GString Class Reference

#include <gstring.h>

Collaboration diagram for GString:

Public Member Functions
void	String_Method_Optimization ()
void	reparam_and_getTangents_with_LST (double **fstring)
void	init (string infilename, string xyzfile)
void	init (string infilename, int runNum, int nprocs)
double	min_rms_structure_distance (double struct1, double struct2, int natoms)
void	print_string (int STEPS, double **allcoords, string xyzstring)
void	print_string_clump (int STEPS, double grad, double **allcoords, string xyzstring)
void	write_string_file (int iter)
void	write_SVfile (int iter)
void	write_geom_file (int iter)
void	shift_node (int nnOld, int nnNew)
void	build_fstring (double **fstring)
Public Attributes
double **	allcoords
Private Member Functions
void	set_fsm_active (int nnR, int nnP)
void	growth_iters (int max_iter, double &totalgrad, double &gradrms, double endenergy, string strfileg, int &tscontinue, double gaddmax, int osteps, int oesteps, double *dqa, double dqmaga, double **ictan)
void	opt_iters (int max_iter, double &totalgrad, double &gradrms, double endenergy, string strfileg, int &tscontinue, double gaddmax, int osteps, int oesteps, double *dqa, double dqmaga, double **ictan, int finder, int climber, int do_tp, int &tp)
int	isomer_init (string isofilename)
void	set_ssm_bonds (ICoord &ic1)
double	get_ssm_dqmag (double bdist)
int	past_ts ()
	Checks if string is past_ts. Used by SSM.
int	find_peaks (int type)
	Finds peaks, used by opt_iters to know which node to climb.
int	find_uphill (double cutoff)
void	trim_string ()
void	trim_string (int nextmin)
int	add_linear ()
int	break_planes_ssm (ICoord ic1)
void	get_eigenv_bofill ()
void	get_eigenv_finite (int enode)
	calls get_eigenv_finite after constructing tangent
void	get_eigenv_finite (int enode, double **ictan)
	modifies hessian using RP direction
void	starting_string (double *dq, int nnodes)
	Grows the initial nodes for SE and DE. nnodes is 4 for DE and 3 for SE.
void	starting_string_dm (double *dq)
int	addNode (int n1, int n2, int n3)
int	addCNode (int n1)
	Add space node between n1-1 and n1.
void	add_last_node (int type)
void	com_rotate_move (int iR, int iP, int iN, double ff)
void	scan_r (int eigen)
void	opt_tr ()
void	opt_r ()
void	opt_steps (double dqa, double ictan, int osteps, int oesteps)
int	knnr_vs_opt (int n)
void	ic_reparam_g (double *dqa, double dqmaga)
	reparametrizes the string along the constraint during the growth phase, only used by DE
void	ic_reparam (double *dqa, double dqmaga, int type)
	reparametrizes the string along the constraint after the growth phase
void	ic_reparam_h (double *dqa, double dqmaga, int type)
void	ic_reparam_dm (double *dqa, double dqmaga, int type)
void	ic_reparam_new (double *dqa, double dqmaga, int type)
void	tangent_1 (double *ictan)
	Calculates the DE internal coordinate tangent vector.
double	tangent_1b (double *ictan)
	bond tangent for SSM
void	get_tangents_1 (double *dqa, double dqmaga, double **ictan)
	tangents pairwise, returns distance magnitudes also
void	get_tangents_1e (double *dqa, double dqmaga, double **ictan)
void	get_tangents_1g (double *dqa, double dqmaga, double **ictan)
	Finds the tangents during the growth phase. Tangents referenced to left or right during growing phase.
void	get_tangents (double *dqa, double dqmaga, double **ictan)
void	get_tangents_dm (double *dqa, double dqmaga, double **ictan)
void	get_distances (double dqmaga, double *ictan)
void	get_distances_dm (double dqmaga, double *ictan)
int	close_dist_fix (int type)
int	check_close_dist (int n, double dist, int newbonds)
void	add_bonds (int nadd, int *newbonds)
void	add_angles (int nadd, int *newangles)
void	align_rxn ()
void	align_string (ICoord ic1, ICoord ic2)
void	rotate_structure (double xyz0, int a)
void	print_em (int nmaxp)
void	set_prima (string pstring)
int	read_string (string stringfile, double *coordsn, double energies)
void	print_string_clump_p (int STEPS, double grad, double **allcoords, string xyzstring)
int	twin_peaks ()
int	find_ints ()
void	ic_reparam_cut (int min, double *dqa, double dqmaga, int type)
int	check_for_reaction_g (int type)
int	check_for_reaction (int &wts, int &wint)
void	general_init (string infilename)
void	parameter_init (string infilename)
void	structure_init (string xyzfile)
void	allelse_init ()
void	restart_string (string pstring)
Private Attributes
int	isRestart
int	killcounter
int	ngrowth
int	growing
int	oi
int	endearly
int	bondfrags
int	isSSM
int	hessSSM
int	isFSM
int	use_exact_climb
int	ptsn
double	newclimbscale
int	nfound
int	nbond
int	nadd
int	nbrk
int	nangle
int	ntors
int *	bond
int *	add
int *	brk
int *	angles
double *	anglet
int *	tors
double *	tort
int	n0
int	using_break_planes
int	natoms
int	ncpu
int	runNum
int	runend
string	runends
string	infile0
double **	coords
ICoord *	icoords
double **	tangents
double **	grads
double **	perp_grads
int	climb
int	find
int	TSnode0
int	cTSnode
double	lastdispr
double	xdist
int	nnew_bond
int *	new_bond
ICoord	bondsic
ICoord	newic
ICoord	intic
ICoord	int2ic
ICoord	newic_dm
ICoord	intic_dm
ICoord	int2ic_dm
int	ic_reparam_steps
int	pTSnode
double *	pTSnodecoords
int	nsplit
double *	V_profile
double	V0
int *	active
int	nn
int	nnR
int	nnP
int	nnmax
int	nnmax0
double	SCALING
int	INTERP_MODE
int	GROWD
string *	anames
int *	anumbers
double *	amasses
string	stringfilename
int	STEP_OPT_ITERS
int	MAX_OPT_ITERS
double	CONV_TOL
double	ADD_NODE_TOL
double	HESS_INIT
int	CHARGE
int	SPIN
double	NODE_SPACING
int	NUM_INTERP
int	NUM_STEPS
double	DQMAG_SSM_MAX
double	DQMAG_SSM_MIN
double	QDISTMAX
double	PEAK4_EDIFF
int	tstype
double	prodelim
int	lastOpt
int	initialOpt
int	gradJobCount
int	gradFailCount
Gradient	grad1

Member Function Documentation

void GString::add_angles	(	int	nadd,
		int *	newangles
	)			`[private]`

void GString::add_bonds	(	int	nadd,
		int *	newbonds
	)			`[private]`

void GString::add_last_node ( int type ) [private]

int GString::add_linear ( ) [private]

int GString::addCNode ( int n1 ) [private]

Add space node between n1-1 and n1.

int GString::addNode	(	int	n1,
		int	n2,
		int	n3
	)			`[private]`

Adds a node between n1 and n3. In SE, n2 is nnmax-1 arbitrarily because the added node is not "between" any node.

void GString::align_rxn ( ) [private]

void GString::align_string	(	ICoord	ic1,
		ICoord	ic2
	)			`[private]`

void GString::allelse_init ( ) [private]

int GString::break_planes_ssm ( ICoord ic1 ) [private]

void GString::build_fstring ( double ** fstring )

int GString::check_close_dist	(	int	n,
		double *	dist,
		int *	newbonds
	)			`[private]`

int GString::check_for_reaction	(	int &	wts,
		int &	wint
	)			`[private]`

int GString::check_for_reaction_g ( int type ) [private]

int GString::close_dist_fix ( int type ) [private]

void GString::com_rotate_move	(	int	iR,
		int	iP,
		int	iN,
		double	ff
	)			`[private]`

int GString::find_ints ( ) [private]

int GString::find_peaks ( int type ) [private]

Finds peaks, used by opt_iters to know which node to climb.

int GString::find_uphill ( double cutoff ) [private]

void GString::general_init ( string infilename ) [private]

void GString::get_distances	(	double *	dqmaga,
		double **	ictan
	)			`[private]`

void GString::get_distances_dm	(	double *	dqmaga,
		double **	ictan
	)			`[private]`

void GString::get_eigenv_bofill ( ) [private]

void GString::get_eigenv_finite	(	int	enode,
		double **	ictan
	)			`[private]`

modifies hessian using RP direction

void GString::get_eigenv_finite ( int enode ) [private]

calls get_eigenv_finite after constructing tangent

double GString::get_ssm_dqmag ( double bdist ) [private]

void GString::get_tangents	(	double **	dqa,
		double *	dqmaga,
		double **	ictan
	)			`[private]`

void GString::get_tangents_1	(	double **	dqa,
		double *	dqmaga,
		double **	ictan
	)			`[private]`

tangents pairwise, returns distance magnitudes also

void GString::get_tangents_1e	(	double **	dqa,
		double *	dqmaga,
		double **	ictan
	)			`[private]`

void GString::get_tangents_1g	(	double **	dqa,
		double *	dqmaga,
		double **	ictan
	)			`[private]`

Finds the tangents during the growth phase. Tangents referenced to left or right during growing phase.

void GString::get_tangents_dm	(	double **	dqa,
		double *	dqmaga,
		double **	ictan
	)			`[private]`

void GString::growth_iters	(	int	max_iter,
		double &	totalgrad,
		double &	gradrms,
		double	endenergy,
		string	strfileg,
		int &	tscontinue,
		double	gaddmax,
		int	osteps,
		int	oesteps,
		double **	dqa,
		double *	dqmaga,
		double **	ictan
	)			`[private]`

Optimization and add node driver for SE and DE during growth phase. max_iter is the max number of iterations for the entire calculation (growth and optimiazation)

void GString::ic_reparam	(	double **	dqa,
		double *	dqmaga,
		int	type
	)			`[private]`

reparametrizes the string along the constraint after the growth phase

rtype==0 using average

void GString::ic_reparam_cut	(	int	min,
		double **	dqa,
		double *	dqmaga,
		int	type
	)			`[private]`

void GString::ic_reparam_dm	(	double **	dqa,
		double *	dqmaga,
		int	type
	)			`[private]`

void GString::ic_reparam_g	(	double **	dqa,
		double *	dqmaga
	)			`[private]`

reparametrizes the string along the constraint during the growth phase, only used by DE

void GString::ic_reparam_h	(	double **	dqa,
		double *	dqmaga,
		int	type
	)			`[private]`

void GString::ic_reparam_new	(	double **	dqa,
		double *	dqmaga,
		int	type
	)			`[private]`

void GString::init	(	string	infilename,
		int	run,
		int	nprocs
	)

initializes starting variables related to the string.xyz file, ISOMERS file, nprocs, etc.

void GString::init	(	string	infilename,
		string	xyzfile
	)

int GString::isomer_init ( string isofilename ) [private]

int GString::knnr_vs_opt ( int n ) [private]

double GString::min_rms_structure_distance	(	double *	struct1,
		double *	struct2,
		int	natoms
	)

void GString::opt_iters	(	int	max_iter,
		double &	totalgrad,
		double &	gradrms,
		double	endenergy,
		string	strfileg,
		int &	tscontinue,
		double	gaddmax,
		int	osteps,
		int	oesteps,
		double **	dqa,
		double *	dqmaga,
		double **	ictan,
		int	finder,
		int	climber,
		int	do_tp,
		int &	tp
	)			`[private]`

Optimization driver for DE and SE during the optimization phase. climber=1 uses climbing image, finder=1 finds the exact TS

void GString::opt_r ( ) [private]

void GString::opt_steps	(	double **	dqa,
		double **	ictan,
		int	osteps,
		int	oesteps
	)			`[private]`

Optimizes each active node. osteps is the number of optimization steps for the nodes oesteps is the number of eigenvector following steps for the TS

void GString::opt_tr ( ) [private]

void GString::parameter_init ( string infilename ) [private]

int GString::past_ts ( ) [private]

Checks if string is past_ts. Used by SSM.

void GString::print_em ( int nmaxp ) [private]

void GString::print_string	(	int	STEPS,
		double **	allcoords,
		string	xyzstring
	)

void GString::print_string_clump	(	int	STEPS,
		double	grad,
		double **	allcoords,
		string	xyzstring
	)

void GString::print_string_clump_p	(	int	STEPS,
		double	grad,
		double **	allcoords,
		string	xyzstring
	)			`[private]`

int GString::read_string	(	string	stringfile,
		double **	coordsn,
		double *	energies
	)			`[private]`

void GString::reparam_and_getTangents_with_LST ( double ** fstring )

void GString::restart_string ( string pstring ) [private]

void GString::rotate_structure	(	double *	xyz0,
		int *	a
	)			`[private]`

void GString::scan_r ( int eigen ) [private]

void GString::set_fsm_active	(	int	nnR,
		int	nnP
	)			`[private]`

void GString::set_prima ( string pstring ) [private]

void GString::set_ssm_bonds ( ICoord & ic1 ) [private]

void GString::shift_node	(	int	nnOld,
		int	nnNew
	)

void GString::starting_string	(	double *	dq,
		int	nnodes
	)			`[private]`

Grows the initial nodes for SE and DE. nnodes is 4 for DE and 3 for SE.

void GString::starting_string_dm ( double * dq ) [private]

void GString::String_Method_Optimization ( )

The main driver for DE and SE methods, growth and optimization. Can only be called after coordinates have been set.

void GString::structure_init ( string xyzfile ) [private]

Reads xyz file defined from commnand line

void GString::tangent_1 ( double * ictan ) [private]

Calculates the DE internal coordinate tangent vector.

double GString::tangent_1b ( double * ictan ) [private]

bond tangent for SSM

void GString::trim_string ( int nextmin ) [private]

void GString::trim_string ( ) [private]

int GString::twin_peaks ( ) [private]

void GString::write_geom_file ( int iter )

void GString::write_string_file ( int iter )

void GString::write_SVfile ( int iter )

Member Data Documentation

int* GString::active [private]

int* GString::add [private]

double GString::ADD_NODE_TOL [private]

double** GString::allcoords

double* GString::amasses [private]

string* GString::anames [private]

int* GString::angles [private]

double* GString::anglet [private]

int* GString::anumbers [private]

int* GString::bond [private]

int GString::bondfrags [private]

ICoord GString::bondsic [private]

int* GString::brk [private]

int GString::CHARGE [private]

int GString::climb [private]

double GString::CONV_TOL [private]

double** GString::coords [private]

int GString::cTSnode [private]

double GString::DQMAG_SSM_MAX [private]

double GString::DQMAG_SSM_MIN [private]

int GString::endearly [private]

int GString::find [private]

Gradient GString::grad1 [private]

int GString::gradFailCount [private]

int GString::gradJobCount [private]

double** GString::grads [private]

int GString::GROWD [private]

int GString::growing [private]

double GString::HESS_INIT [private]

int GString::hessSSM [private]

int GString::ic_reparam_steps [private]

ICoord* GString::icoords [private]

string GString::infile0 [private]

int GString::initialOpt [private]

ICoord GString::int2ic [private]

ICoord GString::int2ic_dm [private]

int GString::INTERP_MODE [private]

ICoord GString::intic [private]

ICoord GString::intic_dm [private]

int GString::isFSM [private]

int GString::isRestart [private]

int GString::isSSM [private]

int GString::killcounter [private]

double GString::lastdispr [private]

int GString::lastOpt [private]

int GString::MAX_OPT_ITERS [private]

int GString::n0 [private]

int GString::nadd [private]

int GString::nangle [private]

int GString::natoms [private]

int GString::nbond [private]

int GString::nbrk [private]

int GString::ncpu [private]

int* GString::new_bond [private]

double GString::newclimbscale [private]

ICoord GString::newic [private]

ICoord GString::newic_dm [private]

int GString::nfound [private]

int GString::ngrowth [private]

int GString::nn [private]

int GString::nnew_bond [private]

int GString::nnmax [private]

int GString::nnmax0 [private]

int GString::nnP [private]

int GString::nnR [private]

double GString::NODE_SPACING [private]

int GString::nsplit [private]

int GString::ntors [private]

int GString::NUM_INTERP [private]

int GString::NUM_STEPS [private]

int GString::oi [private]

double GString::PEAK4_EDIFF [private]

double** GString::perp_grads [private]

double GString::prodelim [private]

int GString::ptsn [private]

int GString::pTSnode [private]

double* GString::pTSnodecoords [private]

double GString::QDISTMAX [private]

int GString::runend [private]

string GString::runends [private]

int GString::runNum [private]

double GString::SCALING [private]

int GString::SPIN [private]

int GString::STEP_OPT_ITERS [private]

string GString::stringfilename [private]

double** GString::tangents [private]

int* GString::tors [private]

double* GString::tort [private]

int GString::TSnode0 [private]

int GString::tstype [private]

int GString::use_exact_climb [private]

int GString::using_break_planes [private]

double GString::V0 [private]

double* GString::V_profile [private]

double GString::xdist [private]

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

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

GString Class Reference

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Member Function Documentation

Member Data Documentation