/*
+ * 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.
+ *
+ * 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.
*
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- * 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.
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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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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <string.h>
#include <math.h>
-#include "string2.h"
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "smalloc.h"
-#include "enxio.h"
-#include "statutil.h"
-#include "names.h"
-#include "copyrite.h"
-#include "macros.h"
-#include "xvgr.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/xvgr.h"
#include "gstat.h"
-#include "physics.h"
-#include "matio.h"
-#include "strdb.h"
+#include "gromacs/math/units.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/strdb.h"
#include "gmx_ana.h"
+#include "gromacs/fileio/trxio.h"
static int search_str2(int nstr, char **str, char *key)
int gmx_enemat(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_enemat[tt] extracts an energy matrix from the energy file ([TT]-f[tt]).",
+ "[THISMODULE] extracts an energy matrix from the energy file ([TT]-f[tt]).",
"With [TT]-groups[tt] a file must be supplied with on each",
"line a group of atoms to be used. For these groups matrix of",
"interaction energies will be extracted from the energy file",
"[TT]SOL[tt][BR]",
"then energy groups with names like 'Coul-SR:Protein-SOL' and ",
"'LJ:Protein-SOL' are expected in the energy file (although",
- "[TT]g_enemat[tt] is most useful if many groups are analyzed",
+ "[THISMODULE] is most useful if many groups are analyzed",
"simultaneously). Matrices for different energy types are written",
"out separately, as controlled by the",
"[TT]-[no]coul[tt], [TT]-[no]coulr[tt], [TT]-[no]coul14[tt], ",
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | 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_TIME,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
+ for (i = 0; (i < egNR+egSP); i++)
+ {
+ egrp_use[i] = FALSE;
+ }
egrp_use[egCOULSR] = bCoulSR;
egrp_use[egLJSR] = bLJSR;
egrp_use[egBHAMSR] = bBhamSR;
sprintf(fn, "%s%s", egrp_nm[m], ftp2fn(efXPM, NFILE, fnm));
sprintf(label, "%s Interaction Energies", egrp_nm[m]);
- out = ffopen(fn, "w");
+ out = gmx_ffopen(fn, "w");
if (emin >= emid)
{
write_xpm(out, 0, label, "Energy (kJ/mol)",
ngroups, ngroups, groupnr, groupnr, emat[m],
emin, emid, emax, rlo, rmid, rhi, &nlevels);
}
- ffclose(out);
+ gmx_ffclose(out);
}
}
}
oenv);
xvgr_legend(out, 0, NULL, oenv);
j = 0;
- for (m = 0; (m < egNR+egSP); m++)
+ if (output_env_get_print_xvgr_codes(oenv))
{
- if (egrp_use[m])
+ char str1[STRLEN], str2[STRLEN];
+ if (output_env_get_xvg_format(oenv) == exvgXMGR)
{
- fprintf(out, "@ legend string %d \"%s\"\n", j++, egrp_nm[m]);
+ sprintf(str1, "@ legend string ");
+ sprintf(str2, " ");
}
- }
- if (bFree)
- {
- fprintf(out, "@ legend string %d \"%s\"\n", j++, "Free");
- }
- if (bFree)
- {
- fprintf(out, "@ legend string %d \"%s\"\n", j++, "Diff");
- }
- fprintf(out, "@TYPE xy\n");
- fprintf(out, "#%3s", "grp");
- for (m = 0; (m < egNR+egSP); m++)
- {
- if (egrp_use[m])
+ else
{
- fprintf(out, " %9s", egrp_nm[m]);
+ sprintf(str1, "@ s");
+ sprintf(str2, " legend ");
}
+
+ for (m = 0; (m < egNR+egSP); m++)
+ {
+ if (egrp_use[m])
+ {
+ fprintf(out, "%s%d%s \"%s\"\n", str1, j++, str2, egrp_nm[m]);
+ }
+ }
+ if (bFree)
+ {
+ fprintf(out, "%s%d%s \"%s\"\n", str1, j++, str2, "Free");
+ }
+ if (bFree)
+ {
+ fprintf(out, "%s%d%s \"%s\"\n", str1, j++, str2, "Diff");
+ }
+ fprintf(out, "@TYPE xy\n");
+ fprintf(out, "#%3s", "grp");
+
+ for (m = 0; (m < egNR+egSP); m++)
+ {
+ if (egrp_use[m])
+ {
+ fprintf(out, " %9s", egrp_nm[m]);
+ }
+ }
+ if (bFree)
+ {
+ fprintf(out, " %9s", "Free");
+ }
+ if (bFree)
+ {
+ fprintf(out, " %9s", "Diff");
+ }
+ fprintf(out, "\n");
}
- if (bFree)
- {
- fprintf(out, " %9s", "Free");
- }
- if (bFree)
- {
- fprintf(out, " %9s", "Diff");
- }
- fprintf(out, "\n");
for (i = 0; (i < ngroups); i++)
{
fprintf(out, "%3.0f", groupnr[i]);
}
fprintf(out, "\n");
}
- ffclose(out);
+ gmx_ffclose(out);
}
else
{
write_matrix(out,ngroups,1,ngroups,groupnr,emat,label,emin,emax,nlevels);
n++;
}
- ffclose(out);
+ gmx_ffclose(out);
*/
}
close_enx(in);
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff