/*
- * $Id: mdrun.c,v 1.139.2.9 2009/05/04 16:13:29 hess Exp $
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 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
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, 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
+ * 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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*
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*
- * For more info, check our website at http://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.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * 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 "gmxpre.h"
+
+#include "membed.h"
#include <signal.h>
#include <stdlib.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "sysstuff.h"
-#include "vec.h"
-#include "statutil.h"
-#include "macros.h"
-#include "main.h"
-#include "futil.h"
-#include "edsam.h"
-#include "index.h"
-#include "physics.h"
-#include "names.h"
-#include "mtop_util.h"
-#include "tpxio.h"
-#include "string2.h"
-#include "membed.h"
-#include "pbc.h"
-#include "readinp.h"
-#include "readir.h"
+
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* information about scaling center */
typedef struct {
char buf[STRLEN], buf2[STRLEN], *temp;
int i, *nmol_rm, nmol, line;
- fpin = ffopen(topfile, "r");
- fpout = ffopen(TEMP_FILENM, "w");
+ fpin = gmx_ffopen(topfile, "r");
+ fpout = gmx_ffopen(TEMP_FILENM, "w");
snew(nmol_rm, mtop->nmoltype);
for (i = 0; i < rm_p->nr; i++)
}
}
- ffclose(fpout);
- /* use ffopen to generate backup of topinout */
- fpout = ffopen(topfile, "w");
- ffclose(fpout);
+ gmx_ffclose(fpout);
+ /* use gmx_ffopen to generate backup of topinout */
+ fpout = gmx_ffopen(topfile, "w");
+ gmx_ffclose(fpout);
rename(TEMP_FILENM, topfile);
#undef TEMP_FILENM
}
get_input(membed_input, &xy_fac, &xy_max, &z_fac, &z_max, &it_xy, &it_z, &probe_rad, &low_up_rm,
&maxwarn, &pieces, &bALLOW_ASYMMETRY);
- tpr_version = get_tpr_version(ftp2fn(efTPX, nfile, fnm));
+ tpr_version = get_tpr_version(ftp2fn(efTPR, nfile, fnm));
if (tpr_version < membed_version)
{
gmx_fatal(FARGS, "Version of *.tpr file to old (%d). "