if (PAR(cr))
{
- gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
+ gmx_fatal(FARGS, "L-BFGS minimization only supports a single rank");
}
if (nullptr != constr)
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# make an "object library" for code that we re-use for both kinds of tests
+# Make an "object library" for test infrastructure code that we re-use
+# in multiple test executables.
add_library(mdrun_test_objlib OBJECT
energyreader.cpp
+ energycomparison.cpp
moduletest.cpp
simulationdatabase.cpp
terminationhelper.cpp
- # PME tests
- pmetest.cpp
+ trajectorycomparison.cpp
+ trajectoryreader.cpp
)
set(testname "MdrunTests")
${exename}
# files with code for tests
compressed_x_output.cpp
- energycomparison.cpp
grompp.cpp
initialconstraints.cpp
interactiveMD.cpp
- rerun.cpp
+ pmetest.cpp
swapcoords.cpp
tabulated_bonded_interactions.cpp
termination.cpp
trajectory_writing.cpp
- trajectorycomparison.cpp
- trajectoryreader.cpp
# pseudo-library for code for testing mdrun
$<TARGET_OBJECTS:mdrun_test_objlib>
# pseudo-library for code for mdrun
gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST)
endif()
+# To avoid running into test timeouts, some end-to-end tests of mdrun
+# functionality are split off. This can be rearranged in future as we
+# see fit.
+set(testname "MdrunNonIntegratorTests")
+set(exename "mdrun-non-integrator-test")
+
+gmx_add_gtest_executable(
+ ${exename}
+ # files with code for tests
+ minimize.cpp
+ rerun.cpp
+ # pseudo-library for code for testing mdrun
+ $<TARGET_OBJECTS:mdrun_test_objlib>
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST)
+
+# To permit other end-to-end tests to run with multiple OpenMP
+# threads, test cases that still use the group scheme are separated.
set(testname "LegacyGroupSchemeMdrunTests")
set(exename "legacy-mdrun-test")
gmx_add_gtest_executable(
${exename}
+ # When TPI supports the Verlet scheme, move this into
+ # MdrunNonIntegratorTest
tpitest.cpp
# pseudo-library for code for testing mdrun
$<TARGET_OBJECTS:mdrun_test_objlib>
)
gmx_register_gtest_test(${testname} ${exename} INTEGRATION_TEST)
+# Tests that only make sense to run with multiple ranks and/or real
+# MPI are implemented here.
set(testname "MdrunMpiTests")
set(exename "mdrun-mpi-test")
${exename} MPI
# files with code for tests
domain_decomposition.cpp
+ minimize.cpp
multisim.cpp
multisimtest.cpp
+ pmetest.cpp
replicaexchange.cpp
# pseudo-library for code for testing mdrun
$<TARGET_OBJECTS:mdrun_test_objlib>
# pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
)
-gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 INTEGRATION_TEST)
+if (GMX_GPU AND GMX_USE_OPENCL)
+ gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 OCL_INTEGRATION_TEST)
+else()
+ gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST)
+endif()
#include "energycomparison.h"
+#include <gtest/gtest.h>
+#include <gtest/gtest-spi.h>
+
#include "gromacs/trajectory/energyframe.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringutil.h"
+#include "testutils/refdata.h"
#include "testutils/testasserts.h"
+#include "energyreader.h"
+#include "moduletest.h"
+
namespace gmx
{
namespace test
}
}
+void
+checkEnergiesAgainstReferenceData(const std::string &energyFilename,
+ const EnergyTolerances &energiesToMatch,
+ TestReferenceChecker *checker)
+{
+ const bool thisRankChecks = (gmx_node_rank() == 0);
+
+ if (thisRankChecks)
+ {
+ auto namesOfEnergiesToMatch = getKeys(energiesToMatch);
+ auto energyReader = openEnergyFileToReadFields(energyFilename,
+ namesOfEnergiesToMatch);
+
+ std::unordered_map<std::string, TestReferenceChecker> checkers;
+ for (const auto &energyToMatch : energiesToMatch)
+ {
+ const auto &energyName = energyToMatch.first;
+ checkers[energyName] = checker->checkCompound("Energy", energyName.c_str());
+ const auto &energyTolerance = energyToMatch.second;
+ checkers[energyName].setDefaultTolerance(energyTolerance);
+ }
+
+ // We can't assume that frame names based purely on frame
+ // contents are unique. For example, CG can write multiple
+ // frames with the same step number. But we need a unique
+ // identifier so we match the intended reference data, so we
+ // keep track of the number of the frame read from the file.
+ int frameNumber = 0;
+ while (energyReader->readNextFrame())
+ {
+ const EnergyFrame &frame = energyReader->frame();
+ const std::string frameName = frame.frameName() + " in frame " + toString(frameNumber);
+
+ for (const auto &energyToMatch : energiesToMatch)
+ {
+ const std::string &energyName = energyToMatch.first;
+ const real energyValue = frame.at(energyName);
+
+ SCOPED_TRACE("Comparing " + energyName + " in " + frameName);
+ checkers[energyName].checkReal(energyValue, frameName.c_str());
+ }
+ ++frameNumber;
+ }
+ }
+ else
+ {
+ EXPECT_NONFATAL_FAILURE(checker->checkUnusedEntries(), ""); // skip checks on other ranks
+ }
+}
+
} // namespace test
} // namespace gmx
namespace test
{
+class TestReferenceChecker;
+
//! Convenience type
using EnergyTolerances = std::unordered_map<std::string, FloatingPointTolerance>;
const EnergyFrame &test,
const EnergyTolerances &tolerances);
+/*! \brief Check a subset of the energies found in an energy file
+ * against reference data.
+ *
+ * Opens the energy file, loops over all frames, matching the
+ * indicated energies against refdata at the given tolerance.
+ *
+ * \param[in] energyFilename The name of an energy file.
+ * \param[in] energiesToMatch Set of energies to match at given tolerances.
+ * \param[in] checker Root checker for reference data.
+ *
+ * \todo This is quite similar to the functionality used in PmeTest,
+ * and we should consider reducing the duplication.
+ */
+void
+checkEnergiesAgainstReferenceData(const std::string &energyFilename,
+ const EnergyTolerances &energiesToMatch,
+ TestReferenceChecker *checker);
+
} // namespace test
} // namespace gmx
--- /dev/null
+Glycine
+ 10
+ 7GLY N 1 4.063 1.415 0.028
+ 7GLY H1 2 4.152 1.370 0.036
+ 7GLY H2 3 3.990 1.348 0.041
+ 7GLY H3 4 4.055 1.456 -0.063
+ 7GLY CA 5 4.052 1.522 0.132
+ 7GLY HA1 6 4.075 1.480 0.229
+ 7GLY HA2 7 4.124 1.599 0.111
+ 7GLY C 8 3.921 1.596 0.127
+ 7GLY OT1 9 3.921 1.716 0.153
+ 7GLY OT2 10 3.903 1.695 0.218
+ 8.05623 5.63712 7.44504
--- /dev/null
+[ System ]
+ 1 2 3 4 5 6 7 8 9 10
--- /dev/null
+; Include forcefield parameters
+#include "charmm27.ff/forcefield.itp"
+
+#include "glycine_vacuo.itp"
+
+[ system ]
+; Name
+Glycine
+
+[ molecules ]
+; Compound #mols
+Glycine 1
--- /dev/null
+Glycine
+ 10
+ 7GLY N 1 4.063 1.415 0.028
+ 7GLY H1 2 4.152 1.370 0.036
+ 7GLY H2 3 3.990 1.348 0.041
+ 7GLY H3 4 4.055 1.456 -0.063
+ 7GLY CA 5 4.052 1.522 0.132
+ 7GLY HA1 6 4.075 1.480 0.229
+ 7GLY HA2 7 4.124 1.599 0.111
+ 7GLY C 8 3.921 1.596 0.127
+ 7GLY OT1 9 3.921 1.716 0.153
+ 7GLY OT2 10 3.903 1.695 0.218
+ 8.05623 5.63712 7.44504
--- /dev/null
+[ moleculetype ]
+; Name nrexcl
+Glycine 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 7 GLY rtp GLY q 0.0
+ 1 NH3 7 GLY N 1 -0.3 14.007 ; qtot -0.3
+ 2 HC 7 GLY H1 2 0.33 1.008 ; qtot 0.03
+ 3 HC 7 GLY H2 3 0.33 1.008 ; qtot 0.36
+ 4 HC 7 GLY H3 4 0.33 1.008 ; qtot 0.69
+ 5 CT2 7 GLY CA 5 0.13 12.011 ; qtot 0.82
+ 6 HB 7 GLY HA1 6 0.09 1.008 ; qtot 0.91
+ 7 HB 7 GLY HA2 7 0.09 1.008 ; qtot 1
+ 8 CC 7 GLY C 8 0.34 12.011 ; qtot 1.34
+ 9 OC 7 GLY OT1 9 -0.67 15.9994 ; qtot 0.67
+ 10 OC 7 GLY OT2 10 -0.67 15.9994 ; qtot 0
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+
+[ pairs ]
+; ai aj funct c0 c1 c2 c3
+ 1 9 1
+ 1 10 1
+ 2 6 1
+ 2 7 1
+ 2 8 1
+ 3 6 1
+ 3 7 1
+ 3 8 1
+ 4 6 1
+ 4 7 1
+ 4 8 1
+ 6 9 1
+ 6 10 1
+ 7 9 1
+ 7 10 1
+
+[ angles ]
+; ai aj ak funct c0 c1 c2 c3
+ 2 1 3 5
+ 2 1 4 5
+ 2 1 5 5
+ 3 1 4 5
+ 3 1 5 5
+ 4 1 5 5
+ 1 5 6 5
+ 1 5 7 5
+ 1 5 8 5
+ 6 5 7 5
+ 6 5 8 5
+ 7 5 8 5
+ 5 8 9 5
+ 5 8 10 5
+ 9 8 10 5
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3 c4 c5
+ 2 1 5 6 9
+ 2 1 5 7 9
+ 2 1 5 8 9
+ 3 1 5 6 9
+ 3 1 5 7 9
+ 3 1 5 8 9
+ 4 1 5 6 9
+ 4 1 5 7 9
+ 4 1 5 8 9
+ 1 5 8 9 9
+ 1 5 8 10 9
+ 6 5 8 9 9
+ 6 5 8 10 9
+ 7 5 8 9 9
+ 7 5 8 10 9
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3
+ 8 5 10 9 2
--- /dev/null
+[ System ]
+ 1 2 3 4 5 6 7 8 9 10
--- /dev/null
+; Include forcefield parameters
+#include "charmm27.ff/forcefield.itp"
+
+#include "glycine_vacuo.itp"
+
+[ system ]
+; Name
+Glycine
+
+[ molecules ]
+; Compound #mols
+Glycine 1
--- /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 energy minimization functionality.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \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/stringutil.h"
+
+#include "testutils/mpitest.h"
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+#include "energycomparison.h"
+#include "energyreader.h"
+#include "moduletest.h"
+#include "simulationdatabase.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+/*! \brief Test fixture base for energy minimizaiton
+ *
+ * This test ensures mdrun can run an energy minimization, reaching
+ * a reproducible final energy.
+ *
+ * The choices for tolerance are arbitrary but sufficient. */
+class EnergyMinimizationTest : public MdrunTestFixture,
+ public ::testing::WithParamInterface <
+ std::tuple < std::string, std::string>>
+{
+};
+
+/*! \brief Database of empirical tolerances for EM integrators on the various systems. */
+std::unordered_map<std::string, FloatingPointTolerance> potentialEnergyToleranceForSystem_g =
+{{
+ {
+ "argon12",
+ relativeToleranceAsPrecisionDependentUlp(-1, 10, 200)
+ },
+ {
+ "spc5",
+ relativeToleranceAsPrecisionDependentUlp(-50, 150, 3500)
+ },
+ {
+ "glycine_vacuo",
+ relativeToleranceAsPrecisionDependentUlp(1000, 100, 100)
+ },
+ {
+ "alanine_vsite_vacuo",
+ relativeToleranceAsPrecisionDependentUlp(-160, 100, 400)
+ },
+ {
+ "glycine_no_constraints_vacuo",
+ relativeToleranceAsPrecisionDependentUlp(2000, 100, 100)
+ }
+ }};
+
+TEST_P(EnergyMinimizationTest, WithinTolerances)
+{
+ auto params = GetParam();
+ auto simulationName = std::get<0>(params);
+ auto minimizer = std::get<1>(params);
+ SCOPED_TRACE(formatString("Comparing '%s' energy minimization for simulation '%s'",
+ minimizer.c_str(), simulationName.c_str()));
+
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(),
+ minimizer.c_str(),
+ "no", "no");
+ mdpFieldValues["nsteps"] = "4";
+
+ int maxWarningsTolerated = (minimizer == "l-bfgs") ? 1 : 0;
+ // prepare the .tpr file
+ {
+ // TODO evolve grompp to report the number of warnings issued, so
+ // tests always expect the right number.
