/*
+ * 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.
- * 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
+ * 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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+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
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- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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 <string.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
-#include "string2.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "statutil.h"
-#include "disre.h"
-#include "names.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "enxio.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/math/vec.h"
#include "gmx_ana.h"
+#include "gromacs/fileio/trxio.h"
#define TIME_EXPLICIT 0
#define TIME_CONTINUE 1
int *set;
gmx_bool bVerbose = TRUE;
- if ((getenv("VERBOSE")) != NULL)
+ if ((getenv("GMX_ENER_VERBOSE")) != NULL)
{
bVerbose = FALSE;
}
}
}
-static void update_ee(t_energy *lastee, gmx_large_int_t laststep,
- t_energy *startee, gmx_large_int_t startstep,
+static void update_ee(t_energy *lastee, gmx_int64_t laststep,
+ t_energy *startee, gmx_int64_t startstep,
t_energy *ee, int step,
t_energy *outee, int nre)
{
*/
if (startstep > 0)
{
- gmx_large_int_t q = laststep+step;
- gmx_large_int_t p = startstep+1;
+ gmx_int64_t q = laststep+step;
+ gmx_int64_t p = startstep+1;
prestart_esum = startee[i].esum-startee[i].e;
sigmacorr = prestart_esum-(p-1)*startee[i].e;
prestart_sigma = startee[i].eav-
}
static void update_ee_sum(int nre,
- gmx_large_int_t *ee_sum_step,
- gmx_large_int_t *ee_sum_nsteps,
- gmx_large_int_t *ee_sum_nsum,
+ gmx_int64_t *ee_sum_step,
+ gmx_int64_t *ee_sum_nsteps,
+ gmx_int64_t *ee_sum_nsum,
t_energy *ee_sum,
t_enxframe *fr, int out_step)
{
- gmx_large_int_t nsteps, nsum, fr_nsum;
+ gmx_int64_t nsteps, nsum, fr_nsum;
int i;
nsteps = *ee_sum_nsteps;
"in the later file is used. By specifying [TT]-settime[tt] you will be",
"asked for the start time of each file. The input files are taken",
"from the command line,",
- "such that the command [TT]eneconv -f *.edr -o fixed.edr[tt] should do",
+ "such that the command [TT]gmx eneconv -f *.edr -o fixed.edr[tt] should do",
"the trick. [PAR]",
"With [IT]one file[it] specified for [TT]-f[tt]:[BR]",
"Reads one energy file and writes another, applying the [TT]-dt[tt],",
gmx_enxnm_t *enm = NULL;
#endif
t_enxframe *fr, *fro;
- gmx_large_int_t ee_sum_step = 0, ee_sum_nsteps, ee_sum_nsum;
+ gmx_int64_t ee_sum_step = 0, ee_sum_nsteps, ee_sum_nsum;
t_energy *ee_sum;
- gmx_large_int_t lastfilestep, laststep, startstep, startstep_file = 0;
+ gmx_int64_t lastfilestep, laststep, startstep, startstep_file = 0;
int noutfr;
int nre, nremax, this_nre, nfile, f, i, j, kkk, nset, *set = NULL;
double last_t;
"Stop on errors in the file" }
};
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa),
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa),
pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
nset = 0;
timestep = 0.0;
snew(fnms, argc);
- nfile = 0;
lastfilestep = 0;
laststep = startstep = 0;
}
else
{
- fro->nsum = gmx_large_int_to_int(ee_sum_nsum,
- "energy average summation");
+ fro->nsum = gmx_int64_to_int(ee_sum_nsum,
+ "energy average summation");
/* Copy the energy sums */
for (i = 0; i < nre; i++)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff