gmx_arpack.h File Reference

#include "config.h"

Include dependency graph for gmx_arpack.h:

Description

Selected routines from ARPACK.

This file contains a subset of ARPACK functions to perform diagonalization and SVD for sparse matrices in Gromacs.

Consult the main ARPACK site for detailed documentation: http://www.caam.rice.edu/software/ARPACK/

Below, we just list the options and any specific differences from ARPACK. The code is essentially the same, but the routines have been made thread-safe by using extra workspace arrays.

Functions
void	dsaupd (int *ido, const char *bmat, int *n, const char *which, int *nev, double *tol, double *resid, int *ncv, double *v, int *ldv, int *iparam, int *ipntr, double *workd, int *iwork, double *workl, int *lworkl, int *info)
	Implicitly Restarted Arnoldi Iteration, double precision. More...
void	dseupd (int *rvec, const char *howmny, int *select, double *d, double *z, int *ldz, double *sigma, const char *bmat, int *n, const char *which, int *nev, double *tol, double *resid, int *ncv, double *v, int *ldv, int *iparam, int *ipntr, double *workd, double *workl, int *lworkl, int *info)
	Get eigenvalues/vectors after Arnoldi iteration, double prec. More...
void	ssaupd (int *ido, const char *bmat, int *n, const char *which, int *nev, float *tol, float *resid, int *ncv, float *v, int *ldv, int *iparam, int *ipntr, float *workd, int *iwork, float *workl, int *lworkl, int *info)
	Implicitly Restarted Arnoldi Iteration, single precision. More...
void	sseupd (int *rvec, const char *howmny, int *select, float *d, float *z, int *ldz, float *sigma, const char *bmat, int *n, const char *which, int *nev, float *tol, float *resid, int *ncv, float *v, int *ldv, int *iparam, int *ipntr, float *workd, float *workl, int *lworkl, int *info)
	Get eigenvalues/vectors after Arnoldi iteration, single prec. More...

Function Documentation

void dsaupd	(	int *	ido,
		const char *	bmat,
		int *	n,
		const char *	which,
		int *	nev,
		double *	tol,
		double *	resid,
		int *	ncv,
		double *	v,
		int *	ldv,
		int *	iparam,
		int *	ipntr,
		double *	workd,
		int *	iwork,
		double *	workl,
		int *	lworkl,
		int *	info
	)

Implicitly Restarted Arnoldi Iteration, double precision.

Reverse communication interface for the Implicitly Restarted Arnoldi Iteration. For symmetric problems this reduces to a variant of the Lanczos method. See the ARPACK site for details.

Parameters

ido	Reverse communication flag. Set to 0 first time. Upon return with ido=-1 or ido=1 you should calculate Y=A*X and recall the routine. Return with ido=2 means Y=B*X should be calculated. ipntr[0] is the pointer in workd for X, ipntr[1] is the index for Y. Return with ido=99 means it finished.
bmat	'I' for standard eigenproblem, 'G' for generalized.
n	Order of eigenproblem.
which	Which eigenvalues to calculate. 'LA' for largest algebraic, 'SA' for smallest algebraic, 'LM' for largest magnitude, 'SM' for smallest magnitude, and finally 'BE' (both ends) to calculate half from each end of the spectrum.
nev	Number of eigenvalues to calculate. 0<nev<n.
tol	Tolerance. Machine precision of it is 0.
resid	Optional starting residual vector at input if info=1, otherwise a random one is used. Final residual vector on return.
ncv	Number of columns in matrix v.
v	N*NCV matrix. V contain the Lanczos basis vectors.
ldv	Leading dimension of v.
iparam	Integer array, size 11. Same contents as arpack.
ipntr	Integer array, size 11. Points to starting locations in the workd/workl arrays. Same contents as arpack.
workd	Double precision work array, length 3*n+4. Provide the same array for all calls, and don't touch it. IMPORTANT: This is 4 units larger than standard ARPACK!
iwork	Integer work array, size 80. Provide the same array for all calls, and don't touch it. IMPORTANT: New argument compared to standard ARPACK!
workl	Double precision work array, length lwork.
lworkl	Length of the work array workl. Must be at least ncv*(ncv+8)
info	Set info to 0 to use random initial residual vector, or to 1 if you provide a one. On output, info=0 means normal exit, 1 that max number of iterations was reached, and 3 that no shifts could be applied. Negative numbers correspond to errors in the arguments provided.

void dseupd	(	int *	rvec,
		const char *	howmny,
		int *	select,
		double *	d,
		double *	z,
		int *	ldz,
		double *	sigma,
		const char *	bmat,
		int *	n,
		const char *	which,
		int *	nev,
		double *	tol,
		double *	resid,
		int *	ncv,
		double *	v,
		int *	ldv,
		int *	iparam,
		int *	ipntr,
		double *	workd,
		double *	workl,
		int *	lworkl,
		int *	info
	)

Get eigenvalues/vectors after Arnoldi iteration, double prec.

See the ARPACK site for details. You must have finished the interative part with dsaupd() before calling this function.

