src/tools/eigio.c

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
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  17  * If you want to redistribute modifications, please consider that
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  31  */
  32 static char *SRCID_eigio_c = "$Id$";
  33 #include "smalloc.h"
  34 #include "vec.h"
  35 #include "eigio.h"
  36 #include "trnio.h"
  37 #include "tpxio.h"
  38
  39 void read_eigenvectors(char *file,int *natoms,bool *bFit,
  40                        rvec **xref,bool *bDMR,
  41                        rvec **xav,bool *bDMA,
  42                        int *nvec, int **eignr, rvec ***eigvec)
  43 {
  44   t_trnheader head;
  45   int    status,i,snew_size;
  46   rvec   *x;
  47   matrix box;
  48   bool   bOK;
  49
  50   *bDMR=FALSE;
  51
  52   /* read (reference (t=-1) and) average (t=0) structure */
  53   status=open_trn(file,"r");
  54   fread_trnheader(status,&head,&bOK);
  55   *natoms=head.natoms;
  56   snew(*xav,*natoms);
  57   fread_htrn(status,&head,box,*xav,NULL,NULL);
  58   if ((head.t>=-1.1) && (head.t<=-0.9)) {
  59     snew(*xref,*natoms);
  60     for(i=0; i<*natoms; i++)
  61       copy_rvec((*xav)[i],(*xref)[i]);
  62     *bDMR = (head.lambda > 0.5);
  63     *bFit = (head.lambda > -0.5);
  64     if (*bFit)
  65       fprintf(stderr,"Read %smass weighted reference structure with %d atoms from %s\n", *bDMR ? "" : "non ",*natoms,file);
  66     else {
  67        fprintf(stderr,"Eigenvectors in %s were determined without fitting\n",
  68                file);
  69        sfree(*xref);
  70        *xref=NULL;
  71     }
  72     fread_trnheader(status,&head,&bOK);
  73     fread_htrn(status,&head,box,*xav,NULL,NULL);
  74   }
  75   else {
  76     *bFit=TRUE;
  77     *xref=NULL;
  78   }
  79   *bDMA = (head.lambda > 0.5);
  80   if ((head.t<=-0.01) || (head.t>=0.01))
  81     fprintf(stderr,"WARNING: %s does not start with t=0, which should be the "
  82             "average structure. This might not be a eigenvector file. "
  83             "Some things might go wrong.\n",
  84             file);
  85   else
  86     fprintf(stderr,
  87             "Read %smass weighted average/minimum structure with %d atoms from %s\n",
  88             *bDMA ? "" : "non ",*natoms,file);
  89
  90   snew(x,*natoms);
  91   snew_size=0;
  92   *nvec=0;
  93   while (fread_trnheader(status,&head,&bOK)) {
  94     fread_htrn(status,&head,box,x,NULL,NULL);
  95     if (*nvec >= snew_size) {
  96       snew_size+=10;
  97       srenew(*eignr,snew_size);
  98       srenew(*eigvec,snew_size);
  99     }
 100     i=(int)(head.t+0.01);
 101     if ((head.t-i<=-0.01) || (head.t-i>=0.01))
 102       fatal_error(0,"%s contains a frame with non-integer time (%f), this "
 103                   "time should be an eigenvector index. "
 104                   "This might not be a eigenvector file.",file,head.t);
 105     (*eignr)[*nvec]=i-1;
 106     snew((*eigvec)[*nvec],*natoms);
 107     for(i=0; i<*natoms; i++)
 108       copy_rvec(x[i],(*eigvec)[*nvec][i]);
 109     (*nvec)++;
 110   }
 111   sfree(x);
 112   fprintf(stderr,"Read %d eigenvectors (dim=%d)\n\n",*nvec,*natoms*DIM);
 113 }
 114
 115 void write_eigenvectors(char *trnname,int natoms,real mat[],
 116                         bool bReverse,int begin,int end,
 117                         int WriteXref,rvec *xref,bool bDMR,
 118                         rvec xav[],bool bDMA)
 119 {
 120   int    trnout;
 121   int    ndim,i,j,d,vec;
 122   matrix zerobox;
 123   rvec   *x;
 124
 125   ndim = natoms*DIM;
 126   clear_mat(zerobox);
 127   snew(x,natoms);
 128
 129   fprintf (stderr,
 130            "\nWriting %saverage structure\nand eigenvectors 1 to %d to %s\n",
 131            (WriteXref==eWXR_YES) ? "reference and " : "",
 132            end,trnname);
 133
 134   trnout = open_tpx(trnname,"w");
 135   if (WriteXref == eWXR_YES)
 136     /* misuse lambda: 0/1 mass weighted fit no/yes */
 137     fwrite_trn(trnout,-1,-1,bDMR ? 1.0 : 0.0,zerobox,natoms,xref,NULL,NULL);
 138   else if (WriteXref == eWXR_NOFIT)
 139     /* misuse lambda: -1 no fit */
 140     fwrite_trn(trnout,-1,-1,-1.0,zerobox,natoms,x,NULL,NULL);
 141
 142   /* misuse lambda: 0/1 mass weighted analysis no/yes */
 143   fwrite_trn(trnout,0,0,bDMA ? 1.0 : 0.0,zerobox,natoms,xav,NULL,NULL);
 144
 145   for(i=begin; i<=end; i++) {
 146     if (!bReverse)
 147       vec = i-1;
 148     else
 149       vec = ndim-i;
 150     for (j=0; j<natoms; j++)
 151       for(d=0; d<DIM; d++)
 152         x[j][d]=mat[vec*ndim+DIM*j+d];
 153     fwrite_trn(trnout,i,(real)i,0,zerobox,natoms,x,NULL,NULL);
 154   }
 155   close_trn(trnout);
 156
 157   sfree(x);
 158 }