/*
+ * 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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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "smalloc.h"
#include <math.h>
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "statutil.h"
-#include "string2.h"
-#include "vec.h"
-#include "index.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "do_fit.h"
+#include <stdlib.h>
+
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "cmat.h"
-#include "viewit.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/do_fit.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 norm_princ(t_atoms *atoms, int isize, atom_id *index, int natoms,
rvec *x)
int gmx_rms(int argc, char *argv[])
{
- const char
- *desc[] =
+ const char *desc[] =
{
- "[TT]g_rms[tt] compares two structures by computing the root mean square",
+ "[THISMODULE] compares two structures by computing the root mean square",
"deviation (RMSD), the size-independent [GRK]rho[grk] similarity parameter",
"([TT]rho[tt]) or the scaled [GRK]rho[grk] ([TT]rhosc[tt]), ",
"see Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).",
"Option [TT]-m[tt] produces a matrix in [TT].xpm[tt] format of",
"comparison values of each structure in the trajectory with respect to",
"each other structure. This file can be visualized with for instance",
- "[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].[PAR]",
+ "[TT]xv[tt] and can be converted to postscript with [gmx-xpm2ps].[PAR]",
"Option [TT]-fit[tt] controls the least-squares fitting of",
"the structures on top of each other: complete fit (rotation and",
int ePBC;
t_iatom *iatom = NULL;
- matrix box;
+ matrix box = {{0}};
rvec *x, *xp, *xm = NULL, **mat_x = NULL, **mat_x2, *mat_x2_j = NULL, vec1,
vec2;
t_trxstatus *status;
};
#define NFILE asize(fnm)
- if (!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,
+ 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;
bPrev = (prev > 0);
if (bPrev)
{
+ fprintf(stderr, "WARNING: using option -prev with large trajectories will\n"
+ " require a lot of memory and could lead to crashes\n");
prev = abs(prev);
if (freq != 1)
{
del_yaxis[i] = delta_maxy*i/del_lev;
}
sprintf(buf, "%s %s vs. delta t", gn_rms[0], whatname[ewhat]);
- fp = ffopen("delta.xpm", "w");
+ fp = gmx_ffopen("delta.xpm", "w");
write_xpm(fp, 0, buf, "density", output_env_get_time_label(oenv), whatlabel[ewhat],
delta_xsize, del_lev+1, del_xaxis, del_yaxis,
delta, 0.0, delta_max, rlo, rhi, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
}
if (opt2bSet("-bin", NFILE, fnm))
{
gmx_fatal(FARGS, "Error writing to output file");
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
}
if (bBond)
for (i = 0; (i < teller); i++)
{
if (bSplit && i > 0 &&
- abs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
+ fabs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
{
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(fp, "%12.7f", time[bPrev ? freq*i : i]);
for (j = 0; (j < nrms); j++)
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
if (bMirror)
{
}
for (i = 0; (i < teller); i++)
{
- if (bSplit && i > 0 && abs(time[i]) < 1e-5)
+ if (bSplit && i > 0 && fabs(time[i]) < 1e-5)
{
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(fp, "%12.7f", time[i]);
for (j = 0; (j < nrms); j++)
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
if (bAv)
{
fprintf(fp, "%10d %10g\n", j, rlstot/teller);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
if (bNorm)
{
fprintf(fp, "%10d %10g\n", j, rlsnorm[j]/teller);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
do_view(oenv, opt2fn_null("-a", NFILE, fnm), "-graphtype bar");
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff