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 ebb142cf27711e6ccaaa75c057e9c28024b18d48..8e644bf21a7f95b1547f773f18646709211766a4 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.h
+++ b/src/gromacs/mdlib/nbnxn_search.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * 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.
@@ -36,7 +36,8 @@
 #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" {
@@ -59,12 +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.
@@ -117,6 +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,