KNNR Class Reference

#include <knnr.h>

Public Member Functions
int	begin (int runnum, int natoms0)
double	test_points (int k0)
double	grad_knnr (double coords, double &E1, double grads, double *Ut, int k)
int	add_extra_points ()
void	add_point (double energy, double xyz, double grad, double *hess)
void	freemem ()
Public Attributes
int	npts
int	printl
Private Member Functions
int	read_ics (int &nbonds, int bonds, int &nangles, int angles, int &ntor, int **torsions, string filename)
int	read_xyzs (double energies, double xyz, string filenames)
double	read_one_xyz (int n, string filename, double *coords)
void	xyz_read (string anames, double coords, string xyzfile)
int	read_hess (int nic, string *filenames)
void	read_one_hess (int n, int nic, string filename)
int	get_files (string fileprefix, string filesuffix, string *files)
void	get_distances (int npts, double **xyz, ICoord &ic1, ICoord &ic2)
double	get_distance (double xyz1, double xyz2, ICoord &ic1, ICoord &ic2)
void	get_distances_u (int npts, int pt, ICoord &ic1, ICoord &ic2)
double	get_distance_u (double xyz1, double xyz2, ICoord &ic1, ICoord &ic2)
void	get_dqpic (double *dq1, ICoord &ic1, ICoord &ic2)
void	setup_ic (ICoord &ic1, ICoord &ic2)
void	release_ic (ICoord &ic1, ICoord &ic2)
int	find_knn (int pt, int k, int knn, double knnd, int type)
double	predict_point (int pt, int k, ICoord &ic1, ICoord &ic2)
int	find_knn_xyz (double coords, int k, int knn, double *knnd, ICoord &ic1, ICoord &ic2)
int	compare_add_files (int npts1, string filesxyz1, string filesgrad1, string fileshess1, string newfilesxyz, string newfilesgrad, string newfileshess)
void	reassign_mem (int npts1)
Private Attributes
string	file0
int	runnum
string *	filesxyz
string *	filesgrad
string *	fileshess
int	natoms
double **	xyz
int *	anumbers
string *	anames
int *	id
double *	distances
double *	distancesu
double *	energies
double **	grads
double **	hess
int *	useH
int	nic
int	nbonds
int	nangles
int	ntor

Member Function Documentation

int KNNR::add_extra_points ( )

void KNNR::add_point	(	double	energy,
		double *	xyz,
		double *	grad,
		double *	hess
	)

int KNNR::begin	(	int	runnum,
		int	natoms0
	)

int KNNR::compare_add_files	(	int	npts1,
		string *	filesxyz1,
		string *	filesgrad1,
		string *	fileshess1,
		string *	newfilesxyz,
		string *	newfilesgrad,
		string *	newfileshess
	)			`[private]`

int KNNR::find_knn	(	int	pt,
		int	k,
		int *	knn,
		double *	knnd,
		int	type
	)			`[private]`

int KNNR::find_knn_xyz	(	double *	coords,
		int	k,
		int *	knn,
		double *	knnd,
		ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

void KNNR::freemem ( )

double KNNR::get_distance	(	double *	xyz1,
		double *	xyz2,
		ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

double KNNR::get_distance_u	(	double *	xyz1,
		double *	xyz2,
		ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

void KNNR::get_distances	(	int	npts,
		double **	xyz,
		ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

void KNNR::get_distances_u	(	int	npts,
		int	pt,
		ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

void KNNR::get_dqpic	(	double *	dq1,
		ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

int KNNR::get_files	(	string	fileprefix,
		string	filesuffix,
		string *	files
	)			`[private]`

double KNNR::grad_knnr	(	double *	coords,
		double &	E1,
		double *	grads,
		double *	Ut,
		int	k
	)

double KNNR::predict_point	(	int	pt,
		int	k,
		ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

CPMZ here

int KNNR::read_hess	(	int	nic,
		string *	filenames
	)			`[private]`

int KNNR::read_ics	(	int &	nbonds,
		int **	bonds,
		int &	nangles,
		int **	angles,
		int &	ntor,
		int **	torsions,
		string	filename
	)			`[private]`

void KNNR::read_one_hess	(	int	n,
		int	nic,
		string	filename
	)			`[private]`

double KNNR::read_one_xyz	(	int	n,
		string	filename,
		double *	coords
	)			`[private]`

int KNNR::read_xyzs	(	double *	energies,
		double **	xyz,
		string *	filenames
	)			`[private]`

void KNNR::reassign_mem ( int npts1 ) [private]

void KNNR::release_ic	(	ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

void KNNR::setup_ic	(	ICoord &	ic1,
		ICoord &	ic2
	)			`[private]`

double KNNR::test_points ( int k0 )

void KNNR::xyz_read	(	string *	anames,
		double *	coords,
		string	xyzfile
	)			`[private]`

Member Data Documentation

string* KNNR::anames [private]

int* KNNR::anumbers [private]

double* KNNR::distances [private]

double* KNNR::distancesu [private]

double* KNNR::energies [private]

string KNNR::file0 [private]

string* KNNR::filesgrad [private]

string* KNNR::fileshess [private]

string* KNNR::filesxyz [private]

double** KNNR::grads [private]

double** KNNR::hess [private]

int* KNNR::id [private]

int KNNR::nangles [private]

int KNNR::natoms [private]

int KNNR::nbonds [private]

int KNNR::nic [private]

int KNNR::npts

int KNNR::ntor [private]

int KNNR::printl

int KNNR::runnum [private]

int* KNNR::useH [private]

double** KNNR::xyz [private]

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

/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/knnr.h
/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/knnr.cpp

KNNR Class Reference

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Member Function Documentation

Member Data Documentation