+ CommandLine caller;
+ caller.append("grompp");
+ caller.addOption("-maxwarn", maxWarningsTolerated);
+ runner_.useTopGroAndNdxFromDatabase(simulationName);
+ runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ EXPECT_EQ(0, runner_.callGrompp(caller));
+ }
+
+ // do mdrun, preparing to check the energies later
+ runner_.edrFileName_ = fileManager_.getTemporaryFilePath("minimize.edr");
+ {
+ CommandLine mdrunCaller;
+ mdrunCaller.append("mdrun");
+ if (minimizer == "l-bfgs" && getNumberOfTestMpiRanks() > 1)
+ {
+ // Ideally we would use this death test, but it is not
+ // stable enough in Jenkins, so we just skip it.
+ //EXPECT_DEATH_IF_SUPPORTED(runner_.callMdrun(mdrunCaller),
+ // "L-BFGS minimization only supports a single rank");
+ return;
+ }
+ else
+ {
+ ASSERT_EQ(0, runner_.callMdrun(mdrunCaller));
+ }
+ }
+
+ EnergyTolerances energiesToMatch
+ {{
+ {
+ interaction_function[F_EPOT].longname, potentialEnergyToleranceForSystem_g.at(simulationName)
+ },
+ }};
+
+ TestReferenceData refData;
+ auto checker = refData.rootChecker()
+ .checkCompound("Simulation", simulationName)
+ .checkCompound("Minimizer", minimizer);
+ checkEnergiesAgainstReferenceData(runner_.edrFileName_,
+ energiesToMatch,
+ &checker);
+}
+
+//! Containers of systems and integrators to test.
+//! \{
+std::vector<std::string> unconstrainedSystemsToTest_g = { "argon12", "glycine_no_constraints_vacuo" };
+std::vector<std::string> minimizersToTest_g = { "steep", "cg", "l-bfgs" };
+
+std::vector<std::string> constrainedSystemsToTest_g = { "spc5", "glycine_vacuo", "alanine_vsite_vacuo" };
+std::vector<std::string> minimizersToTestWithConstraints_g = { "steep", "cg" };
+//! \}
+
+// 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.
+INSTANTIATE_TEST_CASE_P(MinimizersWorkWithConstraints, EnergyMinimizationTest,
+ ::testing::Combine(::testing::ValuesIn(constrainedSystemsToTest_g),
+ ::testing::ValuesIn(minimizersToTestWithConstraints_g)));
+INSTANTIATE_TEST_CASE_P(MinimizersWork, EnergyMinimizationTest,
+ ::testing::Combine(::testing::ValuesIn(unconstrainedSystemsToTest_g),
+ ::testing::ValuesIn(minimizersToTest_g)));
+
+} // namespace
+} // namespace test
+} // namespace gmx
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="spc5">
+ <Minimizer Name="steep">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">-9.6231425679441998</Real>
+ <Real Name="Time 1.000000 Step 1 in frame 1">-16.824484254501229</Real>
+ <Real Name="Time 2.000000 Step 2 in frame 2">-27.187878502925926</Real>
+ <Real Name="Time 3.000000 Step 3 in frame 3">-37.906539302378249</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 4">-47.991046443359224</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="spc5">
+ <Minimizer Name="cg">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">-9.6231425679441998</Real>
+ <Real Name="Time 0.000000 Step 0 in frame 1">-14.332060088206859</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 2">-55.862253955236056</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="glycine_vacuo">
+ <Minimizer Name="steep">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">2188.6237281397243</Real>
+ <Real Name="Time 1.000000 Step 1 in frame 1">1675.0453966455655</Real>
+ <Real Name="Time 2.000000 Step 2 in frame 2">1195.8320906920646</Real>
+ <Real Name="Time 3.000000 Step 3 in frame 3">739.9882576159057</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 4">319.37689948961605</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="glycine_vacuo">
+ <Minimizer Name="cg">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">2188.6237281397243</Real>
+ <Real Name="Time 0.000000 Step 0 in frame 1">1842.8583301483945</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 2">151.7430178757935</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="alanine_vsite_vacuo">
