/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 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
+ * 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.
*
- * GROningen MAchine for Chemical Simulations
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, 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
- * of the License, or (at your option) any later version.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * 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
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * 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 papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#include <copyrite.h>
-#include <filenm.h>
-#include <macros.h>
-#include <pbc.h>
-#include <smalloc.h>
-#include <statutil.h>
-#include <vec.h>
-#include <xvgr.h>
-
+#include "gmxpre.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
int gmx_dyecoupl(int argc, char *argv[])
{
const char *desc[] =
{
- "This tool extracts dye dynamics from trajectory files.",
+ "[THISMODULE] extracts dye dynamics from trajectory files.",
"Currently, R and kappa^2 between dyes is extracted for (F)RET",
"simulations with assumed dipolar coupling as in the Foerster equation.",
"It further allows the calculation of R(t) and kappa^2(t), R and",
int ndon, nacc;
atom_id *donindex, *accindex;
char *grpnm;
- t_atoms *atoms = NULL;
t_trxstatus *status;
t_trxframe fr;
rrange, krange, rincr, kincr, Rfrac;
int rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
- parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* Check command line options for filenames and set bool flags when switch used*/
}
printf("Select group with donor atom pairs defining the transition moment\n");
- get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
+ get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
printf("Select group with acceptor atom pairs defining the transition moment\n");
- get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
+ get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
/*check if groups are identical*/
grident = TRUE;
if (bRKout)
{
- ffclose(rkfp);
+ gmx_ffclose(rkfp);
}
if (bDatout)
{
- ffclose(datfp);
+ gmx_ffclose(datfp);
}
if (bInstEffout)
{
- ffclose(iefp);
+ gmx_ffclose(iefp);
}
fprintf(rhfp, "%12.7f %12.7f\n", (i + 0.5) * rincr + rmin,
rhist[i]);
}
- ffclose(rhfp);
+ gmx_ffclose(rhfp);
}
if (bKhistout)
fprintf(khfp, "%12.7f %12.7f\n", (i + 0.5) * kincr + kmin,
khist[i]);
}
- ffclose(khfp);
+ gmx_ffclose(khfp);
}
printf("\nAverages:\n");
gmx_fatal(FARGS, "Could not read first frame of the trajectory.\n");
}
- thanx(stderr);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff