+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * 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
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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+ * If you want to redistribute modifications to GROMACS, please
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+ * 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 http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief End-to-end tests checking sanity of results of simulations
+ * containing constant acceleration groups
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/mpitest.h"
+#include "testutils/simulationdatabase.h"
+#include "testutils/testmatchers.h"
+
+#include "moduletest.h"
+#include "simulatorcomparison.h"
+#include "trajectoryreader.h"
+
+namespace gmx::test
+{
+namespace
+{
+/*! \brief Test fixture checking the velocities of aomts
+ *
+ * This tests that velocities of non-accelerated atoms are zero
+ * and that velocities of accelarated atoms match acceleration*time.
+ * This code assumes the first half the atoms are non-accelerated
+ * and the second half are accelerated
+ */
+using AccelerationGroupTestParams = std::tuple<std::string, std::string>;
+class AccelerationGroupTest :
+ public MdrunTestFixture,
+ public ::testing::WithParamInterface<AccelerationGroupTestParams>
+{
+public:
+ //! Check that the velocities are zero or accelerated
+ static void checkVelocities(const std::string& trajectoryName,
+ const RVec acceleration,
+ const FloatingPointTolerance& tolerance)
+ {
+ const size_t c_groupSize = 3;
+
+ const std::vector<RVec> zeroVelocities(c_groupSize, RVec{ 0, 0, 0 });
+
+ TrajectoryFrameReader trajectoryFrameReader(trajectoryName);
+ while (trajectoryFrameReader.readNextFrame())
+ {
+ const auto frame = trajectoryFrameReader.frame();
+ GMX_RELEASE_ASSERT(frame.v().size() == 2 * c_groupSize,
+ "Expect velocities for both atom groups");
+
+ const RVec referenceVelocity = real(frame.time()) * acceleration;
+ const std::vector<RVec> referenceVelocities(c_groupSize, referenceVelocity);
+
+ SCOPED_TRACE("Checking velocities of non-accelerated atoms");
+ ArrayRef<const RVec> nonAcceleratedVelocities = frame.v().subArray(0, c_groupSize);
+ EXPECT_THAT(nonAcceleratedVelocities, Pointwise(RVecEq(tolerance), zeroVelocities));
+
+ SCOPED_TRACE("Checking velocities of accelerated atoms");
+ ArrayRef<const RVec> acceleratedVelocities = frame.v().subArray(c_groupSize, c_groupSize);
+ EXPECT_THAT(acceleratedVelocities, Pointwise(RVecEq(tolerance), referenceVelocities));
+ }
+ }
+};
+
+TEST_P(AccelerationGroupTest, WithinTolerances)
+{
+ const auto& params = GetParam();
+ const auto& integrator = std::get<0>(params);
+ const auto& tcoupling = std::get<1>(params);
+ const auto& simulationName = "spc2";
+
+ // Prepare mdp input
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName, integrator, tcoupling, "no");
+ mdpFieldValues["nsteps"] = "8";
+ mdpFieldValues["dt"] = "0.002";
+ mdpFieldValues["nstxout"] = "0";
+ mdpFieldValues["nstvout"] = "8";
+ mdpFieldValues["nstfout"] = "0";
+ mdpFieldValues["comm-mode"] = "none";
+ // The two groups will not see each other when the cut-off is 0.9 nm
+ mdpFieldValues["coulombtype"] = "reaction-field";
+ mdpFieldValues["rcoulomb"] = "0.8";
+ mdpFieldValues["rvdw"] = "0.8";
+ mdpFieldValues["verlet-buffer-tolerance"] = "-1";
+ mdpFieldValues["rlist"] = "0.9";
+ // Couple the (non-)accelerated groups separately, so their velocties are independent
+ mdpFieldValues["tc-grps"] = "firstWaterMolecule secondWaterMolecule";
+ mdpFieldValues["ref-t"] = "0.001 0.001";
+ // Use weak coupling so we can check vecolities of atoms with a tight tolerance
+ mdpFieldValues["tau-t"] = "10.0 10.0";
+ const RVec c_acceleration = { 2.0, 3.0, 1.5 };
+ mdpFieldValues["acc-grps"] = "secondWaterMolecule";
+ mdpFieldValues["accelerate"] = "2.0 3.0 1.5";
+ // Set initial velocities to zero
+ mdpFieldValues["gen-vel"] = "yes";
+ mdpFieldValues["gen-temp"] = "0";
+
+ // Run grompp
+ runner_.useTopGroAndNdxFromDatabase(simulationName);
+ runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ runGrompp(&runner_);
+ // Run mdrun
+ runMdrun(&runner_);
+
+ // T-coupling causes changes in the velocities up to 1e-4
+ auto tolerance = absoluteTolerance((GMX_DOUBLE && tcoupling == "no") ? 1e-10 : 1e-4);
+
+ // Check the velocities of the non-accelerated and accelerated groups
+ checkVelocities(runner_.fullPrecisionTrajectoryFileName_, c_acceleration, tolerance);
+}
+
+// The v-rescale case check that Ekin computation and temperature coupling
+// can be performed independently for atoms groups, so the accelerations
+// are not affected. This can be useful in practice.
+INSTANTIATE_TEST_SUITE_P(AccelerationWorks,
+ AccelerationGroupTest,
+ ::testing::Combine(::testing::Values("md", "md-vv"),
+ ::testing::Values("no", "v-rescale")));
+} // namespace
+} // namespace gmx::test
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff