-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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.
*
- * This source code is part of
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- * GROningen MAchine for Chemical Simulations
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- * 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
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-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.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 "copyrite.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "tpxio.h"
-#include "do_fit.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
#include "gmx_ana.h"
+#include "gromacs/math/do_fit.h"
static void get_refx(output_env_t oenv, const char *trxfn, int nfitdim, int skip,
int gnx, int *index,
w_rls[a] = (bMW ? top->atoms.atom[index[a]].m : 1.0);
tot_mass += w_rls[a];
}
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
do
{
}
nfr_all++;
}
- while (read_next_x(oenv, status, &ti[nfr], natoms, x, box));
+ while (read_next_x(oenv, status, &ti[nfr], x, box));
close_trj(status);
sfree(x);
int gmx_rotmat(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_rotmat[tt] plots the rotation matrix required for least squares fitting",
+ "[THISMODULE] plots the rotation matrix required for least squares fitting",
"a conformation onto the reference conformation provided with",
"[TT]-s[tt]. Translation is removed before fitting.",
"The output are the three vectors that give the new directions",
"This tool is useful for, for instance,",
"determining the orientation of a molecule",
"at an interface, possibly on a trajectory produced with",
- "[TT]trjconv -fit rotxy+transxy[tt] to remove the rotation",
+ "[TT]gmx trjconv -fit rotxy+transxy[tt] to remove the rotation",
"in the [IT]x-y[it] plane.",
"[PAR]",
"Option [TT]-ref[tt] determines a reference structure for fitting,",
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | 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_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x_ref, NULL, box, bMW);
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr, box);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
gmx_rmpbc(gpbc, top.atoms.nr, box, x_ref);
R[YY][XX], R[YY][YY], R[YY][ZZ],
R[ZZ][XX], R[ZZ][YY], R[ZZ][ZZ]);
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
close_trj(status);
- ffclose(out);
+ gmx_ffclose(out);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff