src/gmxlib/mtxio.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
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  15  * This program is free software; you can redistribute it and/or
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 /* This module provides routines to read/write sparse or full storage
  40  * matrices from/to files. It is normally used for the Hessian matrix
  41  * in normal mode analysis.
  42  */
  43
  44 #include "xdrf.h"
  45 #include "smalloc.h"
  46 #include "gmxfio.h"
  47 #include "copyrite.h"
  48 #include "gmx_fatal.h"
  49 #include "mtxio.h"
  50 #include "gmxfio.h"
  51
  52
  53 /* Just a number to identify our file type */
  54 #define GMX_MTXIO_MAGIC_NUMBER  0x34ce8fd2
  55
  56 #define GMX_MTXIO_FULL_MATRIX     0
  57 #define GMX_MTXIO_SPARSE_MATRIX   1
  58
  59
  60
  61 /* Matrix file format definition:
  62  *
  63  * All entries are stored in XDR format.
  64  *
  65  * 1. Magic number integer, should be GMX_MTXIO_MAGIC_NUMBER
  66  * 2. An XDR string specifying the Gromacs version used to generate the file.
  67  * 3. Integer to denote precision. 1 if double, 0 if single precision.
  68  * 4. Two integers specifying number of rows and columns.
  69  * 5. Integer to denote storage type:
  70 *    GMX_MTXIO_FULL_MATRIX or GMX_MTXIO_SPARSE_MATRIX
  71  *
  72  * 6. Matrix data.
  73  *    a) In case of full matrix, this is nrow*ncol floating-point values.
  74  *    b) In case of sparse matrix the data is:
  75  *       - Integer specifying compressed_symmetric format (1=yes, 0=no)
  76  *       - Integer specifying number of rows (again)
  77  *       - nrow integers specifying the number of data entries on each row ("ndata")
  78  *       - All the actual entries for each row, stored contiguous.
  79  *         Each entry consists of an integer column index and floating-point data value.
  80  */
  81
  82 void gmx_mtxio_write(const char *             filename,
  83                      int                      nrow,
  84                      int                      ncol,
  85                      real *                   full_matrix,
  86                      gmx_sparsematrix_t *     sparse_matrix)
  87 {
  88     t_fileio *fio;
  89     XDR *   xd;
  90     int     i,j,prec;
  91     bool    bDum = TRUE;
  92     bool    bRead = FALSE;
  93     size_t  sz;
  94
  95     if(full_matrix!=NULL && sparse_matrix!=NULL)
  96     {
  97         gmx_fatal(FARGS,"Both full AND sparse matrix specified to gmx_mtxio_write().\n");
  98     }
  99
 100     fio = gmx_fio_open(filename,"w");
 101     gmx_fio_checktype(fio);
 102     xd = gmx_fio_getxdr(fio);
 103
 104     /* Write magic number */
 105     i = GMX_MTXIO_MAGIC_NUMBER;
 106     gmx_fio_do_int(fio, i);
 107
 108     /* Write generating Gromacs version */
 109     gmx_fio_write_string(fio, GromacsVersion());
 110
 111     /* Write 1 for double, 0 for single precision */
 112     if(sizeof(real)==sizeof(double))
 113         prec = 1;
 114     else
 115         prec = 0;
 116     gmx_fio_do_int(fio, prec);
 117
 118     gmx_fio_do_int(fio, nrow);
 119     gmx_fio_do_int(fio, ncol);
 120
 121     if(full_matrix!=NULL)
 122     {
 123         /* Full matrix storage format */
 124         i = GMX_MTXIO_FULL_MATRIX;
 125         gmx_fio_do_int(fio, i);
 126         sz = nrow*ncol;
 127         bDum=gmx_fio_ndo_real(fio, full_matrix,sz);
 128     }
 129     else
 130     {
 131         /* Sparse storage */
 132         i = GMX_MTXIO_SPARSE_MATRIX;
 133         gmx_fio_do_int(fio, i);
 134
 135         gmx_fio_do_bool(fio, sparse_matrix->compressed_symmetric);
 136         gmx_fio_do_int(fio, sparse_matrix->nrow);
 137         if(sparse_matrix->nrow != nrow)
 138         {
