Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / mdlib / wall.c

diff --git a/src/gromacs/mdlib/wall.c b/src/gromacs/mdlib/wall.c
index 32210f7dca70cb9b0b06493907e57b659351bbd3..bdc5c90e404b06e96cd38a06e86a28b205c7f669 100644 (file)
--- a/src/gromacs/mdlib/wall.c
+++ b/src/gromacs/mdlib/wall.c
@@ -1,53 +1,54 @@
-/*  -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * 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
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, 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) 2001-2008, 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.
  *
- * 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 <math.h>
 #include <string.h>
-#include "maths.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "smalloc.h"
-#include "force.h"
+
 #include "gromacs/fileio/filenm.h"
-#include "nrnb.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
 
 void make_wall_tables(FILE *fplog, const output_env_t oenv,
                       const t_inputrec *ir, const char *tabfn,
@@ -159,7 +160,7 @@ real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
             }
             else
             {
-                lamfac = 0;
+                lamfac = lambda;
                 type   = md->typeB;
             }
         }
@@ -168,7 +169,7 @@ real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
             lamfac = 1;
             type   = md->typeA;
         }
-        for (i = md->start; i < md->start+md->homenr; i++)
+        for (i = 0; i < md->homenr; i++)
         {
             for (w = 0; w < nwall; w++)
             {