src/gromacs/fileio/mtxio.c

   1 /*
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  37 #include "mtxio.h"
  38
  39 #include "config.h"
  40
  41 /* This module provides routines to read/write sparse or full storage
  42  * matrices from/to files. It is normally used for the Hessian matrix
  43  * in normal mode analysis.
  44  */
  45
  46 #include "gromacs/fileio/gmxfio.h"
  47 #include "gromacs/fileio/xdrf.h"
  48 #include "gromacs/linearalgebra/sparsematrix.h"
  49 #include "gromacs/utility/baseversion.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/smalloc.h"
  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     gmx_bool    bDum  = TRUE;
  92     gmx_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, gmx_version());
 110
 111     /* Write 1 for double, 0 for single precision */
 112     if (sizeof(real) == sizeof(double))
 113     {
 114         prec = 1;
 115     }
 116     else
 117     {
 118         prec = 0;
 119     }
 120     gmx_fio_do_int(fio, prec);
 121
 122     gmx_fio_do_int(fio, nrow);
 123     gmx_fio_do_int(fio, ncol);
 124
 125     if (full_matrix != NULL)
 126     {
 127         /* Full matrix storage format */
 128         i = GMX_MTXIO_FULL_MATRIX;
 129         gmx_fio_do_int(fio, i);
 130         sz   = nrow*ncol;
 131         bDum = gmx_fio_ndo_real(fio, full_matrix, sz);
 132     }
 133     else
 134     {
 135         /* Sparse storage */
 136         i = GMX_MTXIO_SPARSE_MATRIX;
 137         gmx_fio_do_int(fio, i);
 138
 139         gmx_fio_do_gmx_bool(fio, sparse_matrix->compressed_symmetric);
 140         gmx_fio_do_int(fio, sparse_matrix->nrow);
 141         if (sparse_matrix->nrow != nrow)
 142         {
 143             gmx_fatal(FARGS, "Internal inconsistency in sparse matrix.\n");
 144         }
 145         bDum = gmx_fio_ndo_int(fio, sparse_matrix->ndata, sparse_matrix->nrow);
 146         for (i = 0; i < sparse_matrix->nrow; i++)
 147         {
 148             for (j = 0; j < sparse_matrix->ndata[i]; j++)
 149             {
 150                 gmx_fio_do_int(fio, sparse_matrix->data[i][j].col);
 151                 gmx_fio_do_real(fio, sparse_matrix->data[i][j].value);
 152             }
 153         }
 154     }
 155     gmx_fio_close(fio);
 156 }
 157
 158
 159 void
 160 gmx_mtxio_read (const char *            filename,
 161                 int *                   nrow,
 162                 int *                   ncol,
 163                 real **                 full_matrix,
 164                 gmx_sparsematrix_t **   sparse_matrix)
 165 {
 166     t_fileio   *fio;
 167     XDR     *   xd;
 168     int         i, j, prec;
 169     gmx_bool    bDum  = TRUE;
 170     gmx_bool    bRead = TRUE;
 171     char        gmxver[256];
 172     size_t      sz;
 173
 174     fio = gmx_fio_open(filename, "r");
 175     gmx_fio_checktype(fio);
 176     xd = gmx_fio_getxdr(fio);
 177
 178     /* Read and check magic number */
 179     i = GMX_MTXIO_MAGIC_NUMBER;
 180     gmx_fio_do_int(fio, i);
 181
 182     if (i != GMX_MTXIO_MAGIC_NUMBER)
 183     {
 184         gmx_fatal(FARGS,
 185                   "No matrix data found in file. Note that the Hessian matrix format changed\n"
 186                   "in Gromacs 3.3 to enable portable files and sparse matrix storage.\n");
 187     }
 188
 189     /* Read generating Gromacs version */
 190     gmx_fio_do_string(fio, gmxver);
 191
 192     /* Write 1 for double, 0 for single precision */
 193     if (sizeof(real) == sizeof(double))
 194     {
 195         prec = 1;
 196     }
 197     else
 198     {
 199         prec = 0;
 200     }
 201     gmx_fio_do_int(fio, prec);
 202
 203     fprintf(stderr, "Reading %s precision matrix generated by Gromacs %s\n",
 204             (prec == 1) ? "double" : "single", gmxver);
 205
 206     gmx_fio_do_int(fio, i);
 207     *nrow = i;
 208     gmx_fio_do_int(fio, i);
 209     *ncol = i;
 210
 211     gmx_fio_do_int(fio, i);
 212
 213     if (i == GMX_MTXIO_FULL_MATRIX && NULL != full_matrix)
 214     {
 215         printf("Full matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
 216
 217         sz = (*nrow) * (*ncol);
 218         snew((*full_matrix), sz);
 219         bDum = gmx_fio_ndo_real(fio, (*full_matrix), sz);
 220     }
 221     else if (NULL != sparse_matrix)
 222     {
 223         /* Sparse storage */
 224         printf("Sparse matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
 225
 226         snew((*sparse_matrix), 1);
 227         gmx_fio_do_gmx_bool(fio, (*sparse_matrix)->compressed_symmetric);
 228         gmx_fio_do_int(fio, (*sparse_matrix)->nrow);
 229         if ((*sparse_matrix)->nrow != *nrow)
 230         {
 231             gmx_fatal(FARGS, "Internal inconsistency in sparse matrix.\n");
 232         }
 233         snew((*sparse_matrix)->ndata, (*sparse_matrix)->nrow);
 234         snew((*sparse_matrix)->nalloc, (*sparse_matrix)->nrow);
 235         snew((*sparse_matrix)->data, (*sparse_matrix)->nrow);
 236         bDum = gmx_fio_ndo_int(fio, (*sparse_matrix)->ndata,
 237                                (*sparse_matrix)->nrow);
 238
 239         for (i = 0; i < (*sparse_matrix)->nrow; i++)
 240         {
 241             (*sparse_matrix)->nalloc[i] = (*sparse_matrix)->ndata[i] + 10;
 242             snew(((*sparse_matrix)->data[i]), (*sparse_matrix)->nalloc[i]);
 243
 244             for (j = 0; j < (*sparse_matrix)->ndata[i]; j++)
 245             {
 246                 gmx_fio_do_int(fio, (*sparse_matrix)->data[i][j].col);
 247                 gmx_fio_do_real(fio, (*sparse_matrix)->data[i][j].value);
 248             }
 249         }
 250     }
 251     gmx_fio_close(fio);
 252 }