Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / mdlib / nbnxn_search.h

diff --git a/src/gromacs/mdlib/nbnxn_search.h b/src/gromacs/mdlib/nbnxn_search.h
index a5117ccc4768b8a1811a752246aa8ac3ef5773da..8e644bf21a7f95b1547f773f18646709211766a4 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.h
+++ b/src/gromacs/mdlib/nbnxn_search.h
@@ -1,48 +1,48 @@
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustr
+/*
+ * This file is part of the GROMACS molecular simulation package.
  *
+ * 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.
  *
- *                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) 2001-2012, 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.
  */
 
 #ifndef _nbnxn_search_h
 #define _nbnxn_search_h
 
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-
 /* Returns the j-cluster size for kernel of type nb_kernel_type */
 int nbnxn_kernel_to_cj_size(int nb_kernel_type);
 
@@ -60,12 +60,13 @@ real nbnxn_get_rlist_effective_inc(int cluster_size, real atom_density);
 void nbnxn_init_search(nbnxn_search_t    * nbs_ptr,
                        ivec               *n_dd_cells,
                        gmx_domdec_zones_t *zones,
+                       gmx_bool            bFEP,
                        int                 nthread_max);
 
 /* Put the atoms on the pair search grid.
  * Only atoms a0 to a1 in x are put on the grid.
  * The atom_density is used to determine the grid size.
- * When atom_density=-1, the density is determined from a1-a0 and the corners.
+ * When atom_density<=0, the density is determined from a1-a0 and the corners.
  * With domain decomposition part of the n particles might have migrated,
  * but have not been removed yet. This count is given by nmoved.
  * When move[i] < 0 particle i has migrated and will not be put on the grid.
@@ -118,6 +119,7 @@ void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
  * number or roughly equally sized ci blocks in nbl.
  * When set >0 ci lists will be chopped up when the estimate
  * for the number of equally sized lists is below min_ci_balanced.
+ * With perturbed particles, also a group scheme style nbl_fep list is made.
  */
 void nbnxn_make_pairlist(const nbnxn_search_t  nbs,
                          nbnxn_atomdata_t     *nbat,