/*
+ * 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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+ * 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
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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 "gstat.h"
-#include "txtdump.h"
-#include "eigio.h"
-#include "mtop_util.h"
-#include "physics.h"
-#include "main.h"
-#include "gmx_ana.h"
-
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/linearalgebra/eigensolver.h"
-#include "gromacs/linearalgebra/mtxio.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static double cv_corr(double nu, double T)
{
int gmx_nmeig(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_nmeig[tt] calculates the eigenvectors/values of a (Hessian) matrix,",
- "which can be calculated with [TT]mdrun[tt].",
+ "[THISMODULE] calculates the eigenvectors/values of a (Hessian) matrix,",
+ "which can be calculated with [gmx-mdrun].",
"The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
"The structure is written first with t=0. The eigenvectors",
"are written as frames with the eigenvector number as timestamp.",
- "The eigenvectors can be analyzed with [TT]g_anaeig[tt].",
+ "The eigenvectors can be analyzed with [gmx-anaeig].",
"An ensemble of structures can be generated from the eigenvectors with",
- "[TT]g_nmens[tt]. When mass weighting is used, the generated eigenvectors",
+ "[gmx-nmens]. When mass weighting is used, the generated eigenvectors",
"will be scaled back to plain Cartesian coordinates before generating the",
"output. In this case, they will no longer be exactly orthogonal in the",
"standard Cartesian norm, but in the mass-weighted norm they would be.[PAR]",
"degree of freedom at the given temperature.",
"The total correction is printed on the terminal screen.",
"The recommended way of getting the corrections out is:[PAR]",
- "[TT]g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr][tt][PAR]",
+ "[TT]gmx nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr][tt][PAR]",
"The [TT]-constr[tt] option should be used when bond constraints were used during the",
"simulation [BB]for all the covalent bonds[bb]. If this is not the case, ",
"you need to analyze the [TT]quant_corr.xvg[tt] file yourself.[PAR]",
t_filenm fnm[] = {
{ efMTX, "-f", "hessian", ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efXVG, "-of", "eigenfreq", ffWRITE },
{ efXVG, "-ol", "eigenval", ffWRITE },
{ efXVG, "-os", "spectrum", ffOPTWR },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, 0,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* Read tpr file for volume and number of harmonic terms */
- read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &tpx, TRUE, &version, &generation);
+ read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &tpx, TRUE, &version, &generation);
snew(top_x, tpx.natoms);
- read_tpx(ftp2fn(efTPX, NFILE, fnm), NULL, box, &natoms,
+ read_tpx(ftp2fn(efTPR, NFILE, fnm), NULL, box, &natoms,
top_x, NULL, NULL, &mtop);
if (bCons)
{
{
fprintf (out, "%6d %15g\n", begin+i, eigenvalues[i]);
}
- ffclose(out);
+ gmx_ffclose(out);
if (opt2bSet("-qc", NFILE, fnm))
qutot += qu;
}
}
- ffclose(out);
+ gmx_ffclose(out);
if (NULL != spec)
{
for (j = 0; (j < maxspec); j++)
{
fprintf(spec, "%10g %10g\n", 1.0*j, spectrum[j]);
}
- ffclose(spec);
+ gmx_ffclose(spec);
}
if (NULL != qc)
{
nharm, nvsite);
printf("Total correction to cV = %g J/mol K\n", qcvtot);
printf("Total correction to H = %g kJ/mol\n", qutot);
- ffclose(qc);
+ gmx_ffclose(qc);
please_cite(stdout, "Caleman2011b");
}
/* Writing eigenvectors. Note that if mass scaling was used, the eigenvectors
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff