/*
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*
- * This source code is part of
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* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include <ctype.h>
-#include "macros.h"
-#include "smalloc.h"
-#include "typedefs.h"
-#include "statutil.h"
-#include "tpxio.h"
-#include "string2.h"
-#include "vec.h"
-#include "macros.h"
-#include "index.h"
-#include "gmx_random.h"
-#include "pbc.h"
-#include "rmpbc.h"
-#include "xvgr.h"
-#include "futil.h"
-#include "matio.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/random/random.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/matio.h"
#include "cmat.h"
-#include "do_fit.h"
-#include "trnio.h"
-#include "viewit.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gmx_ana.h"
#include "gromacs/linearalgebra/eigensolver.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/utility/fatalerror.h"
/* print to two file pointers at once (i.e. stderr and log) */
-static inline
+static gmx_inline
void lo_ffprintf(FILE *fp1, FILE *fp2, const char *buf)
{
fprintf(fp1, "%s", buf);
}
/* just print a prepared buffer to fp1 and fp2 */
-static inline
+static gmx_inline
void ffprintf(FILE *fp1, FILE *fp2, const char *buf)
{
lo_ffprintf(fp1, fp2, buf);
}
/* prepare buffer with one argument, then print to fp1 and fp2 */
-static inline
+static gmx_inline
void ffprintf_d(FILE *fp1, FILE *fp2, char *buf, const char *fmt, int arg)
{
sprintf(buf, fmt, arg);
}
/* prepare buffer with one argument, then print to fp1 and fp2 */
-static inline
+static gmx_inline
void ffprintf_g(FILE *fp1, FILE *fp2, char *buf, const char *fmt, real arg)
{
sprintf(buf, fmt, arg);
}
/* prepare buffer with one argument, then print to fp1 and fp2 */
-static inline
+static gmx_inline
void ffprintf_s(FILE *fp1, FILE *fp2, char *buf, const char *fmt, const char *arg)
{
sprintf(buf, fmt, arg);
}
/* prepare buffer with two arguments, then print to fp1 and fp2 */
-static inline
+static gmx_inline
void ffprintf_dd(FILE *fp1, FILE *fp2, char *buf, const char *fmt, int arg1, int arg2)
{
sprintf(buf, fmt, arg1, arg2);
}
/* prepare buffer with two arguments, then print to fp1 and fp2 */
-static inline
+static gmx_inline
void ffprintf_gg(FILE *fp1, FILE *fp2, char *buf, const char *fmt, real arg1, real arg2)
{
sprintf(buf, fmt, arg1, arg2);
}
/* prepare buffer with two arguments, then print to fp1 and fp2 */
-static inline
+static gmx_inline
void ffprintf_ss(FILE *fp1, FILE *fp2, char *buf, const char *fmt, const char *arg1, const char *arg2)
{
sprintf(buf, fmt, arg1, arg2);
"max %d between two specific clusters\n", ntranst, maxtrans);
if (transfn)
{
- fp = ffopen(transfn, "w");
+ fp = gmx_ffopen(transfn, "w");
i = min(maxtrans+1, 80);
write_xpm(fp, 0, "Cluster Transitions", "# transitions",
"from cluster", "to cluster",
clust->ncl, clust->ncl, axis, axis, trans,
0, maxtrans, rlo, rhi, &i);
- ffclose(fp);
+ gmx_ffclose(fp);
}
if (ntransfn)
{
{
fprintf(fp, "%5d %5d\n", i+1, ntrans[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
sfree(ntrans);
for (i = 0; i < clust->ncl; i++)
if (clustidfn)
{
fp = xvgropen(clustidfn, "Clusters", output_env_get_xvgr_tlabel(oenv), "Cluster #", oenv);
- fprintf(fp, "@ s0 symbol 2\n");
- fprintf(fp, "@ s0 symbol size 0.2\n");
- fprintf(fp, "@ s0 linestyle 0\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ s0 symbol 2\n");
+ fprintf(fp, "@ s0 symbol size 0.2\n");
+ fprintf(fp, "@ s0 linestyle 0\n");
+ }
for (i = 0; i < nf; i++)
{
fprintf(fp, "%8g %8d\n", time[i], clust->cl[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
if (sizefn)
{
fp = xvgropen(sizefn, "Cluster Sizes", "Cluster #", "# Structures", oenv);
- fprintf(fp, "@g%d type %s\n", 0, "bar");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@g%d type %s\n", 0, "bar");
+ }
}
snew(structure, nf);
fprintf(log, "\n%3s | %3s %4s | %6s %4s | cluster members\n",
int gmx_cluster(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_cluster[tt] can cluster structures using several different methods.",
+ "[THISMODULE] can cluster structures using several different methods.",
"Distances between structures can be determined from a trajectory",
"or read from an [TT].xpm[tt] matrix file with the [TT]-dm[tt] option.",
"RMS deviation after fitting or RMS deviation of atom-pair distances",
};
FILE *fp, *log;
- int i, i1, i2, j, nf, nrms;
+ int nf, i, i1, i2, j;
+ gmx_int64_t nrms = 0;
matrix box;
rvec *xtps, *usextps, *x1, **xx = NULL;
{ efXVG, "-sz", "clust-size", ffOPTWR},
{ efXPM, "-tr", "clust-trans", ffOPTWR},
{ efXVG, "-ntr", "clust-trans", ffOPTWR},
- { efXVG, "-clid", "clust-id.xvg", ffOPTWR},
+ { efXVG, "-clid", "clust-id", ffOPTWR},
{ efTRX, "-cl", "clusters.pdb", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
&oenv))
{
}
}
}
- /* Initiate arrays */
- snew(d1, isize);
- snew(d2, isize);
- for (i = 0; (i < isize); i++)
- {
- snew(d1[i], isize);
- snew(d2[i], isize);
- }
if (bReadTraj)
{
else /* !bReadMat */
{
rms = init_mat(nf, method == m_diagonalize);
- nrms = (nf*(nf-1))/2;
+ nrms = ((gmx_int64_t)nf*((gmx_int64_t)nf-1))/2;
if (!bRMSdist)
{
fprintf(stderr, "Computing %dx%d RMS deviation matrix\n", nf, nf);
+ /* Initialize work array */
snew(x1, isize);
- for (i1 = 0; (i1 < nf); i1++)
+ for (i1 = 0; i1 < nf; i1++)
{
- for (i2 = i1+1; (i2 < nf); i2++)
+ for (i2 = i1+1; i2 < nf; i2++)
{
for (i = 0; i < isize; i++)
{
rmsd = rmsdev(isize, mass, xx[i2], x1);
set_mat_entry(rms, i1, i2, rmsd);
}
- nrms -= (nf-i1-1);
- fprintf(stderr, "\r# RMSD calculations left: %d ", nrms);
+ nrms -= (gmx_int64_t) (nf-i1-1);
+ fprintf(stderr, "\r# RMSD calculations left: " "%"GMX_PRId64 " ", nrms);
}
+ sfree(x1);
}
else /* bRMSdist */
{
fprintf(stderr, "Computing %dx%d RMS distance deviation matrix\n", nf, nf);
- for (i1 = 0; (i1 < nf); i1++)
+
+ /* Initiate work arrays */
+ snew(d1, isize);
+ snew(d2, isize);
+ for (i = 0; (i < isize); i++)
+ {
+ snew(d1[i], isize);
+ snew(d2[i], isize);
+ }
+ for (i1 = 0; i1 < nf; i1++)
{
calc_dist(isize, xx[i1], d1);
for (i2 = i1+1; (i2 < nf); i2++)
set_mat_entry(rms, i1, i2, rms_dist(isize, d1, d2));
}
nrms -= (nf-i1-1);
- fprintf(stderr, "\r# RMSD calculations left: %d ", nrms);
+ fprintf(stderr, "\r# RMSD calculations left: " "%"GMX_PRId64 " ", nrms);
+ }
+ /* Clean up work arrays */
+ for (i = 0; (i < isize); i++)
+ {
+ sfree(d1[i]);
+ sfree(d2[i]);
}
+ sfree(d1);
+ sfree(d2);
}
fprintf(stderr, "\n\n");
}
{
fprintf(fp, "%10d %10g\n", i, eigenvalues[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
break;
case m_monte_carlo:
orig = init_mat(rms->nn, FALSE);
bAverage, write_ncl, write_nst, rmsmin, bFit, log,
rlo_bot, rhi_bot, oenv);
}
- ffclose(log);
+ gmx_ffclose(log);
if (bBinary && !bAnalyze)
{
}
}
fprintf(stderr, "\n");
- ffclose(fp);
+ gmx_ffclose(fp);
if (NULL != orig)
{
fp = opt2FILE("-om", NFILE, fnm, "w");
write_xpm(fp, 0, title, "RMSD (nm)", buf, buf,
nf, nf, time, time, orig->mat, 0.0, orig->maxrms,
rlo_top, rhi_top, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
done_mat(&orig);
sfree(orig);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff