-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
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*
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- * This source code is part of
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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 "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "tpxio.h"
-#include "rmpbc.h"
-#include "physics.h"
-#include "nrjac.h"
-#include "confio.h"
-#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void low_print_data(FILE *fp, real time, rvec x[], int n, atom_id *index,
gmx_bool bDim[], const char *sffmt)
fprintf(fp, "%-5d %10.3f %10.3f %10.3f\n", 1+i,
sum[index[i]][XX], sum[index[i]][YY], sum[index[i]][ZZ]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
max = 0;
maxi = 0;
for (i = 0; i < isize; i++)
{
fprintf(fp, "%10.3e %10d\n", i*binwidth, histo[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
int gmx_traj(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_traj[tt] plots coordinates, velocities, forces and/or the box.",
+ "[THISMODULE] plots coordinates, velocities, forces and/or the box.",
"With [TT]-com[tt] the coordinates, velocities and forces are",
"calculated for the center of mass of each group.",
"When [TT]-mol[tt] is set, the numbers in the index file are",
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efXVG, "-ox", "coord.xvg", ffOPTWR },
- { efTRX, "-oxt", "coord.xtc", ffOPTWR },
- { efXVG, "-ov", "veloc.xvg", ffOPTWR },
- { efXVG, "-of", "force.xvg", ffOPTWR },
- { efXVG, "-ob", "box.xvg", ffOPTWR },
- { efXVG, "-ot", "temp.xvg", ffOPTWR },
- { efXVG, "-ekt", "ektrans.xvg", ffOPTWR },
- { efXVG, "-ekr", "ekrot.xvg", ffOPTWR },
- { efXVG, "-vd", "veldist.xvg", ffOPTWR },
- { efPDB, "-cv", "veloc.pdb", ffOPTWR },
- { efPDB, "-cf", "force.pdb", ffOPTWR },
- { efXVG, "-av", "all_veloc.xvg", ffOPTWR },
- { efXVG, "-af", "all_force.xvg", ffOPTWR }
+ { efXVG, "-ox", "coord", ffOPTWR },
+ { efTRX, "-oxt", "coord", ffOPTWR },
+ { efXVG, "-ov", "veloc", ffOPTWR },
+ { efXVG, "-of", "force", ffOPTWR },
+ { efXVG, "-ob", "box", ffOPTWR },
+ { efXVG, "-ot", "temp", ffOPTWR },
+ { efXVG, "-ekt", "ektrans", ffOPTWR },
+ { efXVG, "-ekr", "ekrot", ffOPTWR },
+ { efXVG, "-vd", "veldist", ffOPTWR },
+ { efPDB, "-cv", "veloc", ffOPTWR },
+ { efPDB, "-cf", "force", ffOPTWR },
+ { efXVG, "-av", "all_veloc", ffOPTWR },
+ { efXVG, "-af", "all_force", ffOPTWR }
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (bMol)
{
read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, flags);
+
+ if ((bOV || bOF) && fn2ftp(ftp2fn(efTRX, NFILE, fnm)) == efXTC)
+ {
+ gmx_fatal(FARGS, "Cannot extract velocities or forces since your input XTC file does not contain them.");
+ }
+
if (bCV || bCF)
{
snew(sumx, fr.natoms);
if (bOX)
{
- ffclose(outx);
+ gmx_ffclose(outx);
}
if (bOXT)
{
}
if (bOV)
{
- ffclose(outv);
+ gmx_ffclose(outv);
}
if (bOF)
{
- ffclose(outf);
+ gmx_ffclose(outf);
}
if (bOB)
{
- ffclose(outb);
+ gmx_ffclose(outb);
}
if (bOT)
{
- ffclose(outt);
+ gmx_ffclose(outt);
}
if (bEKT)
{
- ffclose(outekt);
+ gmx_ffclose(outekt);
}
if (bEKR)
{
- ffclose(outekr);
+ gmx_ffclose(outekr);
}
if (bVD)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff