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.
37 * This implements molecule setup tests
39 * \author Victor Holanda <victor.holanda@cscs.ch>
40 * \author Joe Jordan <ejjordan@kth.se>
41 * \author Prashanth Kanduri <kanduri@cscs.ch>
42 * \author Sebastian Keller <keller@cscs.ch>
43 * \author Artem Zhmurov <zhmurov@gmail.com>
45 #include "nblib/integrator.h"
46 #include "gromacs/pbcutil/pbc.h"
47 #include "nblib/molecules.h"
48 #include "nblib/particletype.h"
49 #include "nblib/simulationstate.h"
50 #include "nblib/topology.h"
52 #include "testutils/testasserts.h"
61 TEST(NBlibTest, IntegratorWorks)
67 ParticleType particleType(ParticleTypeName("H"), Mass(1.0));
68 Molecule molecule(MoleculeName("SomeMolecule"));
69 molecule.addParticle(ParticleName("SomeAtom"), particleType);
71 ParticleTypesInteractions interactions;
72 interactions.add(particleType.name(), C6{ 0 }, C12{ 0 });
74 TopologyBuilder topologyBuilder;
75 topologyBuilder.addMolecule(molecule, numAtoms);
76 topologyBuilder.addParticleTypesInteractions(interactions);
77 Topology topology = topologyBuilder.buildTopology();
79 std::vector<Vec3> x(numAtoms, { 0.0, 0.0, 0.0 });
80 std::vector<Vec3> v(numAtoms, { 0.0, 0.0, 0.0 });
81 std::vector<Vec3> f(numAtoms, { 1.0, 2.0, 0.0 });
85 std::vector<Vec3> x0(x);
86 std::vector<Vec3> v0(v);
88 SimulationState simulationState(x, v, f, box, topology);
89 put_atoms_in_box(PbcType::Xyz, box.legacyMatrix(), x0);
91 LeapFrog integrator(simulationState.topology(), simulationState.box());
93 gmx::test::FloatingPointTolerance tolerance = gmx::test::absoluteTolerance(numSteps * 0.000005);
94 for (int step = 0; step < numSteps; step++)
96 real totalTime = step * dt;
101 for (int i = 0; i < numAtoms; i++)
103 for (int d = 0; d < dimSize; d++)
105 // Analytical solution for constant-force particle movement
106 int typeIndex = simulationState.topology().getParticleTypeIdOfAllParticles()[i];
107 real im = 1.0 / simulationState.topology().getParticleTypes()[typeIndex].mass();
109 x0[i][d] + v0[i][d] * totalTime + 0.5 * f[i][d] * totalTime * totalTime * im;
110 vAnalytical[d] = v0[i][d] + f[i][d] * totalTime * im;
112 EXPECT_REAL_EQ_TOL(xAnalytical[d], simulationState.coordinates()[i][d], tolerance)
114 "Coordinate {} of atom {} is different from analytical solution "
120 EXPECT_REAL_EQ_TOL(vAnalytical[d], simulationState.velocities()[i][d], tolerance)
122 "Velocity component {} of atom {} is different from analytical "
123 "solution at step {}.",
128 integrator.integrate(dt,
129 simulationState.coordinates(),
130 simulationState.velocities(),
131 simulationState.forces());