/*
- * $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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- * bugs must be traceable. We will be happy to consider code for
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+ * GROMACS is distributed in the hope that it will be useful,
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*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
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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 <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 "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/utility/cstringutil.h"
#include "membed.h"
-#include "pbc.h"
-#include "readinp.h"
-#include "readir.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxpreprocess/readir.h"
/* information about scaling center */
typedef struct {
/* generate the list of membrane molecules that overlap with the molecule to be embedded. *
* The molecule to be embedded is already reduced in size. */
static int gen_rm_list(rm_t *rm_p, t_block *ins_at, t_block *rest_at, t_pbc *pbc, gmx_mtop_t *mtop,
- rvec *r, rvec *r_ins, mem_t *mem_p, pos_ins_t *pos_ins, real probe_rad,
+ rvec *r, mem_t *mem_p, pos_ins_t *pos_ins, real probe_rad,
int low_up_rm, gmx_bool bALLOW_ASYMMETRY)
{
int i, j, k, l, at, at2, mol_id;
}
/*remove all lipids and waters overlapping and update all important structures (e.g. state and mtop)*/
-static void rm_group(t_inputrec *ir, gmx_groups_t *groups, gmx_mtop_t *mtop, rm_t *rm_p, t_state *state,
+static void rm_group(gmx_groups_t *groups, gmx_mtop_t *mtop, rm_t *rm_p, t_state *state,
t_block *ins_at, pos_ins_t *pos_ins)
{
int i, j, k, n, rm, mol_id, at, block;
}
/* Write a topology where the number of molecules is correct for the system after embedding */
-static void top_update(const char *topfile, char *ins, rm_t *rm_p, gmx_mtop_t *mtop)
+static void top_update(const char *topfile, rm_t *rm_p, gmx_mtop_t *mtop)
{
#define TEMP_FILENM "temp.top"
int bMolecules = 0;
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
}
set_pbc(pbc, inputrec->ePBC, state->box);
snew(rm_p, 1);
- lip_rm = gen_rm_list(rm_p, ins_at, rest_at, pbc, mtop, state->x, r_ins, mem_p, pos_ins,
+ lip_rm = gen_rm_list(rm_p, ins_at, rest_at, pbc, mtop, state->x, mem_p, pos_ins,
probe_rad, low_up_rm, bALLOW_ASYMMETRY);
lip_rm -= low_up_rm;
}
/*remove all lipids and waters overlapping and update all important structures*/
- rm_group(inputrec, groups, mtop, rm_p, state, ins_at, pos_ins);
+ rm_group(groups, mtop, rm_p, state, ins_at, pos_ins);
rm_bonded_at = rm_bonded(ins_at, mtop);
if (rm_bonded_at != ins_at->nr)
if (ftp2bSet(efTOP, nfile, fnm))
{
- top_update(opt2fn("-mp", nfile, fnm), ins, rm_p, mtop);
+ top_update(opt2fn("-mp", nfile, fnm), rm_p, mtop);
}
sfree(pbc);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff