src/gromacs/fileio/mtxio.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "mtxio.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/gmxfio_xdr.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 /* Matrix file format definition:
  61  *
  62  * All entries are stored in XDR format.
  63  *
  64  * 1. Magic number integer, should be GMX_MTXIO_MAGIC_NUMBER
  65  * 2. An XDR string specifying the Gromacs version used to generate the file.
  66  * 3. Integer to denote precision. 1 if double, 0 if single precision.
  67  * 4. Two integers specifying number of rows and columns.
  68  * 5. Integer to denote storage type:
  69  *    GMX_MTXIO_FULL_MATRIX or GMX_MTXIO_SPARSE_MATRIX
  70  *
  71  * 6. Matrix data.
  72  *    a) In case of full matrix, this is nrow*ncol floating-point values.
  73  *    b) In case of sparse matrix the data is:
  74  *       - Integer specifying compressed_symmetric format (1=yes, 0=no)
  75  *       - Integer specifying number of rows (again)
  76  *       - nrow integers specifying the number of data entries on each row ("ndata")
  77  *       - All the actual entries for each row, stored contiguous.
  78  *         Each entry consists of an integer column index and floating-point data value.
  79  */
  80
  81 void gmx_mtxio_write(const char* filename, int nrow, int ncol, real* full_matrix, gmx_sparsematrix_t* sparse_matrix)
  82 {
  83     t_fileio* fio;
  84     int       i, j, prec;
  85     size_t    sz;
  86
  87     if (full_matrix != nullptr && sparse_matrix != nullptr)
  88     {
  89         gmx_fatal(FARGS, "Both full AND sparse matrix specified to gmx_mtxio_write().\n");
  90     }
  91
  92     fio = gmx_fio_open(filename, "w");
  93
  94     /* Write magic number */
  95     i = GMX_MTXIO_MAGIC_NUMBER;
  96     gmx_fio_do_int(fio, i);
  97
  98     /* Write generating Gromacs version */
  99     gmx_fio_write_string(fio, gmx_version());
 100
 101     /* Write 1 for double, 0 for single precision */
 102     if (sizeof(real) == sizeof(double))
 103     {
 104         prec = 1;
 105     }
 106     else
 107     {
 108         prec = 0;
 109     }
 110     gmx_fio_do_int(fio, prec);
 111
 112     gmx_fio_do_int(fio, nrow);
 113     gmx_fio_do_int(fio, ncol);
 114
 115     if (full_matrix != nullptr)
 116     {
 117         /* Full matrix storage format */
 118         i = GMX_MTXIO_FULL_MATRIX;
 119         gmx_fio_do_int(fio, i);
 120         sz = nrow * ncol;
 121         gmx_fio_ndo_real(fio, full_matrix, sz);
 122     }
 123     else
 124     {
 125         /* Sparse storage */
 126         i = GMX_MTXIO_SPARSE_MATRIX;
 127         gmx_fio_do_int(fio, i);
 128
 129         gmx_fio_do_gmx_bool(fio, sparse_matrix->compressed_symmetric);
 130         gmx_fio_do_int(fio, sparse_matrix->nrow);
 131         if (sparse_matrix->nrow != nrow)
 132         {
 133             gmx_fatal(FARGS, "Internal inconsistency in sparse matrix.\n");
 134         }
 135         gmx_fio_ndo_int(fio, sparse_matrix->ndata, sparse_matrix->nrow);
 136         for (i = 0; i < sparse_matrix->nrow; i++)
 137         {
 138             for (j = 0; j < sparse_matrix->ndata[i]; j++)
 139             {
 140                 gmx_fio_do_int(fio, sparse_matrix->data[i][j].col);
 141                 gmx_fio_do_real(fio, sparse_matrix->data[i][j].value);
 142             }
 143         }
 144     }
 145     gmx_fio_close(fio);
 146 }
 147
 148
 149 void gmx_mtxio_read(const char* filename, int* nrow, int* ncol, real** full_matrix, gmx_sparsematrix_t** sparse_matrix)
 150 {
 151     t_fileio* fio;
 152     int       i, j, prec;
 153     char      gmxver[256];
 154     size_t    sz;
 155
 156     fio = gmx_fio_open(filename, "r");
 157
 158     /* Read and check magic number */
 159     i = GMX_MTXIO_MAGIC_NUMBER;
 160     gmx_fio_do_int(fio, i);
 161
 162     if (i != GMX_MTXIO_MAGIC_NUMBER)
 163     {
 164         gmx_fatal(FARGS,
 165                   "No matrix data found in file. Note that the Hessian matrix format changed\n"
 166                   "in GROMACS 3.3 to enable portable files and sparse matrix storage.\n");
 167     }
 168
 169     /* Read generating Gromacs version */
 170     gmx_fio_do_string(fio, gmxver);
 171
 172     /* Write 1 for double, 0 for single precision */
 173     if (sizeof(real) == sizeof(double))
 174     {
 175         prec = 1;
 176     }
 177     else
 178     {
 179         prec = 0;
 180     }
 181     gmx_fio_do_int(fio, prec);
 182
 183     fprintf(stderr, "Reading %s precision matrix generated by GROMACS %s\n",
 184             (prec == 1) ? "double" : "single", gmxver);
 185
 186     gmx_fio_do_int(fio, i);
 187     *nrow = i;
 188     gmx_fio_do_int(fio, i);
 189     *ncol = i;
 190
 191     gmx_fio_do_int(fio, i);
 192
 193     if (i == GMX_MTXIO_FULL_MATRIX && nullptr != full_matrix)
 194     {
 195         printf("Full matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
 196
 197         sz = (*nrow) * (*ncol);
 198         snew((*full_matrix), sz);
 199         gmx_fio_ndo_real(fio, (*full_matrix), sz);
 200     }
 201     else if (nullptr != sparse_matrix)
 202     {
 203         /* Sparse storage */
 204         printf("Sparse matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
 205
 206         snew((*sparse_matrix), 1);
 207         gmx_fio_do_gmx_bool(fio, (*sparse_matrix)->compressed_symmetric);
 208         gmx_fio_do_int(fio, (*sparse_matrix)->nrow);
 209         if ((*sparse_matrix)->nrow != *nrow)
 210         {
 211             gmx_fatal(FARGS, "Internal inconsistency in sparse matrix.\n");
 212         }
 213         snew((*sparse_matrix)->ndata, (*sparse_matrix)->nrow);
 214         snew((*sparse_matrix)->nalloc, (*sparse_matrix)->nrow);
 215         snew((*sparse_matrix)->data, (*sparse_matrix)->nrow);
 216         gmx_fio_ndo_int(fio, (*sparse_matrix)->ndata, (*sparse_matrix)->nrow);
 217
 218         for (i = 0; i < (*sparse_matrix)->nrow; i++)
 219         {
 220             (*sparse_matrix)->nalloc[i] = (*sparse_matrix)->ndata[i] + 10;
 221             snew(((*sparse_matrix)->data[i]), (*sparse_matrix)->nalloc[i]);
 222
 223             for (j = 0; j < (*sparse_matrix)->ndata[i]; j++)
 224             {
 225                 gmx_fio_do_int(fio, (*sparse_matrix)->data[i][j].col);
 226                 gmx_fio_do_real(fio, (*sparse_matrix)->data[i][j].value);
 227             }
 228         }
 229     }
 230     gmx_fio_close(fio);
 231 }