/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * 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.
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- * 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
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
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+ * 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 http://www.gromacs.org.
*
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+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "cmat.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "matio.h"
-#include "futil.h"
+
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
t_mat *init_mat(int n1, gmx_bool b1D)
{
m->n1 = n1;
m->nn = 0;
m->b1D = b1D;
- m->emat = 0;
m->maxrms = 0;
m->minrms = 1e20;
m->sumrms = 0;
- m->nn = 0;
m->mat = mk_matrix(n1, n1, b1D);
snew(m->erow, n1);
return m;
}
+void copy_t_mat(t_mat *dst, t_mat *src)
+{
+ int i, j;
+
+ if (dst->nn != src->nn)
+ {
+ fprintf(stderr, "t_mat structures not identical in size dst %d src %d\n", dst->nn, src->nn);
+ return;
+ }
+ dst->maxrms = src->maxrms;
+ dst->minrms = src->minrms;
+ dst->sumrms = src->sumrms;
+ for (i = 0; (i < src->nn); i++)
+ {
+ for (j = 0; (j < src->nn); j++)
+ {
+ dst->mat[i][j] = src->mat[i][j];
+ }
+ dst->erow[i] = src->erow[i];
+ dst->m_ind[i] = src->m_ind[i];
+ }
+}
+
void enlarge_mat(t_mat *m, int deltan)
{
int i, j;
*m = NULL;
}
-real row_energy(int nn, int row, real *mat)
-{
- real re = 0;
- int i;
-
- for (i = 0; (i < nn); i++)
- {
- re += abs(i-row)*mat[i];
- }
- return re/nn;
-}
-
real mat_energy(t_mat *m)
{
- real re, retot;
- int j, jj;
+ int j;
+ real emat = 0;
- retot = 0;
- for (j = 0; (j < m->nn); j++)
+ for (j = 0; (j < m->nn-1); j++)
{
- jj = m->m_ind[j];
- re = row_energy(m->nn, jj, m->mat[j]);
- m->erow[j] = re;
- retot += re;
+ emat += sqr(m->mat[j][j+1]);
}
- m->emat = retot/m->nn;
- return m->emat;
+ return emat;
}
-void swap_rows(t_mat *m, int isw, int jsw)
+void swap_rows(t_mat *m, int iswap, int jswap)
{
real *tmp, ttt;
- int i;
+ int i, itmp;
+
+ /* Swap indices */
+ itmp = m->m_ind[iswap];
+ m->m_ind[iswap] = m->m_ind[jswap];
+ m->m_ind[jswap] = itmp;
+
+ /* Swap rows (since the matrix is an array of pointers) */
+ tmp = m->mat[iswap];
+ m->mat[iswap] = m->mat[jswap];
+ m->mat[jswap] = tmp;
- /* Swap rows */
- tmp = m->mat[isw];
- m->mat[isw] = m->mat[jsw];
- m->mat[jsw] = tmp;
/* Swap columns */
for (i = 0; (i < m->nn); i++)
{
- ttt = m->mat[isw][i];
- m->mat[isw][i] = m->mat[jsw][i];
- m->mat[jsw][i] = ttt;
+ ttt = m->mat[i][iswap];
+ m->mat[i][iswap] = m->mat[i][jswap];
+ m->mat[i][jswap] = ttt;
}
}
{
fprintf(fp, "%10g %10d\n", i/fac, histo[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
sfree(histo);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff