ICoord Class Reference

#include <icoord.h>

Collaboration diagram for ICoord:

Public Member Functions
void	update_bfgs ()
void	update_bfgsp (int makeHint)
void	update_bofill ()
void	save_hess ()
double	getR (int i)
void	make_Hint ()
void	Hintp_to_Hint ()
int	davidson_H (int neigen)
int	ic_create ()
	creates the internal coordinates
int	ic_create_nobonds ()
int	mm_grad ()
int	mm_grad (ICoord shadow)
int	grad_to_q ()
	Transforms the gradient in Cartesian representation to delocalized internal coordinate representation.
int	ic_to_xyz ()
	back transforms from delocalized IC representation to Cartesian represention
int	ic_to_xyz_opt ()
int	grad_init (string infilename, int ncpu, int run, int rune, int use_knnr, int q1)
int	get_tangent ()
int	distance_matrix_ic (ICoord ic1, ICoord ic2)
int	union_ic (ICoord ic1, ICoord ic2)
int	copy_ic (ICoord ic1)
void	write_ic (string filename)
int	read_ics (string filename)
int	opt ()
int	opt (string xyzfile, ICoord shadow)
int	opt (string xyzfile)
void	opt_constraint (double *C)
double	opt_a (int nnewb, int newb, int nnewt, int newt, string xyzfile_string, int nsteps)
double	opt_b (string xyzfile_string, int nsteps)
	optimizes the node to the minimum without a constraint
double	opt_c (string xyzfile_string, int nsteps, double C, double C0)
	Optimizes the node subject to a constraint, nsteps times.
double	opt_r (string xyzfile_string, int nsteps, double C, double C0, double *D, int type)
double	opt_eigen_ts (string xyzfile_string, int nsteps, double C, double C0)
void	update_ic ()
void	mm_init ()
int	bmat_alloc ()
int	bmat_free ()
int	bmatp_finite ()
int	bmatp_create ()
	forms the original B matrix
int	bmatp_to_U ()
	Diagonalizes G to form U.
int	bmat_create ()
	Determines q the components of the molecular geometry in the DI space. Also forms the active B matrix.
int	bond_exists (int b1, int b2)
int	bond_num (int b1, int b2)
int	angle_num (int b1, int b2, int b3)
int	tor_num (int b1, int b2, int b3, int b4)
int	hpair (int a1, int a2)
int	h2count ()
int	same_struct (double *xyz)
int	init (string xyzfile)
int	init (int natoms, string anames, int anumbers, double *xyz)
int	alloc (int size)
int	reset (int natoms, string anames, int anumbers, double *xyz)
int	reset (double *xyz)
void	print_q ()
void	print_ic ()
void	print_bonds ()
void	print_xyz ()
void	print_xyz_save (string filename)
void	print_xyz_save (string xyzfile_string, double energy)
double	distance (int i, int j)
double	angle_val (int i, int j, int k)
double	torsion_val (int i, int j, int k, int l)
void	freemem ()
int	create_prima (int nnodes, int nbonds, int nangles, int ntor, double **tangents)
void	save_hesspu (string filename)
void	save_hessp (string filename)
void	read_hessp (string filename)
void	read_hessxyz (string filename, int write)
Public Attributes
int	revertOpt
Gradient	grad1
string	printout
double	FMAG
double	OPTTHRESH
double	MAXAD
double	DMAX
double	DMIN0
double	SCALEQN0
double	SCALEQN
double	V0
int *	frozen
double	farBond
int	isTSnode
int	nneg
int	newHess
int	optCG
