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37 #ifndef GMX_LINEARALGEBRA_SPARSEMATRIX_H
38 #define GMX_LINEARALGEBRA_SPARSEMATRIX_H
42 #include "../utility/basedefinitions.h"
43 #include "../utility/real.h"
50 gmx_sparsematrix_entry
54 } gmx_sparsematrix_entry_t;
56 /*! \brief Sparse matrix storage format
58 * This structure specifies a storage format for a sparse matrix.
59 * The memory requirements are only proportional to the number
60 * of nonzero elements, and it provides a reasonably fast way to
61 * perform matrix-vector multiplications.
63 * The data format is very similar to a neighborlist. It is optimized
64 * for fast access, but it is difficult to add entries. If you are
65 * constructing a matrix you should either do it in exactly the order
66 * specified here, or use some other more flexible intermediate structure.
68 * The index array is of size nrow+1. All non-zero matrix elements
69 * on row i are stored in positions index[i] through index[i+1]-1 in
70 * the arrays column and value. The column array contains the column
71 * index for each entry, in ascending order, and the corresponding
72 * position in the value array contains the floating point matrix element.
74 * index[nrow] should be equal to the total number of elements stored.
76 * Thus, to find the value of matrix element [5,4] you should loop
77 * over positions index[5] to index[6]-1 in column until you either find
78 * the value 4, or a higher value (meaning the element was zero).
80 * It is fairly easy to construct the matrix on-the-fly if you can do
84 * If compressed_symmetric is set to TRUE, you should only store EITHER the upper OR
85 * lower triangle (and the diagonal), and the other half is assumed to be
86 * symmetric. Otherwise, if compressed_symmetric==FALSE, no symmetry is implied and all
87 * elements should be stored.
89 * The symmetry compression saves us a factor 2 both in storage and
90 * matrix multiplication CPU-time, which can be very useful for huge eigenproblems.
92 * If you are unsure, just set compressed_symmetric to FALSE and list all elements. If
93 * you enable it but still list all elements (both upper and lower triangle) you will be sorry...
95 * Internally, the sparse data is stored as a separate list for each row, where the list
96 * element is a structure with a column and (floating-point) data value. This makes it
97 * possible, although not completely transparent, to update values in random access order.
98 * The drawback is that the structure will allocate nrow memory regions.
99 * The matrix data could be stored in a single contiguous array with indices for each row,
100 * but then we could only insert elements at the end without copying the entire matrix.
104 * In other words: Not perfect, but it works.
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 */
118 /*! \brief Allocate a new sparse matrix structure
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.
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.
129 gmx_sparsematrix_init (int nrow);
132 /*! \brief Release all resources used by a sparse matrix structure
134 * All arrays in the structure will be freed, and the structure itself.
137 gmx_sparsematrix_destroy (gmx_sparsematrix_t * A);
140 /*! \brief Print sparse matrix to a stream.
142 * Mainly used for debugging. Be warned that the real sparse matrices used
143 * in Gromacs runs can be HUGE (think 100,000 rows).
146 gmx_sparsematrix_print (FILE * stream,
147 gmx_sparsematrix_t * A);
149 /* Adds value at row,col. If the value did not exist
150 * previously it is added, otherwise it is incremented with difference.
152 * The column sort order might change, so you need to run fix_sparsematrix
153 * once you are done changing the matrix.
156 gmx_sparsematrix_value (gmx_sparsematrix_t * A,
161 /* Adds value at row,col. If the value did not exist
162 * previously it is added, otherwise it is incremented with difference.
164 * The column sort order might change, so you need to run fix_sparsematrix
165 * once you are done changing the matrix.
168 gmx_sparsematrix_increment_value(gmx_sparsematrix_t * A,
175 /*! \brief Sort elements in each column and remove zeros.
177 * Sparse matrix access is faster when the elements are stored in
178 * increasing column order in each row. In some cases previously non-zero
179 * elements will be zero after adding more data, and this routine also removes
180 * those entries to reduce the storage requirements.
182 * It never hurts to run this routine if you have been updating the matrix...
185 gmx_sparsematrix_compress (gmx_sparsematrix_t * A);
189 /*! \brief Sparse matrix vector multiplication
191 * Calculate y = A * x for a sparse matrix A.
194 gmx_sparsematrix_vector_multiply(gmx_sparsematrix_t * A,