/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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.
-
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- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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* of the License, or (at your option) any later version.
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+ * 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
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+ *
* 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.
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*/
+#include "gmxpre.h"
+
#include "sparsematrix.h"
#include <assert.h>
-#include <stdlib.h>
#include <stdio.h>
+#include <stdlib.h>
-#include "gromacs/legacyheaders/smalloc.h"
-
-
-
+#include "gromacs/utility/smalloc.h"
gmx_sparsematrix_t *
gmx_sparsematrix_init(int nrow)
{
- int i;
+ int i;
gmx_sparsematrix_t *A;
-
- snew(A,1);
-
- A->nrow=nrow;
- snew(A->ndata,nrow);
- snew(A->nalloc,nrow);
- snew(A->data,nrow);
-
- for(i=0;i<nrow;i++)
+
+ snew(A, 1);
+
+ A->nrow = nrow;
+ snew(A->ndata, nrow);
+ snew(A->nalloc, nrow);
+ snew(A->data, nrow);
+
+ for (i = 0; i < nrow; i++)
{
A->ndata[i] = 0;
A->nalloc[i] = 0;
A->data[i] = NULL;
}
- return A;
+ return A;
}
gmx_sparsematrix_destroy(gmx_sparsematrix_t * A)
{
int i;
-
+
/* Release each row */
- for(i=0;i<A->nrow;i++)
+ for (i = 0; i < A->nrow; i++)
{
- if(A->data[i]!=NULL)
+ if (A->data[i] != NULL)
+ {
sfree(A->data[i]);
+ }
}
/* Release the rowdata arrays */
sfree(A->ndata);
sfree(A->nalloc);
sfree(A->data);
/* Release matrix structure itself */
- sfree(A);
+ sfree(A);
}
gmx_sparsematrix_print(FILE * stream,
gmx_sparsematrix_t * A)
{
- int i,j,k;
-
- for(i=0;i<A->nrow;i++)
+ int i, j, k;
+
+ for (i = 0; i < A->nrow; i++)
{
- if(A->ndata[i]==0)
+ if (A->ndata[i] == 0)
{
- for(j=0;j<A->nrow;j++)
- fprintf(stream," %6.3f",0.0);
+ for (j = 0; j < A->nrow; j++)
+ {
+ fprintf(stream, " %6.3f", 0.0);
+ }
}
else
{
- k=0;
- j=0;
- for(j=0;j<A->ndata[i];j++)
+ k = 0;
+ j = 0;
+ for (j = 0; j < A->ndata[i]; j++)
{
- while(k++<A->data[i][j].col)
- fprintf(stream," %6.3f",0.0);
- fprintf(stream," %6.3f",A->data[i][j].value);
+ while (k++ < A->data[i][j].col)
+ {
+ fprintf(stream, " %6.3f", 0.0);
+ }
+ fprintf(stream, " %6.3f", A->data[i][j].value);
+ }
+ while (k++ < A->nrow)
+ {
+ fprintf(stream, " %6.3f", 0.0);
}
- while(k++<A->nrow)
- fprintf(stream," %6.3f",0.0);
}
- fprintf(stream,"\n");
+ fprintf(stream, "\n");
}
-
+
}
real
gmx_sparsematrix_value(gmx_sparsematrix_t * A,
- int row,
+ int row,
int col)
{
gmx_bool found = FALSE;
- int i;
- real value;
-
- assert(row<A->nrow);
+ int i;
+ real value;
+
+ assert(row < A->nrow);
value = 0;
-
+
/* Find previous value */
- for(i=0;i<A->ndata[row] && (found==FALSE);i++)
+ for (i = 0; i < A->ndata[row] && (found == FALSE); i++)
{
- if(A->data[row][i].col==col)
+ if (A->data[row][i].col == col)
{
found = TRUE;
value = A->data[row][i].value;
}
}
-
+
/* value=0 if we didn't find any match */
return value;
}
void
gmx_sparsematrix_increment_value(gmx_sparsematrix_t * A,
- int row,
+ int row,
int col,
real difference)
{
gmx_bool found = FALSE;
- int i;
-
- assert(row<A->nrow);
-
+ int i;
+
+ assert(row < A->nrow);
+
/* Try to find a previous entry with this row/col */
- for(i=0;i<A->ndata[row] && !found;i++)
+ for (i = 0; i < A->ndata[row] && !found; i++)
{
- if(A->data[row][i].col==col)
+ if (A->data[row][i].col == col)
{
- found = TRUE;
+ found = TRUE;
A->data[row][i].value += difference;
}
}
-
+
/* Add a new entry if nothing was found */
- if(!found)
+ if (!found)
{
/* add the value at the end of the row */
- if(A->ndata[row] == A->nalloc[row])
+ if (A->ndata[row] == A->nalloc[row])
{
A->nalloc[row] += 100;
- if(A->data[row]==NULL)
+ if (A->data[row] == NULL)
{
- snew(A->data[row],A->nalloc[row]);
+ snew(A->data[row], A->nalloc[row]);
}
else
{
- srenew(A->data[row],A->nalloc[row]);
+ srenew(A->data[row], A->nalloc[row]);
}
}
A->data[row][A->ndata[row]].col = col;
/* Previous value was 0.0 */
A->data[row][A->ndata[row]].value = difference;
A->ndata[row]++;
- }
+ }
}
{
int c1 = ((gmx_sparsematrix_entry_t *)v1)->col;
int c2 = ((gmx_sparsematrix_entry_t *)v2)->col;
-
- if(c1<c2)
+
+ if (c1 < c2)
+ {
return -1;
- else if(c1>c2)
+ }
+ else if (c1 > c2)
+ {
return 1;
- else
+ }
+ else
+ {
return 0;
+ }
}
void
gmx_sparsematrix_compress(gmx_sparsematrix_t * A)
{
- int i,j;
-
- for (i=0;i<A->nrow;i++)
- {
+ int i, j;
+
+ for (i = 0; i < A->nrow; i++)
+ {
/* Remove last value on this row while it is zero */
- while(A->ndata[i]>0 && A->data[i][A->ndata[i]-1].value==0)
+ while (A->ndata[i] > 0 && A->data[i][A->ndata[i]-1].value == 0)
+ {
A->ndata[i]--;
-
+ }
+
/* Go through values on this row and look for more zero elements */
- for(j=0;j<A->ndata[i];j++)
+ for (j = 0; j < A->ndata[i]; j++)
{
/* If this element was zero, exchange it with the last non-zero
* element on the row (yes, this will invalidate the sort order)
*/
- if(A->data[i][j].value==0)
+ if (A->data[i][j].value == 0)
{
A->data[i][j].value = A->data[i][A->ndata[i]-1].value;
A->data[i][j].col = A->data[i][A->ndata[i]-1].col;
A->ndata[i],
sizeof(gmx_sparsematrix_entry_t),
compare_columns);
- }
+ }
}
real * x,
real * y)
{
- real s,v,xi;
- int i,j,k;
+ real s, v, xi;
+ int i, j, k;
gmx_sparsematrix_entry_t * data; /* pointer to simplify data access */
-
- for (i = 0; i < A->nrow; i ++)
+
+ for (i = 0; i < A->nrow; i++)
+ {
y[i] = 0;
-
- if(A->compressed_symmetric)
+ }
+
+ if (A->compressed_symmetric)
{
- for (i = 0; i < A->nrow; i ++)
+ for (i = 0; i < A->nrow; i++)
{
- xi = x[i];
- s = 0.0;
+ xi = x[i];
+ s = 0.0;
data = A->data[i];
-
- for (k=0;k<A->ndata[i];k++)
+
+ for (k = 0; k < A->ndata[i]; k++)
{
- j = data[k].col;
- v = data[k].value;
+ j = data[k].col;
+ v = data[k].value;
s += v * x[j];
- if(i!=j)
- y[j] += v * xi;
+ if (i != j)
+ {
+ y[j] += v * xi;
+ }
}
- y[i] += s;
- }
+ y[i] += s;
+ }
}
else
{
/* not compressed symmetric storage */
- for (i = 0; i < A->nrow; i ++)
+ for (i = 0; i < A->nrow; i++)
{
- xi = x[i];
- s = 0.0;
+ xi = x[i];
+ s = 0.0;
data = A->data[i];
-
- for (k=0;k<A->ndata[i];k++)
+
+ for (k = 0; k < A->ndata[i]; k++)
{
- j = data[k].col;
- v = data[k].value;
+ j = data[k].col;
+ v = data[k].value;
s += v * x[j];
}
- y[i] += s;
- }
+ y[i] += s;
+ }
}
}
-
-
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff