/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team,
* check out http://www.gromacs.org for more information.
-
+
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
#endif
typedef struct
-gmx_sparsematrix_entry
+ gmx_sparsematrix_entry
{
int col;
real value;
*
* index[nrow] should be equal to the total number of elements stored.
*
- * Thus, to find the value of matrix element [5,4] you should loop
+ * Thus, to find the value of matrix element [5,4] you should loop
* over positions index[5] to index[6]-1 in column until you either find
* the value 4, or a higher value (meaning the element was zero).
*
*
* IMPORTANT:
* If compressed_symmetric is set to TRUE, you should only store EITHER the upper OR
- * lower triangle (and the diagonal), and the other half is assumed to be
- * symmetric. Otherwise, if compressed_symmetric==FALSE, no symmetry is implied and all
+ * lower triangle (and the diagonal), and the other half is assumed to be
+ * symmetric. Otherwise, if compressed_symmetric==FALSE, no symmetry is implied and all
* elements should be stored.
- *
+ *
* The symmetry compression saves us a factor 2 both in storage and
* matrix multiplication CPU-time, which can be very useful for huge eigenproblems.
*
- * If you are unsure, just set compressed_symmetric to FALSE and list all elements. If
+ * If you are unsure, just set compressed_symmetric to FALSE and list all elements. If
* you enable it but still list all elements (both upper and lower triangle) you will be sorry...
*
* Internally, the sparse data is stored as a separate list for each row, where the list
* The matrix data could be stored in a single contiguous array with indices for each row,
* but then we could only insert elements at the end without copying the entire matrix.
*
- * After you have
+ * After you have
*
* In other words: Not perfect, but it works.
- */
-typedef struct
-gmx_sparsematrix
+ */
+typedef struct
+ gmx_sparsematrix
{
gmx_bool compressed_symmetric; /**< Store half elements and assume symmetry. */
int nrow; /**< Number of rows in matrix */
int * ndata; /**< Number of entries on each row (list) */
int * nalloc; /**< Allocated entry list length for each row */
gmx_sparsematrix_entry_t ** data; /**< data[i] is a list with entries on row i */
-}
+}
gmx_sparsematrix_t;
/*! \brief Allocate a new sparse matrix structure
*
* The number of rows is used to allocate the index array entry. Obviously you
- * can reallocate these later yourself if necessary - this is a
+ * can reallocate these later yourself if necessary - this is a
* convenience routine.
*
* By default, the compressed_symmetric flag in the structure will
/*! \brief Release all resources used by a sparse matrix structure
*
- * All arrays in the structure will be freed, and the structure itself.
+ * All arrays in the structure will be freed, and the structure itself.
*/
void
gmx_sparsematrix_destroy (gmx_sparsematrix_t * A);
/* Adds value at row,col. If the value did not exist
* previously it is added, otherwise it is incremented with difference.
- *
+ *
* The column sort order might change, so you need to run fix_sparsematrix
* once you are done changing the matrix.
*/
real
gmx_sparsematrix_value (gmx_sparsematrix_t * A,
- int row,
+ int row,
int col);
/* Adds value at row,col. If the value did not exist
-* previously it is added, otherwise it is incremented with difference.
-*
-* The column sort order might change, so you need to run fix_sparsematrix
-* once you are done changing the matrix.
-*/
+ * previously it is added, otherwise it is incremented with difference.
+ *
+ * The column sort order might change, so you need to run fix_sparsematrix
+ * once you are done changing the matrix.
+ */
void
gmx_sparsematrix_increment_value(gmx_sparsematrix_t * A,
- int row,
+ int row,
int col,
real difference);
/*! \brief Sort elements in each column and remove zeros.
*
- * Sparse matrix access is faster when the elements are stored in
+ * Sparse matrix access is faster when the elements are stored in
* increasing column order in each row. In some cases previously non-zero
* elements will be zero after adding more data, and this routine also removes
* those entries to reduce the storage requirements.
-/*! \brief Sparse matrix vector multiplication
- *
- * Calculate y = A * x for a sparse matrix A.
+/*! \brief Sparse matrix vector multiplication
+ *
+ * Calculate y = A * x for a sparse matrix A.
*/
void
gmx_sparsematrix_vector_multiply(gmx_sparsematrix_t * A,
#endif
-
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff