Remove unnecessary config.h includes

[alexxy/gromacs.git] / src / programs / mdrun / membed.c

diff --git a/src/programs/mdrun/membed.c b/src/programs/mdrun/membed.c
index 94ef5cd5f794632bf5d92f3f7e265e594ab37128..758a5acc479df596d52140a812b8e97adb446c32 100644 (file)
--- a/src/programs/mdrun/membed.c
+++ b/src/programs/mdrun/membed.c
@@ -1,62 +1,57 @@
 /*
- * $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.
  *
- * 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.
+ * 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.
  *
- * 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
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  *
- * 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 "gromacs/fileio/futil.h"
-#include "edsam.h"
-#include "index.h"
-#include "physics.h"
-#include "names.h"
-#include "mtop_util.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 "string2.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 {
@@ -896,8 +891,8 @@ static void top_update(const char *topfile, rm_t *rm_p, gmx_mtop_t *mtop)
     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++)
@@ -962,10 +957,10 @@ static void top_update(const char *topfile, rm_t *rm_p, gmx_mtop_t *mtop)
         }
     }
 
-    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
 }