include/sparsematrix.h

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  38 #ifndef _SPARSEMATRIX_H_
  39 #define _SPARSEMATRIX_H_
  40 #include "visibility.h"
  41 #include "typedefs.h"
  42 #include "types/simple.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 /*! \brief Sparse matrix storage format
  49  *
  50  *  This structure specifies a storage format for a sparse matrix.
  51  *  The memory requirements are only proportional to the number
  52  *  of nonzero elements, and it provides a reasonably fast way to
  53  *  perform matrix-vector multiplications.
  54  *
  55  *  The data format is very similar to a neighborlist. It is optimized
  56  *  for fast access, but it is difficult to add entries. If you are
  57  *  constructing a matrix you should either do it in exactly the order
  58  *  specified here, or use some other more flexible intermediate structure.
  59  *
  60  *  The index array is of size nrow+1. All non-zero matrix elements
  61  *  on row i are stored in positions index[i] through index[i+1]-1 in
  62  *  the arrays column and value. The column array contains the column
  63  *  index for each entry, in ascending order, and the corresponding
  64  *  position in the value array contains the floating point matrix element.
  65  *
  66  *  index[nrow] should be equal to the total number of elements stored.
  67  *
  68  *  Thus, to find the value of matrix element [5,4] you should loop
  69  *  over positions index[5] to index[6]-1 in column until you either find
  70  *  the value 4, or a higher value (meaning the element was zero).
  71  *
  72  *  It is fairly easy to construct the matrix on-the-fly if you can do
  73  *  it row-by-row.
  74  *
  75  *  IMPORTANT:
  76  *  If compressed_symmetric is set to TRUE, you should only store EITHER the upper OR
  77  *  lower triangle (and the diagonal), and the other half is assumed to be
  78  *  symmetric. Otherwise, if compressed_symmetric==FALSE, no symmetry is implied and all
  79  *  elements should be stored.
  80  *
  81  *  The symmetry compression saves us a factor 2 both in storage and
  82  *  matrix multiplication CPU-time, which can be very useful for huge eigenproblems.
  83  *
  84  *  If you are unsure, just set compressed_symmetric to FALSE and list all elements. If
  85  *  you enable it but still list all elements (both upper and lower triangle) you will be sorry...
  86  *
  87  *  Internally, the sparse data is stored as a separate list for each row, where the list
  88  *  element is a structure with a column and (floating-point) data value. This makes it
  89  *  possible, although not completely transparent, to update values in random access order.
  90  *  The drawback is that the structure will allocate nrow memory regions.
  91  *  The matrix data could be stored in a single contiguous array with indices for each row,
  92  *  but then we could only insert elements at the end without copying the entire matrix.
  93  *
  94  *  After you have
  95  *
  96  *  In other words: Not perfect, but it works.
  97  */
  98
  99 typedef struct
 100     gmx_sparsematrix_entry
 101 {
 102     int      col;
 103     real     value;
 104 } gmx_sparsematrix_entry_t;
 105
 106 typedef struct
 107     gmx_sparsematrix
 108 {
 109     gmx_bool                         compressed_symmetric; /*!< Store half elements and assume symmetry. */
 110     int                              nrow;                 /*!< Number of rows in matrix                 */
 111     int     *                        ndata;                /*!< Number of entries on each row (list)     */
 112     int     *                        nalloc;               /*!< Allocated entry list length for each row */
 113     gmx_sparsematrix_entry_t     **  data;                 /*!< data[i] is a list with entries on row i  */
 114 }
 115 gmx_sparsematrix_t;
 116
 117
 118 /*! \Allocate a new sparse matrix structure
 119  *
 120  *  The number of rows is used to allocate the index array entry. Obviously you
 121  *  can reallocate these later yourself if necessary - this is a
 122  *  convenience routine.
 123  *
 124  *  By default, the compressed_symmetric flag in the structure will
 125  *  be FALSE. Set it to TRUE manually if you are only storing either the
 126  *  upper or lower half of the matrix.
 127  */
 128 GMX_LIBGMX_EXPORT
 129 gmx_sparsematrix_t *
 130 gmx_sparsematrix_init            (int                    nrow);
 131
 132
 133 /*! \brief Release all resources used by a sparse matrix structure
 134  *
 135  *  All arrays in the structure will be freed, and the structure itself.
 136  */
 137 GMX_LIBGMX_EXPORT
 138 void
 139 gmx_sparsematrix_destroy         (gmx_sparsematrix_t *   A);
 140
 141
 142 /*! \brief Print sparse matrix to a stream.
 143  *
 144  *  Mainly used for debugging. Be warned that the real sparse matrices used
 145  *  in Gromacs runs can be HUGE (think 100,000 rows).
 146  */
 147 void
 148 gmx_sparsematrix_print           (FILE *                 stream,
 149                                   gmx_sparsematrix_t *   A);
 150
 151 /* Adds value at row,col. If the value did not exist
 152  * previously it is added, otherwise it is incremented with difference.
 153  *
 154  * The column sort order might change, so you need to run fix_sparsematrix
 155  * once you are done changing the matrix.
 156  */
 157 real
 158 gmx_sparsematrix_value          (gmx_sparsematrix_t *    A,
 159                                  int                     row,
 160                                  int                     col);
 161
 162
 163 /* Adds value at row,col. If the value did not exist
 164  * previously it is added, otherwise it is incremented with difference.
 165  *
 166  * The column sort order might change, so you need to run fix_sparsematrix
 167  * once you are done changing the matrix.
 168  */
 169 GMX_LIBGMX_EXPORT
 170 void
 171 gmx_sparsematrix_increment_value(gmx_sparsematrix_t *    A,
 172                                  int                     row,
 173                                  int                     col,
 174                                  real                    difference);
 175
 176
 177
 178 /*! \brief Sort elements in each column and remove zeros.
 179  *
 180  *  Sparse matrix access is faster when the elements are stored in
 181  *  increasing column order in each row. In some cases previously non-zero
 182  *  elements will be zero after adding more data, and this routine also removes
 183  *  those entries to reduce the storage requirements.
 184  *
 185  *  It never hurts to run this routine if you have been updating the matrix...
 186  */
 187 void
 188 gmx_sparsematrix_compress       (gmx_sparsematrix_t *    A);
 189
 190
 191
 192 /*! \brief Sparse matrix vector multiplication
 193  *
 194  * Calculate y = A * x for a sparse matrix A.
 195  */
 196 GMX_LIBGMX_EXPORT
 197 void
 198 gmx_sparsematrix_vector_multiply(gmx_sparsematrix_t *    A,
 199                                  real *                  x,
 200                                  real *                  y);
 201
 202 #ifdef __cplusplus
 203 }
 204 #endif
 205
 206
 207 #endif