/*
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+ *
* This source code is part of
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+ *
* G R O M A C S
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+ *
* GROningen MAchine for Chemical Simulations
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+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
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* To help us fund GROMACS development, we humbly ask that you cite
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#include "statutil.h"
#include "futil.h"
-void read_eigenvectors(const char *file,int *natoms,gmx_bool *bFit,
- rvec **xref,gmx_bool *bDMR,
- rvec **xav,gmx_bool *bDMA,
- int *nvec, int **eignr,
- rvec ***eigvec,real **eigval)
+void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
+ rvec **xref, gmx_bool *bDMR,
+ rvec **xav, gmx_bool *bDMA,
+ int *nvec, int **eignr,
+ rvec ***eigvec, real **eigval)
{
- t_trnheader head;
- int i,snew_size;
- t_fileio *status;
- rvec *x;
- matrix box;
- gmx_bool bOK;
-
- *bDMR=FALSE;
-
- /* read (reference (t=-1) and) average (t=0) structure */
- status=open_trn(file,"r");
- fread_trnheader(status,&head,&bOK);
- *natoms=head.natoms;
- snew(*xav,*natoms);
- fread_htrn(status,&head,box,*xav,NULL,NULL);
-
- if ((head.t>=-1.1) && (head.t<=-0.9))
- {
- snew(*xref,*natoms);
- for(i=0; i<*natoms; i++)
- copy_rvec((*xav)[i],(*xref)[i]);
- *bDMR = (head.lambda > 0.5);
- *bFit = (head.lambda > -0.5);
- if (*bFit)
- {
- fprintf(stderr,"Read %smass weighted reference structure with %d atoms from %s\n", *bDMR ? "" : "non ",*natoms,file);
- }
- else
- {
- fprintf(stderr,"Eigenvectors in %s were determined without fitting\n",file);
- sfree(*xref);
- *xref=NULL;
- }
- fread_trnheader(status,&head,&bOK);
- fread_htrn(status,&head,box,*xav,NULL,NULL);
- }
- else
- {
- *bFit=TRUE;
- *xref=NULL;
- }
- *bDMA = (head.lambda > 0.5);
- if ((head.t<=-0.01) || (head.t>=0.01))
- {
- fprintf(stderr,"WARNING: %s does not start with t=0, which should be the "
- "average structure. This might not be a eigenvector file. "
- "Some things might go wrong.\n",
- file);
- }
- else
- {
- fprintf(stderr,
- "Read %smass weighted average/minimum structure with %d atoms from %s\n",
- *bDMA ? "" : "non ",*natoms,file);
- }
-
- snew(x,*natoms);
- snew_size=10;
- snew(*eignr,snew_size);
- snew(*eigval,snew_size);
- snew(*eigvec,snew_size);
-
- *nvec=0;
- while (fread_trnheader(status,&head,&bOK))
- {
- fread_htrn(status,&head,box,x,NULL,NULL);
- if (*nvec >= snew_size)
- {
- snew_size+=10;
- srenew(*eignr,snew_size);
- srenew(*eigval,snew_size);
- srenew(*eigvec,snew_size);
- }
- i=head.step;
- (*eigval)[*nvec]=head.t;
- (*eignr)[*nvec]=i-1;
- snew((*eigvec)[*nvec],*natoms);
- for(i=0; i<*natoms; i++)
- {
- copy_rvec(x[i],(*eigvec)[*nvec][i]);
- }
- (*nvec)++;
- }
- sfree(x);
- fprintf(stderr,"Read %d eigenvectors (for %d atoms)\n\n",*nvec,*natoms);
+ t_trnheader head;
+ int i, snew_size;
+ t_fileio *status;
+ rvec *x;
+ matrix box;
+ gmx_bool bOK;
+
+ *bDMR = FALSE;
+
+ /* read (reference (t=-1) and) average (t=0) structure */
+ status = open_trn(file, "r");
+ fread_trnheader(status, &head, &bOK);
+ *natoms = head.natoms;
+ snew(*xav, *natoms);
+ fread_htrn(status, &head, box, *xav, NULL, NULL);
+
+ if ((head.t >= -1.1) && (head.t <= -0.9))
+ {
+ snew(*xref, *natoms);
+ for (i = 0; i < *natoms; i++)
+ {
+ copy_rvec((*xav)[i], (*xref)[i]);
+ }
+ *bDMR = (head.lambda > 0.5);
+ *bFit = (head.lambda > -0.5);
+ if (*bFit)
+ {
+ fprintf(stderr, "Read %smass weighted reference structure with %d atoms from %s\n", *bDMR ? "" : "non ", *natoms, file);
+ }
+ else
+ {
+ fprintf(stderr, "Eigenvectors in %s were determined without fitting\n", file);
+ sfree(*xref);
+ *xref = NULL;
+ }
+ fread_trnheader(status, &head, &bOK);
+ fread_htrn(status, &head, box, *xav, NULL, NULL);
+ }
+ else
+ {
+ *bFit = TRUE;
+ *xref = NULL;
+ }
+ *bDMA = (head.lambda > 0.5);
+ if ((head.t <= -0.01) || (head.t >= 0.01))
+ {
+ fprintf(stderr, "WARNING: %s does not start with t=0, which should be the "
+ "average structure. This might not be a eigenvector file. "
+ "Some things might go wrong.\n",
+ file);
+ }
+ else
+ {
+ fprintf(stderr,
+ "Read %smass weighted average/minimum structure with %d atoms from %s\n",
+ *bDMA ? "" : "non ", *natoms, file);
+ }
+
+ snew(x, *natoms);
+ snew_size = 10;
+ snew(*eignr, snew_size);
+ snew(*eigval, snew_size);
+ snew(*eigvec, snew_size);
+
+ *nvec = 0;
+ while (fread_trnheader(status, &head, &bOK))
+ {
+ fread_htrn(status, &head, box, x, NULL, NULL);
+ if (*nvec >= snew_size)
+ {
+ snew_size += 10;
+ srenew(*eignr, snew_size);
+ srenew(*eigval, snew_size);
+ srenew(*eigvec, snew_size);
+ }
+ i = head.step;
+ (*eigval)[*nvec] = head.t;
+ (*eignr)[*nvec] = i-1;
+ snew((*eigvec)[*nvec], *natoms);
+ for (i = 0; i < *natoms; i++)
+ {
+ copy_rvec(x[i], (*eigvec)[*nvec][i]);
+ }
+ (*nvec)++;
+ }
+ sfree(x);
+ fprintf(stderr, "Read %d eigenvectors (for %d atoms)\n\n", *nvec, *natoms);
}
-void write_eigenvectors(const char *trnname,int natoms,real mat[],
- gmx_bool bReverse,int begin,int end,
- int WriteXref,rvec *xref,gmx_bool bDMR,
- rvec xav[], gmx_bool bDMA,real eigval[])
+void write_eigenvectors(const char *trnname, int natoms, real mat[],
+ gmx_bool bReverse, int begin, int end,
+ int WriteXref, rvec *xref, gmx_bool bDMR,
+ rvec xav[], gmx_bool bDMA, real eigval[])
{
t_fileio *trnout;
- int ndim,i,j,d,vec;
- matrix zerobox;
- rvec *x;
-
+ int ndim, i, j, d, vec;
+ matrix zerobox;
+ rvec *x;
+
ndim = natoms*DIM;
clear_mat(zerobox);
- snew(x,natoms);
-
+ snew(x, natoms);
+
fprintf (stderr,
"\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
- (WriteXref==eWXR_YES) ? "reference, " : "",
- begin,end,trnname);
-
- trnout = open_tpx(trnname,"w");
+ (WriteXref == eWXR_YES) ? "reference, " : "",
+ begin, end, trnname);
+
+ trnout = open_tpx(trnname, "w");
if (WriteXref == eWXR_YES)
{
- /* misuse lambda: 0/1 mass weighted fit no/yes */
- fwrite_trn(trnout,-1,-1,bDMR ? 1.0 : 0.0,zerobox,natoms,xref,NULL,NULL);
+ /* misuse lambda: 0/1 mass weighted fit no/yes */
+ fwrite_trn(trnout, -1, -1, bDMR ? 1.0 : 0.0, zerobox, natoms, xref, NULL, NULL);
}
else if (WriteXref == eWXR_NOFIT)
{
- /* misuse lambda: -1 no fit */
- fwrite_trn(trnout,-1,-1,-1.0,zerobox,natoms,x,NULL,NULL);
+ /* misuse lambda: -1 no fit */
+ fwrite_trn(trnout, -1, -1, -1.0, zerobox, natoms, x, NULL, NULL);
}
-
- /* misuse lambda: 0/1 mass weighted analysis no/yes */
- fwrite_trn(trnout,0,0,bDMA ? 1.0 : 0.0,zerobox,natoms,xav,NULL,NULL);
- for(i=0; i<=(end-begin); i++)
+ /* misuse lambda: 0/1 mass weighted analysis no/yes */
+ fwrite_trn(trnout, 0, 0, bDMA ? 1.0 : 0.0, zerobox, natoms, xav, NULL, NULL);
+
+ for (i = 0; i <= (end-begin); i++)
{
-
+
if (!bReverse)
+ {
vec = i;
+ }
else
+ {
vec = ndim-i-1;
-
- for (j=0; j<natoms; j++)
- for(d=0; d<DIM; d++)
- x[j][d]=mat[vec*ndim+DIM*j+d];
-
+ }
+
+ for (j = 0; j < natoms; j++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ x[j][d] = mat[vec*ndim+DIM*j+d];
+ }
+ }
+
/* Store the eigenvalue in the time field */
- fwrite_trn(trnout,begin+i,eigval[vec],0,zerobox,natoms,x,NULL,NULL);
+ fwrite_trn(trnout, begin+i, eigval[vec], 0, zerobox, natoms, x, NULL, NULL);
}
close_trn(trnout);
-
+
sfree(x);
}
-
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff