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/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright 2021- 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.
*
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*/
/*! \inpublicapi \file
* \brief
* Implements functionality to compute virials from force data
*
* \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>
*/
#include "virials.h"
#include <algorithm>
#include "gromacs/mdlib/calcvir.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/vectypes.h"
#include "nblib/box.h"
#include "nblib/exception.h"
namespace nblib
{
void computeVirialTensor(gmx::ArrayRef<const Vec3> coordinates,
gmx::ArrayRef<const Vec3> forces,
gmx::ArrayRef<const Vec3> shiftVectors,
gmx::ArrayRef<const Vec3> shiftForces,
const Box& box,
gmx::ArrayRef<real> virialOutput)
{
if (virialOutput.size() != 9)
{
throw InputException("Virial array size incorrect, should be 9");
}
// set virial output array to zero
std::fill(virialOutput.begin(), virialOutput.end(), 0.0);
// use legacy tensor format
rvec* virial = reinterpret_cast<rvec*>(virialOutput.data());
// compute the virials from surrounding boxes
const rvec* fshift = as_rvec_array(shiftForces.data());
const rvec* shift_vec = as_rvec_array(shiftVectors.data());
calc_vir(numShiftVectors, shift_vec, fshift, virial, false, box.legacyMatrix());
// calculate partial virial, for local atoms only, based on short range
// NOTE: GROMACS uses a variable called mdatoms.homenr which is basically number of atoms in current processor
// Used numAtoms from the coordinate array in its place
auto numAtoms = coordinates.size();
const rvec* f = as_rvec_array(forces.data());
const rvec* x = as_rvec_array(coordinates.data());
calc_vir(numAtoms, x, f, virial, false, box.legacyMatrix());
}
} // namespace nblib
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