/*
+ * 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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*
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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
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
-#include <ctype.h>
#include <math.h>
+#include <string.h>
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "statutil.h"
-#include "maths.h"
-#include "futil.h"
-#include "index.h"
-#include "typedefs.h"
-#include "xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gstat.h"
-#include "gmx_statistics.h"
-#include "tpxio.h"
-#include "pbc.h"
-#include "vec.h"
-#include "confio.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/fileio/confio.h"
#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define FACTOR 1000.0 /* Convert nm^2/ps to 10e-5 cm^2/s */
/* NORMAL = total diffusion coefficient (default). X,Y,Z is diffusion
}
fprintf(out, "\n");
}
- ffclose(out);
+ gmx_ffclose(out);
}
/* called from corr_loop, to do the main calculations */
}
}
}
- ffclose(out);
+ gmx_ffclose(out);
do_view(oenv, fn, "-graphtype bar");
/* Compute variance, stddev and error */
int gmx_msd(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_msd[tt] computes the mean square displacement (MSD) of atoms from",
+ "[THISMODULE] computes the mean square displacement (MSD) of atoms from",
"a set of initial positions. This provides an easy way to compute",
"the diffusion constant using the Einstein relation.",
"The time between the reference points for the MSD calculation",
"types of mean square displacement: [TT]-type[tt], [TT]-lateral[tt]",
"and [TT]-ten[tt]. Option [TT]-ten[tt] writes the full MSD tensor for",
"each group, the order in the output is: trace xx yy zz yx zx zy.[PAR]",
- "If [TT]-mol[tt] is set, [TT]g_msd[tt] plots the MSD for individual molecules",
+ "If [TT]-mol[tt] is set, [THISMODULE] plots the MSD for individual molecules",
"(including making molecules whole across periodic boundaries): ",
"for each individual molecule a diffusion constant is computed for ",
"its center of mass. The chosen index group will be split into ",
"With the option [TT]-rmcomm[tt], the center of mass motion of a ",
"specific group can be removed. For trajectories produced with ",
"GROMACS this is usually not necessary, ",
- "as [TT]mdrun[tt] usually already removes the center of mass motion.",
+ "as [gmx-mdrun] usually already removes the center of mass motion.",
"When you use this option be sure that the whole system is stored",
"in the trajectory file.[PAR]",
"The diffusion coefficient is determined by linear regression of the MSD,",
real dim_factor;
output_env_t oenv;
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
trx_file = ftp2fn_null(efTRX, NFILE, fnm);
tps_file = ftp2fn_null(efTPS, NFILE, fnm);
ndx_file = ftp2fn_null(efNDX, NFILE, fnm);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff