src/tools/eigio.c

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  36 #include "smalloc.h"
  37 #include "vec.h"
  38 #include "eigio.h"
  39 #include "trnio.h"
  40 #include "tpxio.h"
  41
  42 void read_eigenvectors(char *file,int *natoms,bool *bFit,
  43                        rvec **xref,bool *bDMR,
  44                        rvec **xav,bool *bDMA,
  45                        int *nvec, int **eignr, rvec ***eigvec)
  46 {
  47   t_trnheader head;
  48   int    status,i,snew_size;
  49   rvec   *x;
  50   matrix box;
  51   bool   bOK;
  52
  53   *bDMR=FALSE;
  54
  55   /* read (reference (t=-1) and) average (t=0) structure */
  56   status=open_trn(file,"r");
  57   fread_trnheader(status,&head,&bOK);
  58   *natoms=head.natoms;
  59   snew(*xav,*natoms);
  60   fread_htrn(status,&head,box,*xav,NULL,NULL);
  61   if ((head.t>=-1.1) && (head.t<=-0.9)) {
  62     snew(*xref,*natoms);
  63     for(i=0; i<*natoms; i++)
  64       copy_rvec((*xav)[i],(*xref)[i]);
  65     *bDMR = (head.lambda > 0.5);
  66     *bFit = (head.lambda > -0.5);
  67     if (*bFit)
  68       fprintf(stderr,"Read %smass weighted reference structure with %d atoms from %s\n", *bDMR ? "" : "non ",*natoms,file);
  69     else {
  70        fprintf(stderr,"Eigenvectors in %s were determined without fitting\n",
  71                file);
  72        sfree(*xref);
  73        *xref=NULL;
  74     }
  75     fread_trnheader(status,&head,&bOK);
  76     fread_htrn(status,&head,box,*xav,NULL,NULL);
  77   }
  78   else {
  79     *bFit=TRUE;
  80     *xref=NULL;
  81   }
  82   *bDMA = (head.lambda > 0.5);
  83   if ((head.t<=-0.01) || (head.t>=0.01))
  84     fprintf(stderr,"WARNING: %s does not start with t=0, which should be the "
  85             "average structure. This might not be a eigenvector file. "
  86             "Some things might go wrong.\n",
  87             file);
  88   else
  89     fprintf(stderr,
  90             "Read %smass weighted average/minimum structure with %d atoms from %s\n",
  91             *bDMA ? "" : "non ",*natoms,file);
  92
  93   snew(x,*natoms);
  94   snew_size=0;
  95   *nvec=0;
  96   while (fread_trnheader(status,&head,&bOK)) {
  97     fread_htrn(status,&head,box,x,NULL,NULL);
  98     if (*nvec >= snew_size) {
  99       snew_size+=10;
 100       srenew(*eignr,snew_size);
 101       srenew(*eigvec,snew_size);
 102     }
 103     i=(int)(head.t+0.01);
 104     if ((head.t-i<=-0.01) || (head.t-i>=0.01))
 105       fatal_error(0,"%s contains a frame with non-integer time (%f), this "
 106                   "time should be an eigenvector index. "
 107                   "This might not be a eigenvector file.",file,head.t);
 108     (*eignr)[*nvec]=i-1;
 109     snew((*eigvec)[*nvec],*natoms);
 110     for(i=0; i<*natoms; i++)
 111       copy_rvec(x[i],(*eigvec)[*nvec][i]);
 112     (*nvec)++;
 113   }
 114   sfree(x);
 115   fprintf(stderr,"Read %d eigenvectors (dim=%d)\n\n",*nvec,*natoms*DIM);
 116 }
 117
 118 void write_eigenvectors(char *trnname,int natoms,real mat[],
 119                         bool bReverse,int begin,int end,
 120                         int WriteXref,rvec *xref,bool bDMR,
 121                         rvec xav[],bool bDMA)
 122 {
 123   int    trnout;
 124   int    ndim,i,j,d,vec;
 125   matrix zerobox;
 126   rvec   *x;
 127
 128   ndim = natoms*DIM;
 129   clear_mat(zerobox);
 130   snew(x,natoms);
 131
 132   fprintf (stderr,
 133            "\nWriting %saverage structure\nand eigenvectors 1 to %d to %s\n",
 134            (WriteXref==eWXR_YES) ? "reference and " : "",
 135            end,trnname);
 136
 137   trnout = open_tpx(trnname,"w");
 138   if (WriteXref == eWXR_YES)
 139     /* misuse lambda: 0/1 mass weighted fit no/yes */
 140     fwrite_trn(trnout,-1,-1,bDMR ? 1.0 : 0.0,zerobox,natoms,xref,NULL,NULL);
 141   else if (WriteXref == eWXR_NOFIT)
 142     /* misuse lambda: -1 no fit */
 143     fwrite_trn(trnout,-1,-1,-1.0,zerobox,natoms,x,NULL,NULL);
 144
 145   /* misuse lambda: 0/1 mass weighted analysis no/yes */
 146   fwrite_trn(trnout,0,0,bDMA ? 1.0 : 0.0,zerobox,natoms,xav,NULL,NULL);
 147
 148   for(i=begin; i<=end; i++) {
 149     if (!bReverse)
 150       vec = i-1;
 151     else
 152       vec = ndim-i;
 153     for (j=0; j<natoms; j++)
 154       for(d=0; d<DIM; d++)
 155         x[j][d]=mat[vec*ndim+DIM*j+d];
 156     fwrite_trn(trnout,i,(real)i,0,zerobox,natoms,x,NULL,NULL);
 157   }
 158   close_trn(trnout);
 159
 160   sfree(x);
 161 }