2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2020, 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.
38 #include "wholemoleculetransform.h"
40 #include "gromacs/topology/mtop_util.h"
45 WholeMoleculeTransform::WholeMoleculeTransform(const gmx_mtop_t& mtop, const PbcType pbcType) :
48 gmx_localtop_t localTop(mtop.ffparams);
50 gmx_mtop_generate_local_top(mtop, &localTop, false);
52 graph_ = mk_graph(localTop.idef, mtop.natoms);
54 wholeMoleculeCoordinates_.resize(mtop.natoms);
57 void WholeMoleculeTransform::updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box)
59 mk_mshift(nullptr, &graph_, pbcType_, box, as_rvec_array(x.data()));
62 ArrayRef<const RVec> WholeMoleculeTransform::wholeMoleculeCoordinates(ArrayRef<const RVec> x, const matrix box)
64 shift_x(&graph_, box, as_rvec_array(x.data()), as_rvec_array(wholeMoleculeCoordinates_.data()));
66 return wholeMoleculeCoordinates_;