2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2020, 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 basic nblib utility 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>
46 // includesorter/check-source want this include here. IMO a bug
51 #include <gtest/gtest.h>
53 #include "nblib/listed_forces/calculator.h"
54 #include "nblib/listed_forces/dataflow.hpp"
55 #include "nblib/listed_forces/tests/linear_chain_input.hpp"
56 #include "nblib/tests/testhelpers.h"
58 #include "testutils/refdata.h"
59 #include "testutils/testasserts.h"
69 TEST(NBlibTest, ListedForceCalculatorCanConstruct)
71 ListedInteractionData interactions;
73 EXPECT_NO_THROW(ListedForceCalculator listedForceCalculator(interactions, 2, 1, box));
76 template<class TestSeq, class SeqFloat, class SeqDouble>
77 void compareVectors(const TestSeq& forces,
78 [[maybe_unused]] const SeqFloat& refForcesFloat,
79 [[maybe_unused]] const SeqDouble& refForcesDouble)
81 for (size_t i = 0; i < forces.size(); ++i)
83 for (int m = 0; m < dimSize; ++m)
85 EXPECT_FLOAT_DOUBLE_EQ_TOL(
86 forces[i][m], refForcesFloat[i][m], refForcesDouble[i][m],
87 // Todo: why does the tolerance need to be so low?
88 gmx::test::relativeToleranceAsFloatingPoint(refForcesDouble[i][m], 5e-5));
93 class ListedExampleData : public ::testing::Test
99 HarmonicBondType bond1{ 376560, 0.136 };
100 HarmonicBondType bond2{ 313800, 0.1 };
101 std::vector<HarmonicBondType> bonds{ bond1, bond2 };
102 // one bond between atoms 0-1 with bond1 parameters and another between atoms 1-2 with bond2 parameters
103 std::vector<InteractionIndex<HarmonicBondType>> bondIndices{ { 0, 1, 0 }, { 1, 2, 1 } };
105 DefaultAngle angle(Degrees(108.53), 397.5);
106 std::vector<DefaultAngle> angles{ angle };
107 std::vector<InteractionIndex<DefaultAngle>> angleIndices{ { 0, 1, 2, 0 } };
109 pickType<HarmonicBondType>(interactions).indices = bondIndices;
110 pickType<HarmonicBondType>(interactions).parameters = bonds;
112 pickType<DefaultAngle>(interactions).indices = angleIndices;
113 pickType<DefaultAngle>(interactions).parameters = angles;
115 // initial position for the methanol atoms from the spc-water example
116 x = std::vector<gmx::RVec>{ { 1.97, 1.46, 1.209 }, { 1.978, 1.415, 1.082 }, { 1.905, 1.46, 1.03 } };
117 forces = std::vector<gmx::RVec>(3, gmx::RVec{ 0, 0, 0 });
120 std::valarray<gmx::BasicVector<float>>{ { -22.8980637, 128.801575, 363.505951 },
121 { -43.2698593, -88.0130997, -410.639252 },
122 { 66.167923, -40.788475, 47.1333084 } };
123 refAngleForcesFloat =
124 std::valarray<gmx::BasicVector<float>>{ { 54.7276611, -40.1688995, 17.6805191 },
125 { -81.8118973, 86.1988525, 60.1752243 },
126 { 27.0842342, -46.0299492, -77.8557434 } };
128 refBondForcesDouble = std::valarray<gmx::BasicVector<double>>{
129 { -22.89764839974935, 128.79927224858977, 363.50016834602064 },
130 { -43.24622441913251, -88.025652017772231, -410.61635172385434 },
131 { 66.14387281888186, -40.773620230817542, 47.116183377833721 }
133 refAngleForcesDouble = std::valarray<gmx::BasicVector<double>>{
134 { 54.726206806506234, -40.167809526198099, 17.680008528590257 },
135 { -81.809781666748606, 86.196545126117257, 60.173723525141448 },
136 { 27.083574860242372, -46.028735599919159, -77.853732053731704 }
139 refBondEnergyFloat = 0.2113433;
140 refAngleEnergyFloat = 0.112774156;
142 refBondEnergyDouble = 0.2113273434867636;
143 refAngleEnergyDouble = 0.11276812148357591;
145 box.reset(new Box(3, 3, 3));
146 pbc.reset(new PbcHolder(*box));
149 std::vector<gmx::RVec> x;
150 std::vector<gmx::RVec> forces;
152 ListedInteractionData interactions;
154 std::shared_ptr<Box> box;
155 std::shared_ptr<PbcHolder> pbc;
158 std::valarray<gmx::BasicVector<float>> refBondForcesFloat, refAngleForcesFloat;
159 std::valarray<gmx::BasicVector<double>> refBondForcesDouble, refAngleForcesDouble;
161 float refBondEnergyFloat, refAngleEnergyFloat;
162 double refBondEnergyDouble, refAngleEnergyDouble;
165 TEST_F(ListedExampleData, ComputeHarmonicBondForces)
167 auto indices = pickType<HarmonicBondType>(interactions).indices;
168 auto bonds = pickType<HarmonicBondType>(interactions).parameters;
169 real energy = computeForces(indices, bonds, x, &forces, *pbc);
171 EXPECT_FLOAT_DOUBLE_EQ_TOL(energy, refBondEnergyFloat, refBondEnergyDouble,
172 gmx::test::relativeToleranceAsFloatingPoint(refBondEnergyDouble, 1e-5));
174 compareVectors(forces, refBondForcesFloat, refBondForcesDouble);
177 TEST_F(ListedExampleData, ComputeHarmonicAngleForces)
179 auto indices = pickType<DefaultAngle>(interactions).indices;
180 auto angles = pickType<DefaultAngle>(interactions).parameters;
181 real energy = computeForces(indices, angles, x, &forces, *pbc);
183 EXPECT_FLOAT_DOUBLE_EQ_TOL(energy, refAngleEnergyFloat, refAngleEnergyDouble,
184 gmx::test::relativeToleranceAsFloatingPoint(refAngleEnergyDouble, 1e-5));
186 compareVectors(forces, refAngleForcesFloat, refAngleForcesDouble);
189 TEST_F(ListedExampleData, CanReduceForces)
191 auto energies = reduceListedForces(interactions, x, &forces, *pbc);
192 real totalEnergy = std::accumulate(begin(energies), end(energies), 0.0);
194 EXPECT_FLOAT_DOUBLE_EQ_TOL(totalEnergy, refBondEnergyFloat + refAngleEnergyFloat,
195 refBondEnergyDouble + refAngleEnergyDouble,
196 gmx::test::relativeToleranceAsFloatingPoint(refBondEnergyDouble, 1e-5));
198 compareVectors(forces, refBondForcesFloat + refAngleForcesFloat,
199 refBondForcesDouble + refAngleForcesDouble);
203 void compareArray(const ListedForceCalculator::EnergyType& energies,
204 const ListedForceCalculator::EnergyType& refEnergies)
206 for (size_t i = 0; i < energies.size(); ++i)
208 EXPECT_REAL_EQ_TOL(energies[i], refEnergies[i],
209 gmx::test::relativeToleranceAsFloatingPoint(refEnergies[i], 1e-5));
214 //! \brief sets up an interaction tuple for a linear chain with nParticles
215 class LinearChainDataFixture : public ::testing::Test
218 void SetUp() override
220 LinearChainData data(430);
223 interactions = data.interactions;
225 refForces = data.forces;
226 // pbc.reset(new PbcHolder(*box));
228 refEnergies = reduceListedForces(interactions, x, &refForces, NoPbc{});
231 void testEnergies(const ListedForceCalculator::EnergyType& energies) const
233 compareArray(energies, refEnergies);
236 void testForces(const std::vector<gmx::RVec>& forces) const
238 compareVectors(forces, refForces, refForces);
241 std::vector<gmx::RVec> x;
242 ListedInteractionData interactions;
243 std::shared_ptr<Box> box;
244 // std::shared_ptr<PbcHolder> pbc;
247 std::vector<gmx::RVec> refForces;
248 ListedForceCalculator::EnergyType refEnergies;
251 TEST_F(LinearChainDataFixture, Multithreading)
253 ListedForceCalculator lfCalculator(interactions, x.size(), 4, *box);
255 std::vector<Vec3> forces(x.size(), Vec3{ 0, 0, 0 });
256 ListedForceCalculator::EnergyType energies;
257 lfCalculator.compute(x, forces, energies);
259 testEnergies(energies);