int	do_bfgs
int	noptdone
double	path_overlap
int	path_overlap_n
double	path_overlap_e_g
int	nicd
int	nicd0
double *	bondd
double *	anglev
double *	torv
double *	torv0
double *	torfix
double *	imptorv
int **	bonds
int	nbonds
int **	angles
int	nangles
int **	torsions
int	ntor
double *	grad
double *	gradq
double *	pgradq
double *	gradqprim
double *	pgradqprim
double *	dq0
double *	dqm1
double *	dqprim
double *	Hint
double *	Hintp
double *	Hinv
double *	q
int	useExactH
int	isOpt
int	stage1opt
double	pgradrms
double	gradrms
int	isDavid
int	id
int	pid
int	natoms
double *	coords
double *	coordsts
double *	coords0
string *	anames
int *	anumbers
int *	coordn
int	nimptor
string	runends
string	runend2
double *	bmatp
double *	Ut
double *	Ut0
int	use_constraint
int	ridge
Private Member Functions
void	structure_read (string xyzfile)
void	alloc_mem ()
void	make_bonds ()
void	coord_num ()
void	make_angles ()
void	make_torsions ()
void	make_frags ()
void	bond_frags ()
void	hbond_frags ()
void	linear_ties ()
void	h2o_torsions ()
void	tm_ties ()
void	make_imptor ()
void	make_imptor_nobonds ()
int	make_nonbond ()
void	update_bonds ()
void	update_angles ()
void	update_torsion ()
void	update_imptor ()
void	update_nonbond ()
void	create_xyz ()
double	close_bond (int i)
double	close_angle (int i)
double	close_tor (int i)
double	ffbondd (int i, int j)
double	ffbonde (int i, int j)
double	ffangled (int i, int j)
double	ffanglee (int i, int j)
double	fftord (int i, int j, int k, int l)
double	fftore (int i, int j, int k, int l)
double	fftorm (int i, int j, int k, int l)
double	ffimptore (int i, int j, int k, int l)
double	ffimptord (int i, int j, int k, int l)
int	isTM (int anum)
void	print_grad ()
void	print_gradq ()
void	bond_grad_all ()
void	bond_grad_1 (int i, int j)
double	bond_stretch (int i, int j)
void	angle_grad_all ()
void	angle_grad_1 (int i, int j, int k)
void	torsion_grad_all ()
void	torsion_grad_1 (int i, int j, int k, int l)
void	imptor_grad_all ()
void	imptor_grad_1 (int i, int j, int k, int l)
void	vdw_grad_all ()
void	vdw_grad_1 (int i, int j, double scale)
void	update_ic_qn ()
void	update_ic_eigen ()
void	update_ic_eigen_h (double C, double D)
void	update_ic_eigen_ts (double *C)
void	walk_up ()
void	force_notbonds ()
void	bmatp_dqbdx (int a1, int a2, double *dqbdx)
void	bmatp_dqadx (int a1, int a2, int a3, double *dqadx)
void	bmatp_dqtdx (int a1, int a2, int a3, int a4, double *dqtdx)
void	print_xyzf (ofstream xyzfile)
double	prima_force ()
void	lin_grad_1 (int i, int j, double scale)
void	get_gm ()
void	create_mwHint_EV (double Lm, double Lme)
Private Attributes
int	g_inited
double *	amasses
double *	amasses3
double *	dxm1
double	dEpre
double	smag
int **	imptor
int	nfrags
int *	frags
int	max_bonds
int	max_angles
int	max_torsions
int	max_imptor
int	max_nonbond
int	n_nonbond
int **	nonbond
double *	nonbondd
int	ixflag
double *	ffR
double *	ffeps
double *	bmat
double *	bmatti
int	nnodes
double *	prima
int *	aprima
double *	Cp
double	mdist
char *	sbuff
double *	Gmh
double *	Gmih

Member Function Documentation

int ICoord::alloc ( int size )

void ICoord::alloc_mem ( ) [private]

void ICoord::angle_grad_1	(	int	i,
		int	j,
		int	k
	)			`[private]`

void ICoord::angle_grad_all ( ) [private]

int ICoord::angle_num	(	int	b1,
		int	b2,
		int	b3
	)

double ICoord::angle_val	(	int	i,
		int	j,
		int	k
	)

int ICoord::bmat_alloc ( )

int ICoord::bmat_create ( )

Determines q the components of the molecular geometry in the DI space. Also forms the active B matrix.

int ICoord::bmat_free ( )

int ICoord::bmatp_create ( )

forms the original B matrix

void ICoord::bmatp_dqadx	(	int	a1,
		int	a2,
		int	a3,
		double *	dqadx
	)			`[private]`

void ICoord::bmatp_dqbdx	(	int	a1,
		int	a2,
		double *	dqbdx
	)			`[private]`

void ICoord::bmatp_dqtdx	(	int	a1,
		int	a2,
		int	a3,
		int	a4,
		double *	dqtdx
	)			`[private]`

int ICoord::bmatp_finite ( )

int ICoord::bmatp_to_U ( )

Diagonalizes G to form U.

int ICoord::bond_exists	(	int	b1,
		int	b2
	)

void ICoord::bond_frags ( ) [private]

void ICoord::bond_grad_1	(	int	i,
		int	j
	)			`[private]`

void ICoord::bond_grad_all ( ) [private]

int ICoord::bond_num	(	int	b1,
		int	b2
	)

double ICoord::bond_stretch	(	int	i,
		int	j
	)			`[private]`

double ICoord::close_angle ( int i ) [private]

double ICoord::close_bond ( int i ) [private]

double ICoord::close_tor ( int i ) [private]

void ICoord::coord_num ( ) [private]

int ICoord::copy_ic ( ICoord ic1 )

void ICoord::create_mwHint_EV	(	double *	Lm,
		double *	Lme
	)			`[private]`

int ICoord::create_prima	(	int	nnodes,
		int	nbonds,
		int	nangles,
		int	ntor,
		double **	tangents
	)

void ICoord::create_xyz ( ) [private]

int ICoord::davidson_H ( int neigen )

double ICoord::distance	(	int	i,
		int	j
	)

int ICoord::distance_matrix_ic	(	ICoord	ic1,
		ICoord	ic2
	)

double ICoord::ffangled	(	int	i,
		int	j
	)			`[private]`

double ICoord::ffanglee	(	int	i,
		int	j
	)			`[private]`

double ICoord::ffbondd	(	int	i,
		int	j
	)			`[private]`

double ICoord::ffbonde	(	int	i,
		int	j
	)			`[private]`

double ICoord::ffimptord	(	int	i,
		int	j,
		int	k,
		int	l
	)			`[private]`

double ICoord::ffimptore	(	int	i,
		int	j,
		int	k,
		int	l
	)			`[private]`

double ICoord::fftord	(	int	i,
		int	j,
		int	k,
		int	l
	)			`[private]`

double ICoord::fftore	(	int	i,
		int	j,
		int	k,
		int	l
	)			`[private]`

double ICoord::fftorm	(	int	i,
		int	j,
		int	k,
		int	l
	)			`[private]`

void ICoord::force_notbonds ( ) [private]

void ICoord::freemem ( )

void ICoord::get_gm ( ) [private]

int ICoord::get_tangent ( )

double ICoord::getR ( int i )

int ICoord::grad_init	(	string	infilename,
		int	ncpu,
		int	run,
		int	rune,
		int	use_knnr,
		int	q1
	)

int ICoord::grad_to_q ( )

Transforms the gradient in Cartesian representation to delocalized internal coordinate representation.

int ICoord::h2count ( )

void ICoord::h2o_torsions ( ) [private]

void ICoord::hbond_frags ( ) [private]

void ICoord::Hintp_to_Hint ( )

int ICoord::hpair	(	int	a1,
		int	a2
	)

int ICoord::ic_create ( )

creates the internal coordinates

int ICoord::ic_create_nobonds ( )

int ICoord::ic_to_xyz ( )

back transforms from delocalized IC representation to Cartesian represention

int ICoord::ic_to_xyz_opt ( )

void ICoord::imptor_grad_1	(	int	i,
		int	j,
		int	k,
		int	l
	)			`[private]`

void ICoord::imptor_grad_all ( ) [private]

int ICoord::init	(	int	natoms,
		string *	anames,
		int *	anumbers,
		double *	xyz
	)

int ICoord::init ( string xyzfile )

int ICoord::isTM ( int anum ) [private]

void ICoord::lin_grad_1	(	int	i,
		int	j,
		double	scale
	)			`[private]`

void ICoord::linear_ties ( ) [private]

void ICoord::make_angles ( ) [private]

void ICoord::make_bonds ( ) [private]

void ICoord::make_frags ( ) [private]

void ICoord::make_Hint ( )

void ICoord::make_imptor ( ) [private]

void ICoord::make_imptor_nobonds ( ) [private]

int ICoord::make_nonbond ( ) [private]

void ICoord::make_torsions ( ) [private]

int ICoord::mm_grad ( ICoord shadow )

int ICoord::mm_grad ( )

void ICoord::mm_init ( )

int ICoord::opt ( string xyzfile )

int ICoord::opt	(	string	xyzfile,
		ICoord	shadow
	)

int ICoord::opt ( )

double ICoord::opt_a	(	int	nnewb,
		int *	newb,
		int	nnewt,
		int *	newt,
		string	xyzfile_string,
		int	nsteps
	)

double ICoord::opt_b	(	string	xyzfile_string,
		int	nsteps
	)

optimizes the node to the minimum without a constraint

double ICoord::opt_c	(	string	xyzfile_string,
		int	nsteps,
		double *	C,
		double *	C0
	)

Optimizes the node subject to a constraint, nsteps times.

void ICoord::opt_constraint ( double * C )

take constraint vector, project it out of all Ut orthonormalize vectors last vector becomes C (projection onto space)

double ICoord::opt_eigen_ts	(	string	xyzfile_string,
		int	nsteps,
		double *	C,
		double *	C0
	)

double ICoord::opt_r	(	string	xyzfile_string,
		int	nsteps,
		double *	C,
		double *	C0,
		double *	D,
		int	type
	)

double ICoord::prima_force ( ) [private]

void ICoord::print_bonds ( )

void ICoord::print_grad ( ) [private]

void ICoord::print_gradq ( ) [private]

void ICoord::print_ic ( )

void ICoord::print_q ( )

void ICoord::print_xyz ( )

void ICoord::print_xyz_save	(	string	xyzfile_string,
		double	energy
	)

void ICoord::print_xyz_save ( string filename )

void ICoord::print_xyzf ( ofstream xyzfile ) [private]

void ICoord::read_hessp ( string filename )

void ICoord::read_hessxyz	(	string	filename,
		int	write
	)

int ICoord::read_ics ( string filename )

int ICoord::reset ( double * xyz )

int ICoord::reset	(	int	natoms,
		string *	anames,
		int *	anumbers,
		double *	xyz
	)

int ICoord::same_struct ( double * xyz )

void ICoord::save_hess ( )

void ICoord::save_hessp ( string filename )

void ICoord::save_hesspu ( string filename )

void ICoord::structure_read ( string xyzfile ) [private]

void ICoord::tm_ties ( ) [private]

int ICoord::tor_num	(	int	b1,
		int	b2,
		int	b3,
		int	b4
	)

void ICoord::torsion_grad_1	(	int	i,
		int	j,
		int	k,
		int	l
	)			`[private]`

void ICoord::torsion_grad_all ( ) [private]

double ICoord::torsion_val	(	int	i,
		int	j,
		int	k,
		int	l
	)

int ICoord::union_ic	(	ICoord	ic1,
		ICoord	ic2
	)

void ICoord::update_angles ( ) [private]

void ICoord::update_bfgs ( )

void ICoord::update_bfgsp ( int makeHint )

void ICoord::update_bofill ( )

void ICoord::update_bonds ( ) [private]

void ICoord::update_ic ( )

void ICoord::update_ic_eigen ( ) [private]

void ICoord::update_ic_eigen_h	(	double *	C,
		double *	D
	)			`[private]`

void ICoord::update_ic_eigen_ts ( double * C ) [private]

void ICoord::update_ic_qn ( ) [private]

void ICoord::update_imptor ( ) [private]

void ICoord::update_nonbond ( ) [private]

void ICoord::update_torsion ( ) [private]

void ICoord::vdw_grad_1	(	int	i,
		int	j,
		double	scale
	)			`[private]`

void ICoord::vdw_grad_all ( ) [private]

void ICoord::walk_up ( ) [private]

void ICoord::write_ic ( string filename )

Member Data Documentation

double* ICoord::amasses [private]

double* ICoord::amasses3 [private]

string* ICoord::anames

int** ICoord::angles

double* ICoord::anglev

int* ICoord::anumbers

int* ICoord::aprima [private]

double* ICoord::bmat [private]

double* ICoord::bmatp

double* ICoord::bmatti [private]

double* ICoord::bondd

int** ICoord::bonds

int* ICoord::coordn

double* ICoord::coords

double* ICoord::coords0

double* ICoord::coordsts

double* ICoord::Cp [private]

double ICoord::dEpre [private]

double ICoord::DMAX

double ICoord::DMIN0

int ICoord::do_bfgs

double* ICoord::dq0

double* ICoord::dqm1

double* ICoord::dqprim

double* ICoord::dxm1 [private]

double ICoord::farBond

double* ICoord::ffeps [private]

double* ICoord::ffR [private]

double ICoord::FMAG

int* ICoord::frags [private]

int* ICoord::frozen

int ICoord::g_inited [private]

double* ICoord::Gmh [private]

double* ICoord::Gmih [private]

double* ICoord::grad

Gradient ICoord::grad1

double* ICoord::gradq

double* ICoord::gradqprim

double ICoord::gradrms

double* ICoord::Hint

double* ICoord::Hintp

double* ICoord::Hinv

int ICoord::id

int** ICoord::imptor [private]

double* ICoord::imptorv

int ICoord::isDavid

int ICoord::isOpt

int ICoord::isTSnode

int ICoord::ixflag [private]

int ICoord::max_angles [private]

int ICoord::max_bonds [private]

int ICoord::max_imptor [private]

int ICoord::max_nonbond [private]

int ICoord::max_torsions [private]

double ICoord::MAXAD

double ICoord::mdist [private]

int ICoord::n_nonbond [private]

int ICoord::nangles

int ICoord::natoms

int ICoord::nbonds

int ICoord::newHess

int ICoord::nfrags [private]

int ICoord::nicd

int ICoord::nicd0

int ICoord::nimptor

int ICoord::nneg

int ICoord::nnodes [private]

int** ICoord::nonbond [private]

double* ICoord::nonbondd [private]

int ICoord::noptdone

int ICoord::ntor

int ICoord::optCG

double ICoord::OPTTHRESH

double ICoord::path_overlap

double ICoord::path_overlap_e_g

int ICoord::path_overlap_n

double* ICoord::pgradq

double* ICoord::pgradqprim

double ICoord::pgradrms

int ICoord::pid

double* ICoord::prima [private]

string ICoord::printout

double* ICoord::q

int ICoord::revertOpt

int ICoord::ridge

string ICoord::runend2

string ICoord::runends

char* ICoord::sbuff [private]

double ICoord::SCALEQN

double ICoord::SCALEQN0

double ICoord::smag [private]

int ICoord::stage1opt

double* ICoord::torfix

int** ICoord::torsions

double* ICoord::torv

double* ICoord::torv0

int ICoord::use_constraint

int ICoord::useExactH

double* ICoord::Ut

double* ICoord::Ut0

double ICoord::V0

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

/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/icoord.h
/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/bmat.cpp
/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/icoord.cpp
/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/mem.cpp
/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/mm_grad.cpp
/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/optic.cpp
/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/print.cpp

ICoord Class Reference

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Member Function Documentation

Member Data Documentation