2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2020,2021, 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 * \brief Implements a force calculator based on GROMACS data structures.
38 * \author Victor Holanda <victor.holanda@cscs.ch>
39 * \author Joe Jordan <ejjordan@kth.se>
40 * \author Prashanth Kanduri <kanduri@cscs.ch>
41 * \author Sebastian Keller <keller@cscs.ch>
43 #include "nblib/gmxcalculator.h"
44 #include "gromacs/ewald/ewald_utils.h"
45 #include "gromacs/gmxlib/nrnb.h"
46 #include "gromacs/mdlib/rf_util.h"
47 #include "gromacs/mdtypes/enerdata.h"
48 #include "gromacs/mdtypes/forcerec.h"
49 #include "gromacs/mdtypes/interaction_const.h"
50 #include "gromacs/mdtypes/simulation_workload.h"
51 #include "gromacs/nbnxm/nbnxm.h"
52 #include "gromacs/utility/range.h"
53 #include "nblib/exception.h"
54 #include "nblib/simulationstate.h"
59 GmxForceCalculator::GmxForceCalculator()
61 enerd_ = std::make_unique<gmx_enerdata_t>(1, 0);
62 forcerec_ = std::make_unique<t_forcerec>();
63 interactionConst_ = std::make_unique<interaction_const_t>();
64 stepWork_ = std::make_unique<gmx::StepWorkload>();
65 nrnb_ = std::make_unique<t_nrnb>();
68 GmxForceCalculator::~GmxForceCalculator() = default;
70 void GmxForceCalculator::compute(gmx::ArrayRef<const gmx::RVec> coordinateInput,
71 gmx::ArrayRef<gmx::RVec> forceOutput)
73 // update the coordinates in the backend
74 nbv_->convertCoordinates(gmx::AtomLocality::Local, coordinateInput);
76 nbv_->dispatchNonbondedKernel(gmx::InteractionLocality::Local,
84 nbv_->atomdata_add_nbat_f_to_f(gmx::AtomLocality::All, forceOutput);
87 void GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef<const int> particleInfoAllVdw,
88 gmx::ArrayRef<const gmx::RVec> coordinates,
91 auto legacyBox = box.legacyMatrix();
93 if (TRICLINIC(legacyBox))
95 throw InputException("Only rectangular unit-cells are supported here");
97 const rvec lowerCorner = { 0, 0, 0 };
98 const rvec upperCorner = { legacyBox[dimX][dimX], legacyBox[dimY][dimY], legacyBox[dimZ][dimZ] };
100 const real particleDensity = coordinates.size() / det(legacyBox);
102 nbnxn_put_on_grid(nbv_.get(),
108 { 0, int(coordinates.size()) },