2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, 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.
36 #ifndef GMX_NBNXN_ATOMDATA_H
37 #define GMX_NBNXN_ATOMDATA_H
41 #include "gromacs/math/vectypes.h"
42 #include "gromacs/utility/basedefinitions.h"
43 #include "gromacs/utility/real.h"
50 struct nbnxn_atomdata_t;
55 /* Reallocate the nbnxn_atomdata_t for a size of n atoms */
56 void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat, int n);
58 /* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
59 * and fills up to na_round with coordinates that are far away.
61 void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
62 const rvec *x, int nbatFormat,
66 enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE
69 /* Initialize the non-bonded atom data structure.
70 * The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
71 * Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
72 * to the atom data structure.
73 * enbnxninitcombrule sets what combination rule data gets stored in nbat.
75 void nbnxn_atomdata_init(const gmx::MDLogger &mdlog,
76 nbnxn_atomdata_t *nbat,
78 int enbnxninitcombrule,
79 int ntype, const real *nbfp,
83 void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
84 const nbnxn_search *nbs,
85 const t_mdatoms *mdatoms,
88 /* Copy the shift vectors to nbat */
89 void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box,
91 nbnxn_atomdata_t *nbat);
94 * FillLocal tells if the local filler particle coordinates should be zeroed.
96 void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search *nbs,
100 nbnxn_atomdata_t *nbat,
101 gmx_wallcycle *wcycle);
103 /* Add the forces stored in nbat to f, zeros the forces in nbat */
104 void nbnxn_atomdata_add_nbat_f_to_f(nbnxn_search *nbs,
106 nbnxn_atomdata_t *nbat,
108 gmx_wallcycle *wcycle);
110 /* Add the fshift force stored in nbat to fshift */
111 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,