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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
* This tests that sample code can run
*
* \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 <cstdio>
#include <memory>
#include <string>
#include <vector>
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/vectypes.h"
// The entire nblib public API can be included with a single header or individual components
// can be included via their respective headers.
#include "nblib/nblib.h"
int main()
{
// Create an argon particle with a name and a mass.
nblib::ParticleType argonAtom(nblib::ParticleTypeName("Ar"), nblib::Mass(39.94800));
// Create an argon molecule.
nblib::Molecule argonMolecule(nblib::MoleculeName("AR"));
// Add the argon particle to a molecule. The names are for bookkeeping and need not match.
argonMolecule.addParticle(nblib::ParticleName("Argon"), argonAtom);
// Define Lennard-Jones params for argon (parameters from gromos43A1).
nblib::C6 ArC6{ 0.0062647225 }; // C6 parameter
nblib::C12 ArC12{ 9.847044e-06 }; // C12 parameter
// Holder for non-bonded interactions.
nblib::ParticleTypesInteractions interactions;
// Add non-bonded interactions for argon.
interactions.add(argonAtom.name(), ArC6, ArC12);
// The TopologyBuilder builds the Topology!
nblib::TopologyBuilder topologyBuilder;
// Number of Argon particles (molecules) in the system.
int numParticles = 12;
// Add the requested number of argon molecules to a topology.
topologyBuilder.addMolecule(argonMolecule, numParticles);
// Add the argon interactions to the topology.
topologyBuilder.addParticleTypesInteractions(interactions);
// Build the topology.
nblib::Topology topology = topologyBuilder.buildTopology();
// The system needs a bounding box. Only cubic and rectangular boxes are supported.
nblib::Box box(6.05449);
// User defined coordinates.
std::vector<nblib::Vec3> coordinates = {
{ 0.794, 1.439, 0.610 }, { 1.397, 0.673, 1.916 }, { 0.659, 1.080, 0.573 },
{ 1.105, 0.090, 3.431 }, { 1.741, 1.291, 3.432 }, { 1.936, 1.441, 5.873 },
{ 0.960, 2.246, 1.659 }, { 0.382, 3.023, 2.793 }, { 0.053, 4.857, 4.242 },
{ 2.655, 5.057, 2.211 }, { 4.114, 0.737, 0.614 }, { 5.977, 5.104, 5.217 },
};
// User defined velocities.
std::vector<nblib::Vec3> velocities = {
{ 0.0055, -0.1400, 0.2127 }, { 0.0930, -0.0160, -0.0086 }, { 0.1678, 0.2476, -0.0660 },
{ 0.1591, -0.0934, -0.0835 }, { -0.0317, 0.0573, 0.1453 }, { 0.0597, 0.0013, -0.0462 },
{ 0.0484, -0.0357, 0.0168 }, { 0.0530, 0.0295, -0.2694 }, { -0.0550, -0.0896, 0.0494 },
{ -0.0799, -0.2534, -0.0079 }, { 0.0436, -0.1557, 0.1849 }, { -0.0214, 0.0446, 0.0758 },
};
// Force buffer initialization for each particle.
std::vector<nblib::Vec3> forces = {
{ 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
{ 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
{ 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
{ 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
};
// A simulation state contains all the molecular information about the system.
nblib::SimulationState simState(coordinates, velocities, forces, box, topology);
// Kernel options are flags needed for force calculation.
nblib::NBKernelOptions options = nblib::NBKernelOptions();
// Use a simple cutoff rule for Coulomb
options.coulombType = nblib::CoulombType::Cutoff;
// Some performance flags can be set a run time
options.nbnxmSimd = nblib::SimdKernels::SimdNo;
// The force calculator contains all the data needed to compute forces.
auto forceCalculator = nblib::setupGmxForceCalculatorCpu(simState.topology(), options);
// build the pairlist
forceCalculator->updatePairlist(simState.coordinates(), simState.box());
// Integration requires masses, positions, and forces
nblib::LeapFrog integrator(simState.topology(), simState.box());
// Print some diagnostic info
printf("initial forces on particle 0: x %4f y %4f z %4f\n", forces[0][0], forces[0][1], forces[0][2]);
// The forces are computed for the user
gmx::ArrayRef<nblib::Vec3> userForces(simState.forces());
forceCalculator->compute(simState.coordinates(), simState.box(), userForces);
// Print some diagnostic info
printf(" final forces on particle 0: x %4f y %4f z %4f\n",
userForces[0][0],
userForces[0][1],
userForces[0][2]);
// User may modify forces stored in simState.forces() if needed
// Print some diagnostic info
printf("initial position of particle 0: x %4f y %4f z %4f\n",
simState.coordinates()[0][0],
simState.coordinates()[0][1],
simState.coordinates()[0][2]);
// Integrate with a time step of 1 fs
integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
// Print some diagnostic info
printf(" final position of particle 0: x %4f y %4f z %4f\n",
simState.coordinates()[0][0],
simState.coordinates()[0][1],
simState.coordinates()[0][2]);
return 0;
}
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