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37 #ifndef GMX_LINEARALGEBRA_SPARSEMATRIX_H
38 #define GMX_LINEARALGEBRA_SPARSEMATRIX_H
42 #include "../legacyheaders/types/simple.h"
49 gmx_sparsematrix_entry
53 } gmx_sparsematrix_entry_t;
55 /*! \brief Sparse matrix storage format
57 * This structure specifies a storage format for a sparse matrix.
58 * The memory requirements are only proportional to the number
59 * of nonzero elements, and it provides a reasonably fast way to
60 * perform matrix-vector multiplications.
62 * The data format is very similar to a neighborlist. It is optimized
63 * for fast access, but it is difficult to add entries. If you are
64 * constructing a matrix you should either do it in exactly the order
65 * specified here, or use some other more flexible intermediate structure.
67 * The index array is of size nrow+1. All non-zero matrix elements
68 * on row i are stored in positions index[i] through index[i+1]-1 in
69 * the arrays column and value. The column array contains the column
70 * index for each entry, in ascending order, and the corresponding
71 * position in the value array contains the floating point matrix element.
73 * index[nrow] should be equal to the total number of elements stored.
75 * Thus, to find the value of matrix element [5,4] you should loop
76 * over positions index[5] to index[6]-1 in column until you either find
77 * the value 4, or a higher value (meaning the element was zero).
79 * It is fairly easy to construct the matrix on-the-fly if you can do
83 * If compressed_symmetric is set to TRUE, you should only store EITHER the upper OR
84 * lower triangle (and the diagonal), and the other half is assumed to be
85 * symmetric. Otherwise, if compressed_symmetric==FALSE, no symmetry is implied and all
86 * elements should be stored.
88 * The symmetry compression saves us a factor 2 both in storage and
89 * matrix multiplication CPU-time, which can be very useful for huge eigenproblems.
91 * If you are unsure, just set compressed_symmetric to FALSE and list all elements. If
92 * you enable it but still list all elements (both upper and lower triangle) you will be sorry...
94 * Internally, the sparse data is stored as a separate list for each row, where the list
95 * element is a structure with a column and (floating-point) data value. This makes it
96 * possible, although not completely transparent, to update values in random access order.
97 * The drawback is that the structure will allocate nrow memory regions.
98 * The matrix data could be stored in a single contiguous array with indices for each row,
99 * but then we could only insert elements at the end without copying the entire matrix.
103 * In other words: Not perfect, but it works.
108 gmx_bool compressed_symmetric; /**< Store half elements and assume symmetry. */
109 int nrow; /**< Number of rows in matrix */
110 int * ndata; /**< Number of entries on each row (list) */
111 int * nalloc; /**< Allocated entry list length for each row */
112 gmx_sparsematrix_entry_t ** data; /**< data[i] is a list with entries on row i */
117 /*! \brief Allocate a new sparse matrix structure
119 * The number of rows is used to allocate the index array entry. Obviously you
120 * can reallocate these later yourself if necessary - this is a
121 * convenience routine.
123 * By default, the compressed_symmetric flag in the structure will
124 * be FALSE. Set it to TRUE manually if you are only storing either the
125 * upper or lower half of the matrix.
128 gmx_sparsematrix_init (int nrow);
131 /*! \brief Release all resources used by a sparse matrix structure
133 * All arrays in the structure will be freed, and the structure itself.
136 gmx_sparsematrix_destroy (gmx_sparsematrix_t * A);
139 /*! \brief Print sparse matrix to a stream.
141 * Mainly used for debugging. Be warned that the real sparse matrices used
142 * in Gromacs runs can be HUGE (think 100,000 rows).
145 gmx_sparsematrix_print (FILE * stream,
146 gmx_sparsematrix_t * A);
148 /* Adds value at row,col. If the value did not exist
149 * previously it is added, otherwise it is incremented with difference.
151 * The column sort order might change, so you need to run fix_sparsematrix
152 * once you are done changing the matrix.
155 gmx_sparsematrix_value (gmx_sparsematrix_t * A,
160 /* Adds value at row,col. If the value did not exist
161 * previously it is added, otherwise it is incremented with difference.
163 * The column sort order might change, so you need to run fix_sparsematrix
164 * once you are done changing the matrix.
167 gmx_sparsematrix_increment_value(gmx_sparsematrix_t * A,
174 /*! \brief Sort elements in each column and remove zeros.
176 * Sparse matrix access is faster when the elements are stored in
177 * increasing column order in each row. In some cases previously non-zero
178 * elements will be zero after adding more data, and this routine also removes
179 * those entries to reduce the storage requirements.
181 * It never hurts to run this routine if you have been updating the matrix...
184 gmx_sparsematrix_compress (gmx_sparsematrix_t * A);
188 /*! \brief Sparse matrix vector multiplication
190 * Calculate y = A * x for a sparse matrix A.
193 gmx_sparsematrix_vector_multiply(gmx_sparsematrix_t * A,