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/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright 2020- The GROMACS Authors
* and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
* Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* GROMACS is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with GROMACS; if not, see
* https://www.gnu.org/licenses, or write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* If you want to redistribute modifications to GROMACS, please
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*
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*/
/*! \internal \file
* \brief
* Implements nblib integrator
*
* \author Victor Holanda <victor.holanda@cscs.ch>
* \author Joe Jordan <ejjordan@kth.se>
* \author Prashanth Kanduri <kanduri@cscs.ch>
* \author Sebastian Keller <keller@cscs.ch>
* \author Artem Zhmurov <zhmurov@gmail.com>
*/
#include "nblib/integrator.h"
#include <cstddef>
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/vectypes.h"
#include "nblib/particletype.h"
#include "nblib/topology.h"
namespace nblib
{
LeapFrog::LeapFrog(const Topology& topology, const Box& box) : box_(box)
{
inverseMasses_.resize(topology.numParticles());
for (int i = 0; i < topology.numParticles(); i++)
{
int typeIndex = topology.getParticleTypeIdOfAllParticles()[i];
inverseMasses_[i] = 1.0 / topology.getParticleTypes()[typeIndex].mass();
}
}
LeapFrog::LeapFrog(gmx::ArrayRef<const real> inverseMasses, const Box& box) :
inverseMasses_(inverseMasses.begin(), inverseMasses.end()), box_(box)
{
}
void LeapFrog::integrate(const real dt, gmx::ArrayRef<Vec3> x, gmx::ArrayRef<Vec3> v, gmx::ArrayRef<const Vec3> f)
{
for (size_t i = 0; i < x.size(); i++)
{
for (int dim = 0; dim < dimSize; dim++)
{
v[i][dim] += f[i][dim] * dt * inverseMasses_[i];
x[i][dim] += v[i][dim] * dt;
}
}
}
} // namespace nblib
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