+ <Minimizer Name="steep">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">-133.03444555671706</Real>
+ <Real Name="Time 1.000000 Step 1 in frame 1">-144.65547897475835</Real>
+ <Real Name="Time 3.000000 Step 3 in frame 2">-156.9841940951402</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="alanine_vsite_vacuo">
+ <Minimizer Name="cg">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">-133.03444555671706</Real>
+ <Real Name="Time 0.000000 Step 0 in frame 1">-147.76071249343909</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 2">-169.41077894123521</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="argon12">
+ <Minimizer Name="steep">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">-0.97425707583544685</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="argon12">
+ <Minimizer Name="cg">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">-0.97425707583544685</Real>
+ <Real Name="Time 0.000000 Step 0 in frame 1">-0.99064231389395707</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="argon12">
+ <Minimizer Name="l-bfgs">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">-0.97425707583544685</Real>
+ <Real Name="Time 0.000000 Step 0 in frame 1">-0.99064231389395707</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="glycine_no_constraints_vacuo">
+ <Minimizer Name="steep">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">2195.7786482024485</Real>
+ <Real Name="Time 1.000000 Step 1 in frame 1">1676.9767708823963</Real>
+ <Real Name="Time 2.000000 Step 2 in frame 2">1197.7060676659407</Real>
+ <Real Name="Time 3.000000 Step 3 in frame 3">741.59906676238325</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 4">319.39548462989205</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="glycine_no_constraints_vacuo">
+ <Minimizer Name="cg">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">2195.7786482024485</Real>
+ <Real Name="Time 0.000000 Step 0 in frame 1">1848.1873657020258</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 2">156.25879363422524</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Simulation Name="glycine_no_constraints_vacuo">
+ <Minimizer Name="l-bfgs">
+ <Energy Name="Potential">
+ <Real Name="Time 0.000000 Step 0 in frame 0">2195.7786482024485</Real>
+ <Real Name="Time 0.000000 Step 0 in frame 1">1848.1873657020258</Real>
+ <Real Name="Time 4.000000 Step 4 in frame 2">1847.227343785434</Real>
+ </Energy>
+ </Minimizer>
+ </Simulation>
+</ReferenceData>
{
"alanine_vsite_solvated", { {
"constraints", "all-bonds"
+ },
+ {
+ "compressibility", "5e-10"
+ },
+ {
+ "tau-p", "1000"
} }
},
+ // Zwitterionic glycine in vacuo
+ {
+ "glycine_vacuo", { {
+ "constraints", "h-bonds"
+ } }
+ },
+ // Zwitterionic glycine in vacuo, without constraints
+ {
+ "glycine_no_constraints_vacuo", { {
+ "constraints", "none"
+ } }
+ },
// Nonanol molecule in vacuo, topology suitable for testing FEP
// on KE, angles, dihedral restraints, coulomb and vdw
{
* - spc216
* - alanine_vsite_vacuo
* - alanine_vsite_solvated
- * - nonanol
+ * - glycine_vacuo
+ * - glycine_no_constraints_vacuo
+ * - nonanol_vacuo
*
* Some of these systems are pretty minimal, because having
* few atoms means few interactions, highly reproducible
impl_->defaultTolerance_));
}
+TestReferenceChecker TestReferenceChecker::checkCompound(const char *type, const std::string &id)
+{
+ return checkCompound(type, id.c_str());
+}
/*! \brief Throw a TestException if the caller tries to write particular refdata that can't work.
*
* Compound structures can be nested.
*/
TestReferenceChecker checkCompound(const char *type, const char *id);
+ //! \copydoc checkCompound(const char *, const char *)
+ TestReferenceChecker checkCompound(const char *type, const std::string &id);
//! Check a single boolean value.
void checkBoolean(bool value, const char *id);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff