2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2018,2019,2020,2021, 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.
38 * Tests for the energy minimization functionality.
40 * \author Mark Abraham <mark.j.abraham@gmail.com>
41 * \ingroup module_mdrun_integration_tests
51 #include <gtest/gtest.h>
53 #include "gromacs/options/filenameoption.h"
54 #include "gromacs/topology/idef.h"
55 #include "gromacs/topology/ifunc.h"
56 #include "gromacs/trajectory/energyframe.h"
57 #include "gromacs/trajectory/trajectoryframe.h"
58 #include "gromacs/utility/basenetwork.h"
59 #include "gromacs/utility/stringutil.h"
61 #include "testutils/mpitest.h"
62 #include "testutils/refdata.h"
63 #include "testutils/simulationdatabase.h"
64 #include "testutils/testasserts.h"
66 #include "energycomparison.h"
67 #include "energyreader.h"
68 #include "moduletest.h"
77 /*! \brief Test fixture base for energy minimizaiton
79 * This test ensures mdrun can run an energy minimization, reaching
80 * a reproducible final energy.
82 * The choices for tolerance are arbitrary but sufficient. */
83 class EnergyMinimizationTest :
84 public MdrunTestFixture,
85 public ::testing::WithParamInterface<std::tuple<std::string, std::string>>
89 /*! \brief Database of empirical tolerances for EM integrators on the various systems. */
90 std::unordered_map<std::string, FloatingPointTolerance> potentialEnergyToleranceForSystem_g = {
91 { { "argon12", relativeToleranceAsPrecisionDependentUlp(-1, 10, 200) },
92 { "tip3p5", relativeToleranceAsPrecisionDependentUlp(-50, 200, 3800) },
93 { "glycine_vacuo", relativeToleranceAsPrecisionDependentUlp(1000, 100, 100) },
94 { "alanine_vsite_vacuo", relativeToleranceAsPrecisionDependentUlp(-160, 150, 400) },
95 { "glycine_no_constraints_vacuo", relativeToleranceAsPrecisionDependentUlp(2000, 100, 100) } }
98 TEST_P(EnergyMinimizationTest, WithinTolerances)
100 auto params = GetParam();
101 auto simulationName = std::get<0>(params);
102 auto minimizer = std::get<1>(params);
103 SCOPED_TRACE(formatString("Comparing '%s' energy minimization for simulation '%s'",
105 simulationName.c_str()));
107 // TODO At some point we should also test PME-only ranks.
108 int numRanksAvailable = getNumberOfTestMpiRanks();
109 if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
112 "Test system '%s' cannot run with %d ranks.\n"
113 "The supported numbers are: %s\n",
114 simulationName.c_str(),
116 reportNumbersOfPpRanksSupported(simulationName).c_str());
120 auto mdpFieldValues =
121 prepareMdpFieldValues(simulationName.c_str(), minimizer.c_str(), "no", "no");
122 mdpFieldValues["nsteps"] = "4";
124 int maxWarningsTolerated = (minimizer == "l-bfgs") ? 1 : 0;
125 // prepare the .tpr file
127 // TODO evolve grompp to report the number of warnings issued, so
128 // tests always expect the right number.
130 caller.append("grompp");
131 caller.addOption("-maxwarn", maxWarningsTolerated);
132 runner_.useTopGroAndNdxFromDatabase(simulationName);
133 runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
134 EXPECT_EQ(0, runner_.callGrompp(caller));
137 // do mdrun, preparing to check the energies later
138 runner_.edrFileName_ = fileManager_.getTemporaryFilePath("minimize.edr");
140 CommandLine mdrunCaller;
141 mdrunCaller.append("mdrun");
142 if (minimizer == "l-bfgs" && getNumberOfTestMpiRanks() > 1)
144 // Ideally we would use this death test, but it is not
145 // stable enough in CI, so we just skip it.
146 // EXPECT_DEATH_IF_SUPPORTED(runner_.callMdrun(mdrunCaller),
147 // "L-BFGS minimization only supports a single rank");
152 ASSERT_EQ(0, runner_.callMdrun(mdrunCaller));
156 EnergyTermsToCompare energyTermsToCompare{ {
157 { interaction_function[F_EPOT].longname, potentialEnergyToleranceForSystem_g.at(simulationName) },
160 TestReferenceData refData;
161 auto checker = refData.rootChecker()
162 .checkCompound("Simulation", simulationName)
163 .checkCompound("Minimizer", minimizer);
164 checkEnergiesAgainstReferenceData(runner_.edrFileName_, energyTermsToCompare, &checker);
167 //! Containers of systems and integrators to test.
169 std::vector<std::string> unconstrainedSystemsToTest_g = { "argon12",
170 "glycine_no_constraints_vacuo" };
171 std::vector<std::string> minimizersToTest_g = { "steep", "cg", "l-bfgs" };
173 std::vector<std::string> constrainedSystemsToTest_g = { "tip3p5",
175 "alanine_vsite_vacuo" };
176 std::vector<std::string> minimizersToTestWithConstraints_g = { "steep", "cg" };
179 // The time for OpenCL kernel compilation means these tests might time
180 // out. If that proves to be a problem, these can be disabled for
181 // OpenCL builds. However, once that compilation is cached for the
182 // lifetime of the whole test binary process, these tests should run in
183 // such configurations.
184 INSTANTIATE_TEST_SUITE_P(MinimizersWorkWithConstraints,
185 EnergyMinimizationTest,
186 ::testing::Combine(::testing::ValuesIn(constrainedSystemsToTest_g),
187 ::testing::ValuesIn(minimizersToTestWithConstraints_g)));
188 INSTANTIATE_TEST_SUITE_P(MinimizersWork,
189 EnergyMinimizationTest,
190 ::testing::Combine(::testing::ValuesIn(unconstrainedSystemsToTest_g),
191 ::testing::ValuesIn(minimizersToTest_g)));