer2, int LEN1, int LEN2)
void	Utils::copy_structure (double *structure1, double *structure2, int natoms)
void	Utils::alloc_dpointer_1D (double *pointer_name, int LEN)
void	Utils::alloc_dpointer_2D (double **pointer_name, int LEN1, int LEN2)
void	Utils::alloc_dpointer_3D (double ***pointer_name, int LEN1, int LEN2, int LEN3)
void	Utils::get_rotation_matrix (double **rotMat, double *thetas)
void	Utils::Rotate_structure (double **RotMat, double *structure, int natoms)
void	Utils::Rotate_hessian (double **Rot_mat, double **hessian, int natoms)
void	Utils::Rot_around_vec (double *vec, double *structure, int natoms)
void	Utils::mwc_to_ang (double **angs, double **mwc, int nstring, int natoms, double *amasses)
void	Utils::mwc_to_ang (double *angs, double *mwc, int natoms, double *amasses)
void	Utils::ang_to_mwc (double **mwc, double **ang, int nstring, int natoms, double *amasses)
void	Utils::ang_to_mwc (double *mwc, double *ang, int natoms, double *amasses)
void	Utils::mwcgrad_to_anggrad (double **ang_grad, double **mwc_grad, int nstring, int natoms, double *amasses)
void	Utils::mwcgrad_to_anggrad (double *ang_grad, double *mwc_grad, int natoms, double *amasses)
void	Utils::anggrad_to_mwcgrad (double **mwc_grad, double **ang_grad, int nstring, int natoms, double *amasses)
void	Utils::anggrad_to_mwcgrad (double *mwc_grad, double *ang_grad, int natoms, double *amasses)
void	Utils::diagonalize3x3 (double **hmwc, double **smwc, double *w2, int ndiag)
void	Utils::projectfrommatrix3x3 (double *vector, double **hmwc)
double	Utils::randomf (double a, double b)
void	Utils::Mat_times_vec (double **d2S_1, double *dS, double *prod, int LEN)
void	Utils::normalize (double *u, int LEN)
	normalize vector
void	Utils::invertNxN (double **Mat, double **Inverse, int n)
void	Utils::ludcmp (double **a, int n, int *indx, double *d)
void	Utils::lubksb (double **a, int n, int *indx, double b[])
double	Utils::det3x3 (double A[1+3][1+3])
void	Utils::adjoint3x3 (double A[4][4], double Aadj[4][4])
double	Utils::det2x2 (double A[3][3])
void	Utils::gramschmidt (int LEN, double *v_out, double *u_in, double *v_in)
void	Utils::splineTangents (int LEN, double *x, double *y, double *y2, double *y1)
void	Utils::getSpline (int LEN, double *x, double *y, double *y2)
double	Utils::evalSpline (int LEN, double x, double *xa, double *ya, double *y2a)
void	Utils::S_from_angs (double **angs, double *S, double *masses, int LEN, int natoms)
void	Utils::Rmat_from_lincart (double **r, double *xyz, int natoms)
void	Utils::normalize_S (double *normalized_s, double *S, int LEN)
void	Utils::angs_to_mwcs (double **temparray, int nn, int natoms, double *amasses)
void	Utils::anggrads_to_mwcgrads (double **temparray, int nn, int natoms, double *amasses)
double	Utils::dotProd (double *v, double *u, int LEN)
double	Utils::vecMag (double *u, int LEN)
void	Utils::generate_Project_RT_tan (double **Proj, double *structure, double *tangent)
void	Utils::generate_Project_RT (double **Proj, double *structure)

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Function Documentation

int check_array	(	int	size,
		double *	A
	)

int close_val	(	double	x1,
		double	x2,
		double	diff
	)

void cross	(	double *	x,
		double *	r1,
		double *	r2
	)

int Diagonalize	(	double *	A,
		double *	eigen,
		int	size
	)

int Invert	(	double *	A,
		int	m
	)

int mat_root	(	double *	A,
		int	size
	)

int mat_root_inv	(	double *	A,
		int	size
	)

int mat_times_mat	(	double *	C,
		double *	A,
		double *	B,
		int	N,
		int	M,
		int	K
	)

int mat_times_mat	(	double *	C,
		double *	A,
		double *	B,
		int	size
	)

int mat_times_mat_at_bt	(	double *	C,
		double *	A,
		double *	B,
		int	size
	)

int mat_times_mat_bt	(	double *	C,
		double *	A,
		double *	B,
		int	N,
		int	M,
		int	K
	)

int mat_times_mat_bt	(	double *	C,
		double *	A,
		double *	B,
		int	size
	)

int sign

(

double

x

)

int SVD	(	double *	A,
		double *	Ut,
		double *	eigen,
		int	size1,
		int	size2
	)

void trans	(	double *	A,
		double *	B,
		int	m,
		int	n
	)