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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
* consider that scientific software is very special. Version
* control is crucial - bugs must be traceable. We will be happy to
* consider code for inclusion in the official distribution, but
* derived work must not be called official GROMACS. Details are found
* in the README & COPYING files - if they are missing, get the
* official version at https://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out https://www.gromacs.org.
*/
/*! \internal \file
* \brief
* Implements nblib SimulationState
*
* \author Berk Hess <hess@kth.se>
* \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/simulationstate.h"
#include <memory>
#include <utility>
#include <vector>
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/arrayref.h"
#include "nblib/exception.h"
#include "nblib/util/setup.h"
#include "nblib/vector.h"
#include "simulationstateimpl.h"
namespace nblib
{
SimulationState::SimulationState(const std::vector<Vec3>& coordinates,
const std::vector<Vec3>& velocities,
const std::vector<Vec3>& forces,
Box box,
Topology topology) :
simulationStatePtr_(std::make_shared<Impl>(coordinates, velocities, forces, box, topology))
{
}
SimulationState::Impl::Impl(const std::vector<Vec3>& coordinates,
const std::vector<Vec3>& velocities,
const std::vector<Vec3>& forces,
const Box& box,
Topology topology) :
box_(box), topology_(std::move(topology))
{
auto numParticles = topology_.numParticles();
if (int(coordinates.size()) != numParticles)
{
throw InputException("Coordinates array size mismatch");
}
if (int(velocities.size()) != numParticles)
{
throw InputException("Velocities array size mismatch");
}
if (int(forces.size()) != numParticles)
{
throw InputException("Force buffer array size mismatch");
}
if (!isRealValued(coordinates))
{
throw InputException("Input coordinates has at least one NaN");
}
coordinates_ = coordinates;
if (!isRealValued(velocities))
{
throw InputException("Input velocities has at least one NaN");
}
velocities_ = velocities;
forces_ = forces;
// Ensure that the coordinates are in a box following PBC
put_atoms_in_box(PbcType::Xyz, box.legacyMatrix(), coordinates_);
}
const Topology& SimulationState::Impl::topology() const
{
return topology_;
}
Box SimulationState::Impl::box() const
{
return box_;
}
std::vector<Vec3>& SimulationState::Impl::coordinates()
{
return coordinates_;
}
std::vector<Vec3>& SimulationState::Impl::velocities()
{
return velocities_;
}
std::vector<Vec3>& SimulationState::Impl::forces()
{
return forces_;
}
const Topology& SimulationState::topology() const
{
return simulationStatePtr_->topology();
}
Box SimulationState::box() const
{
return simulationStatePtr_->box();
}
std::vector<Vec3>& SimulationState::coordinates()
{
return simulationStatePtr_->coordinates();
}
const std::vector<Vec3>& SimulationState::coordinates() const
{
return simulationStatePtr_->coordinates();
}
std::vector<Vec3>& SimulationState::velocities()
{
return simulationStatePtr_->velocities();
}
std::vector<Vec3>& SimulationState::forces()
{
return simulationStatePtr_->forces();
}
} // namespace nblib
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