 139             gmx_fatal(FARGS,"Internal inconsistency in sparse matrix.\n");
 140         }
 141         bDum=gmx_fio_ndo_int(fio, sparse_matrix->ndata,sparse_matrix->nrow);
 142         for(i=0;i<sparse_matrix->nrow;i++)
 143         {
 144             for(j=0;j<sparse_matrix->ndata[i];j++)
 145             {
 146                 gmx_fio_do_int(fio, sparse_matrix->data[i][j].col);
 147                 gmx_fio_do_real(fio, sparse_matrix->data[i][j].value);
 148             }
 149         }
 150     }
 151     gmx_fio_close(fio);
 152 }
 153
 154
 155 void
 156 gmx_mtxio_read (const char *            filename,
 157                 int *                   nrow,
 158                 int *                   ncol,
 159                 real **                 full_matrix,
 160                 gmx_sparsematrix_t **   sparse_matrix)
 161 {
 162     t_fileio  *fio;
 163     XDR *   xd;
 164     int     i,j,prec;
 165     bool    bDum = TRUE;
 166     bool    bRead = TRUE;
 167     char    gmxver[256];
 168     size_t  sz;
 169
 170     fio = gmx_fio_open(filename,"r");
 171     gmx_fio_checktype(fio);
 172     xd = gmx_fio_getxdr(fio);
 173
 174     /* Read and check magic number */
 175     i = GMX_MTXIO_MAGIC_NUMBER;
 176     gmx_fio_do_int(fio, i);
 177
 178     if(i!=GMX_MTXIO_MAGIC_NUMBER)
 179     {
 180         gmx_fatal(FARGS,
 181                   "No matrix data found in file. Note that the Hessian matrix format changed\n"
 182                   "in Gromacs 3.3 to enable portable files and sparse matrix storage.\n");
 183     }
 184
 185     /* Read generating Gromacs version */
 186     gmx_fio_do_string(fio, gmxver);
 187
 188     /* Write 1 for double, 0 for single precision */
 189     if(sizeof(real)==sizeof(double))
 190         prec = 1;
 191     else
 192         prec = 0;
 193     gmx_fio_do_int(fio, prec);
 194
 195     fprintf(stderr,"Reading %s precision matrix generated by Gromacs %s\n",
 196             (prec == 1) ? "double" : "single",gmxver);
 197
 198     gmx_fio_do_int(fio, i);
 199     *nrow=i;
 200     gmx_fio_do_int(fio, i);
 201     *ncol=i;
 202
 203     gmx_fio_do_int(fio, i);
 204
 205     if(i==GMX_MTXIO_FULL_MATRIX)
 206     {
 207         printf("Full matrix storage format, nrow=%d, ncols=%d\n",*nrow,*ncol);
 208
 209         sz = (*nrow) * (*ncol);
 210         snew((*full_matrix),sz);
 211         bDum=gmx_fio_ndo_real(fio, (*full_matrix),sz);
 212     }
 213     else
 214     {
 215         /* Sparse storage */
 216         printf("Sparse matrix storage format, nrow=%d, ncols=%d\n",*nrow,*ncol);
 217
 218         snew((*sparse_matrix),1);
 219         gmx_fio_do_bool(fio, (*sparse_matrix)->compressed_symmetric);
 220         gmx_fio_do_int(fio, (*sparse_matrix)->nrow);
 221         if((*sparse_matrix)->nrow != *nrow)
 222         {
 223             gmx_fatal(FARGS,"Internal inconsistency in sparse matrix.\n");
 224         }
 225         snew((*sparse_matrix)->ndata,(*sparse_matrix)->nrow);
 226         snew((*sparse_matrix)->nalloc,(*sparse_matrix)->nrow);
 227         snew((*sparse_matrix)->data,(*sparse_matrix)->nrow);
 228         bDum=gmx_fio_ndo_int(fio, (*sparse_matrix)->ndata,
 229                              (*sparse_matrix)->nrow);
 230
 231         for(i=0;i<(*sparse_matrix)->nrow;i++)
 232         {
 233             (*sparse_matrix)->nalloc[i] = (*sparse_matrix)->ndata[i] + 10;
 234             snew(((*sparse_matrix)->data[i]),(*sparse_matrix)->nalloc[i]);
 235
 236             for(j=0;j<(*sparse_matrix)->ndata[i];j++)
 237             {
 238                 gmx_fio_do_int(fio, (*sparse_matrix)->data[i][j].col);
 239                 gmx_fio_do_real(fio, (*sparse_matrix)->data[i][j].value);
 240             }
 241         }
 242     }
 243     gmx_fio_close(fio);
 244 }
 245
 246
 247