Parameters

rvec	1 if you want eigenvectors, 0 if not.
howmny	'A' if you want all nvec vectors, 'S' if you provide a subset selection in select[].
select	Integer array, dimension nev. Indices of the eigenvectors to calculate. Fortran code means we start counting on 1. This array must be given even in howmny is 'A'. (Arpack documentation is wrong on this).
d	Double precision array, length nev. Eigenvalues.
z	Double precision array, n*nev. Eigenvectors.
ldz	Leading dimension of z. Normally n.
sigma	Shift if iparam[6] is 3,4, or 5. Ignored otherwise.
bmat	Provide the same argument as you did to dsaupd()
n	Provide the same argument as you did to dsaupd()
which	Provide the same argument as you did to dsaupd()
nev	Provide the same argument as you did to dsaupd()
tol	Provide the same argument as you did to dsaupd()
resid	Provide the same argument as you did to dsaupd() The array must not be touched between the two function calls!
ncv	Provide the same argument as you did to dsaupd()
v	Provide the same argument as you did to dsaupd() The array must not be touched between the two function calls!
ldv	Provide the same argument as you did to dsaupd()
iparam	Provide the same argument as you did to dsaupd() The array must not be touched between the two function calls!
ipntr	Provide the same argument as you did to dsaupd() The array must not be touched between the two function calls!
workd	Provide the same argument as you did to dsaupd() The array must not be touched between the two function calls!
workl	Double precision work array, length lwork. The array must not be touched between the two function calls!
lworkl	Provide the same argument as you did to dsaupd()
info	Provide the same argument as you did to dsaupd()

void ssaupd	(	int *	ido,
		const char *	bmat,
		int *	n,
		const char *	which,
		int *	nev,
		float *	tol,
		float *	resid,
		int *	ncv,
		float *	v,
		int *	ldv,
		int *	iparam,
		int *	ipntr,
		float *	workd,
		int *	iwork,
		float *	workl,
		int *	lworkl,
		int *	info
	)

Implicitly Restarted Arnoldi Iteration, single precision.

Reverse communication interface for the Implicitly Restarted Arnoldi Iteration. For symmetric problems this reduces to a variant of the Lanczos method. See the ARPACK site for details.

Parameters

ido	Reverse communication flag. Set to 0 first time. Upon return with ido=-1 or ido=1 you should calculate Y=A*X and recall the routine. Return with ido=2 means Y=B*X should be calculated. ipntr[0] is the pointer in workd for X, ipntr[1] is the index for Y. Return with ido=99 means it finished.
bmat	'I' for standard eigenproblem, 'G' for generalized.
n	Order of eigenproblem.
which	Which eigenvalues to calculate. 'LA' for largest algebraic, 'SA' for smallest algebraic, 'LM' for largest magnitude, 'SM' for smallest magnitude, and finally 'BE' (both ends) to calculate half from each end of the spectrum.
nev	Number of eigenvalues to calculate. 0<nev<n.
tol	Tolerance. Machine precision of it is 0.
resid	Optional starting residual vector at input if info=1, otherwise a random one is used. Final residual vector on return.
ncv	Number of columns in matrix v.
v	N*NCV matrix. V contain the Lanczos basis vectors.
ldv	Leading dimension of v.
iparam	Integer array, size 11. Same contents as arpack.
ipntr	Integer array, size 11. Points to starting locations in the workd/workl arrays. Same contents as arpack.
workd	Single precision work array, length 3*n+4. Provide the same array for all calls, and don't touch it. IMPORTANT: This is 4 units larger than standard ARPACK!
iwork	Integer work array, size 80. Provide the same array for all calls, and don't touch it. IMPORTANT: New argument compared to standard ARPACK!
workl	Single precision work array, length lwork.
lworkl	Length of the work array workl. Must be at least ncv*(ncv+8)
info	Set info to 0 to use random initial residual vector, or to 1 if you provide a one. On output, info=0 means normal exit, 1 that max number of iterations was reached, and 3 that no shifts could be applied. Negative numbers correspond to errors in the arguments provided.

void sseupd	(	int *	rvec,
		const char *	howmny,
		int *	select,
		float *	d,
		float *	z,
		int *	ldz,
		float *	sigma,
		const char *	bmat,
		int *	n,
		const char *	which,
		int *	nev,
		float *	tol,
		float *	resid,
		int *	ncv,
		float *	v,
		int *	ldv,
		int *	iparam,
		int *	ipntr,
		float *	workd,
		float *	workl,
		int *	lworkl,
		int *	info
	)

Get eigenvalues/vectors after Arnoldi iteration, single prec.

See the ARPACK site for details. You must have finished the interative part with ssaupd() before calling this function.

Parameters

rvec	1 if you want eigenvectors, 0 if not.
howmny	'A' if you want all nvec vectors, 'S' if you provide a subset selection in select[].
select	Integer array, dimension nev. Indices of the eigenvectors to calculate. Fortran code means we start counting on 1. This array must be given even in howmny is 'A'. (Arpack documentation is wrong on this).
d	Single precision array, length nev. Eigenvalues.
z	Single precision array, n*nev. Eigenvectors.
ldz	Leading dimension of z. Normally n.
sigma	Shift if iparam[6] is 3,4, or 5. Ignored otherwise.
bmat	Provide the same argument as you did to ssaupd()
n	Provide the same argument as you did to ssaupd()
which	Provide the same argument as you did to ssaupd()
nev	Provide the same argument as you did to ssaupd()
tol	Provide the same argument as you did to ssaupd()
resid	Provide the same argument as you did to ssaupd() The array must not be touched between the two function calls!
ncv	Provide the same argument as you did to ssaupd()
v	Provide the same argument as you did to ssaupd() The array must not be touched between the two function calls!
ldv	Provide the same argument as you did to ssaupd()
iparam	Provide the same argument as you did to ssaupd() The array must not be touched between the two function calls!
ipntr	Provide the same argument as you did to ssaupd() The array must not be touched between the two function calls!
workd	Provide the same argument as you did to ssaupd() The array must not be touched between the two function calls!
workl	Single precision work array, length lwork. The array must not be touched between the two function calls!
lworkl	Provide the same argument as you did to ssaupd()
info	Provide the same argument as you did to ssaupd()