#include <cstdio>
+#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxpreprocess/grompp.h"
#include "gromacs/hardware/detecthardware.h"
#include "gromacs/options/basicoptions.h"
tprFileName_(fileManager->getTemporaryFilePath(".tpr")),
logFileName_(fileManager->getTemporaryFilePath(".log")),
edrFileName_(fileManager->getTemporaryFilePath(".edr")),
+ mtxFileName_(fileManager->getTemporaryFilePath(".mtx")),
nsteps_(-2),
fileManager_(*fileManager)
{
return callGrompp(CommandLine());
}
+int
+SimulationRunner::callNmeig()
+{
+ /* Conforming to style guide by not passing a non-const reference
+ to this function. Passing a non-const reference might make it
+ easier to write code that incorrectly re-uses callerRef after
+ the call to this function. */
+
+ CommandLine caller;
+ caller.append("nmeig");
+ caller.addOption("-s", tprFileName_);
+ caller.addOption("-f", mtxFileName_);
+ // Ignore the overall translation and rotation in the
+ // first six eigenvectors.
+ caller.addOption("-first", "7");
+ // No need to check more than a number of output values.
+ caller.addOption("-last", "50");
+ caller.addOption("-xvg", "none");
+
+ return gmx_nmeig(caller.argc(), caller.argv());
+}
+
int
SimulationRunner::callMdrun(const CommandLine &callerRef)
{
caller.addOption("-g", logFileName_);
caller.addOption("-e", edrFileName_);
+ caller.addOption("-mtx", mtxFileName_);
caller.addOption("-o", fullPrecisionTrajectoryFileName_);
caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, 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.
+ *
+ * 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 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
+ * Tests for the normal modes functionality.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include <map>
+#include <memory>
+#include <string>
+#include <tuple>
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/compat/make_unique.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/trajectory/energyframe.h"
+#include "gromacs/trajectory/trajectoryframe.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/mpitest.h"
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/xvgtest.h"
+
+#include "energycomparison.h"
+#include "energyreader.h"
+#include "moduletest.h"
+#include "simulationdatabase.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Helper type
+using MdpField = MdpFieldValues::value_type;
+
+/*! \brief Test fixture base for normal mode analysis
+ *
+ * This test ensures mdrun can run a normal mode analys, reaching
+ * a reproducible eigenvalues following diagonalization.
+ *
+ * The choices for tolerance are arbitrary but sufficient. */
+class NormalModesTest : public MdrunTestFixture,
+ public ::testing::WithParamInterface <
+ std::tuple < std::string, std::string>>
+{
+};
+
+TEST_P(NormalModesTest, WithinTolerances)
+{
+ auto params = GetParam();
+ auto simulationName = std::get<0>(params);
+ auto integrator = std::get<1>(params);
+ SCOPED_TRACE(formatString("Comparing normal modes for '%s'",
+ simulationName.c_str()));
+
+ // TODO At some point we should also test PME-only ranks.
+ int numRanksAvailable = getNumberOfTestMpiRanks();
+ if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
+ {
+ fprintf(stdout, "Test system '%s' cannot run with %d ranks.\n"
+ "The supported numbers are: %s\n",
+ simulationName.c_str(), numRanksAvailable,
+ reportNumbersOfPpRanksSupported(simulationName).c_str());
+ return;
+ }
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(),
+ integrator.c_str(),
+ "no", "no");
+ mdpFieldValues["nsteps"] = "1";
+ mdpFieldValues["rcoulomb"] = "5.6";
+ mdpFieldValues["rlist"] = "5.6";
+ mdpFieldValues["rvdw"] = "5.6";
+ mdpFieldValues["constraints"] = "none";
+ mdpFieldValues.insert(MdpField("coulombtype", "Cut-off"));
+ mdpFieldValues.insert(MdpField("vdwtype", "Cut-off"));
+
+ // prepare the .tpr file
+ {
+ CommandLine caller;
+ caller.append("grompp");
+ runner_.useTopG96AndNdxFromDatabase(simulationName);
+ runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ EXPECT_EQ(0, runner_.callGrompp(caller));
+ }
+ // Do mdrun, preparing to check the normal modes later
+ {
+ CommandLine mdrunCaller;
+ mdrunCaller.append("mdrun");
+ ASSERT_EQ(0, runner_.callMdrun(mdrunCaller));
+ }
+ // Now run gmx nmeig and check the output
+ {
+ ASSERT_EQ(0, runner_.callNmeig());
+ TestReferenceData refData;
+ auto checker = refData.rootChecker()
+ .checkCompound("System", simulationName)
+ .checkCompound("Integrator", integrator);
+ auto settings = XvgMatchSettings();
+ TextInputFile input("eigenval.xvg");
+ checkXvgFile(&input, &checker, settings);
+ }
+}
+
+//! Containers of systems and integrators to test.
+//! \{
+std::vector<std::string> systemsToTest_g = { "scaled-water" };
+std::vector<std::string> integratorsToTest_g = { "nm" };
+
+//! \}
+
+// The time for OpenCL kernel compilation means these tests might time
+// out. If that proves to be a problem, these can be disabled for
+// OpenCL builds. However, once that compilation is cached for the
+// lifetime of the whole test binary process, these tests should run in
+// such configurations.
+#if GMX_DOUBLE
+INSTANTIATE_TEST_CASE_P(NormalModesWorks, NormalModesTest,
+ ::testing::Combine(::testing::ValuesIn(systemsToTest_g),
+ ::testing::ValuesIn(integratorsToTest_g)));
+#endif
+} // namespace
+} // namespace test
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff