/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014, 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.
*
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- * VERSION 3.0
- *
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- *
- * 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
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, 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
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- * files - if they are missing, get the official version at www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
+ * GROMACS is distributed in the hope that it will be useful,
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+ * Lesser General Public License for more details.
*
- * And Hey:
- * Gyas ROwers Mature At Cryogenic Speed
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*
- * finished FD 09/07/08
+ * 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.
*
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "statutil.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
-#include "statutil.h"
-#include "tpxio.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "physics.h"
-#include "index.h"
-#include "gmx_statistics.h"
-#include "gmx_ana.h"
-#include "macros.h"
+#include "gmxpre.h"
+
+#include <assert.h>
+#include <stdlib.h>
+
+#include "gromacs/commandline/pargs.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/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define SQR(x) (pow(x, 2.0))
#define EPSI0 (EPSILON0*E_CHARGE*E_CHARGE*AVOGADRO/(KILO*NANO)) /* EPSILON0 in SI units */
-
static void index_atom2mol(int *n, int *index, t_block *mols)
{
int nat, i, nmol, mol, j;
}
}
- if (abs(qall) > 0.01)
+ if (fabs(qall) > 0.01)
{
printf("\n\nSystem not neutral (q=%f) will not calculate translational part of the dipole moment.\n", qall);
bNEU = FALSE;
}
-static void calc_mjdsp(FILE *fmjdsp, real vol, real temp, real prefactor, rvec mjdsp[], real dsp2[], real time[], int nfr, real refr[])
+static void calc_mjdsp(FILE *fmjdsp, real prefactor, real dsp2[], real time[], int nfr, real refr[])
{
int i;
clear_rvec(mjd_tmp);
clear_rvec(mdvec);
clear_rvec(tmp);
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, fr.natoms, fr.box);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, fr.natoms);
do
{
xshfr[i] = 0.0;
}
}
-
+ assert(time != NULL);
if (nfr == 0)
fprintf(stderr, "Prefactor fit E-H: 1 / 6.0*V*k_B*T: %g\n", prefactorav);
- calc_mjdsp(fmjdsp, volume_av, temp, prefactorav, mjdsp, dsp2, time, nfr, xshfr);
+ calc_mjdsp(fmjdsp, prefactorav, dsp2, time, nfr, xshfr);
/*
* Now we can average and calculate the correlation functions
- if (bACF)
+ if (bACF && (ii < nvfr))
{
fprintf(stderr, "Integral and integrated fit to the current acf yields at t=%f:\n", time[vfr[ii]]);
fprintf(stderr, "sigma=%8.3f (pure integral: %.3f)\n", sgk-malt*pow(time[vfr[ii]], sigma), sgk);
}
else
{
- fprintf(stderr, "Too less points for a fit.\n");
+ fprintf(stderr, "Too few points for a fit.\n");
}
{ efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
{ efNDX, NULL, NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
- { efXVG, "-o", "current.xvg", ffWRITE },
- { efXVG, "-caf", "caf.xvg", ffOPTWR },
- { efXVG, "-dsp", "dsp.xvg", ffWRITE },
- { efXVG, "-md", "md.xvg", ffWRITE },
- { efXVG, "-mj", "mj.xvg", ffWRITE},
- { efXVG, "-mc", "mc.xvg", ffOPTWR }
+ { efXVG, "-o", "current", ffWRITE },
+ { efXVG, "-caf", "caf", ffOPTWR },
+ { efXVG, "-dsp", "dsp", ffWRITE },
+ { efXVG, "-md", "md", ffWRITE },
+ { efXVG, "-mj", "mj", ffWRITE },
+ { efXVG, "-mc", "mc", ffOPTWR }
};
#define NFILE asize(fnm)
const char *desc[] = {
- "[TT]g_current[tt] is a tool for calculating the current autocorrelation function, the correlation",
+ "[THISMODULE] is a tool for calculating the current autocorrelation function, the correlation",
"of the rotational and translational dipole moment of the system, and the resulting static",
"dielectric constant. To obtain a reasonable result, the index group has to be neutral.",
"Furthermore, the routine is capable of extracting the static conductivity from the current ",
/* At first the arguments will be parsed and the system information processed */
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- 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;
+ }
bACF = opt2bSet("-caf", NFILE, fnm);
bINT = opt2bSet("-mc", NFILE, fnm);
temp, trust, bfit, efit, bvit, evit, status, isize, nmols, nshift,
index0, indexm, mass2, qmol, eps_rf, oenv);
- ffclose(fmj);
- ffclose(fmd);
- ffclose(fmjdsp);
+ gmx_ffclose(fmj);
+ gmx_ffclose(fmd);
+ gmx_ffclose(fmjdsp);
if (bACF)
{
- ffclose(outf);
+ gmx_ffclose(outf);
}
if (bINT)
{
- ffclose(mcor);
+ gmx_ffclose(mcor);
}
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff