2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
39 #include "gromacs/math/vectypes.h"
40 #include "gromacs/mdlib/nbnxn_consts.h"
41 #include "gromacs/mdlib/nbnxn_internal.h"
42 #include "gromacs/utility/arrayref.h"
43 #include "gromacs/utility/real.h"
45 struct gmx_domdec_zones_t;
48 class UpdateGroupsCog;
51 /* Put the atoms on the pair search grid.
52 * Only atoms atomStart to atomEnd in x are put on the grid.
53 * The atom_density is used to determine the grid size.
54 * When atomDensity<=0, the density is determined from atomEnd-atomStart and the corners.
55 * With domain decomposition part of the n particles might have migrated,
56 * but have not been removed yet. This count is given by nmoved.
57 * When move[i] < 0 particle i has migrated and will not be put on the grid.
58 * Without domain decomposition move will be NULL.
60 void nbnxn_put_on_grid(nbnxn_search_t nbs,
64 const rvec lowerCorner,
65 const rvec upperCorner,
66 const gmx::UpdateGroupsCog *updateGroupsCog,
71 gmx::ArrayRef<const gmx::RVec> x,
75 nbnxn_atomdata_t *nbat);
77 /* As nbnxn_put_on_grid, but for the non-local atoms
78 * with domain decomposition. Should be called after calling
79 * nbnxn_search_put_on_grid for the local atoms / home zone.
81 void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
82 const struct gmx_domdec_zones_t *zones,
84 gmx::ArrayRef<const gmx::RVec> x,
86 nbnxn_atomdata_t *nbat);
88 /* Return the number of x and y cells in the local grid */
89 void nbnxn_get_ncells(nbnxn_search_t nbs, int *ncx, int *ncy);
91 /* Return the order indices of the atoms on the pairlist search grid */
92 gmx::ArrayRef<const int> nbnxn_get_atomorder(const nbnxn_search* nbs);
94 /* Renumber the atom indices on the grid to consecutive order */
95 void nbnxn_set_atomorder(nbnxn_search_t nbs);
97 /* Return the index position of the atoms on the pairlist search grid */
98 gmx::ArrayRef<const int> nbnxn_get_gridindices(const nbnxn_search* nbs);