src/programs/mdrun/tests/pull.cpp

   1 /*
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   4  * Copyright (c) 2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35
  36 /*! \internal \file
  37  * \brief
  38  * Tests for mdrun pull functionality.
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  * \ingroup module_mdrun_integration_tests
  42  */
  43 #include "gmxpre.h"
  44
  45 #include <map>
  46 #include <memory>
  47 #include <string>
  48 #include <unordered_map>
  49 #include <vector>
  50
  51 #include <gtest/gtest.h>
  52
  53 #include "gromacs/options/filenameoption.h"
  54 #include "gromacs/topology/idef.h"
  55 #include "gromacs/topology/ifunc.h"
  56 #include "gromacs/utility/stringutil.h"
  57
  58 #include "testutils/mpitest.h"
  59 #include "testutils/refdata.h"
  60 #include "testutils/simulationdatabase.h"
  61 #include "testutils/testasserts.h"
  62
  63 #include "energycomparison.h"
  64 #include "moduletest.h"
  65
  66 namespace gmx
  67 {
  68 namespace test
  69 {
  70 namespace
  71 {
  72
  73 /*! \brief Database of energy tolerances on the various systems. */
  74 std::unordered_map<std::string, FloatingPointTolerance> energyToleranceForSystem_g = {
  75     { { "spc216", relativeToleranceAsFloatingPoint(1, 1e-4) } }
  76 };
  77
  78 /*! \brief Database of pressure tolerances on the various systems. */
  79 std::unordered_map<std::string, FloatingPointTolerance> pressureToleranceForSystem_g = {
  80     { { "spc216", relativeToleranceAsFloatingPoint(1, 2e-4) } }
  81 };
  82
  83 const std::unordered_map<std::string, std::vector<std::pair<std::string, std::string>>> c_mdpPullParams = {
  84     { { "umbrella-3D",
  85         { { "pull-ngroups", "2" },
  86           { "pull-ncoords", "1" },
  87           { "pull-nstxout", "0" },
  88           { "pull-nstfout", "0" },
  89           { "pull-group1-name", "r_1" },
  90           { "pull-group2-name", "r_2" },
  91           { "pull-coord1-groups", "1 2" },
  92           { "pull-coord1-type", "umbrella" },
  93           { "pull-coord1-geometry", "distance" },
  94           { "pull-coord1-dim", "Y Y Y" },
  95           { "pull-coord1-init", "0.6" },
  96           { "pull-coord1-k", "100" } } },
  97       { "umbrella-2D",
  98         { { "pull-ngroups", "2" },
  99           { "pull-ncoords", "1" },
 100           { "pull-nstxout", "0" },
 101           { "pull-nstfout", "0" },
 102           { "pull-group1-name", "r_1" },
 103           { "pull-group2-name", "r_2" },
 104           { "pull-coord1-groups", "1 2" },
 105           { "pull-coord1-type", "umbrella" },
 106           { "pull-coord1-geometry", "distance" },
 107           { "pull-coord1-dim", "Y Y N" },
 108           { "pull-coord1-init", "0.4" },
 109           { "pull-coord1-k", "100" } } },
 110       { "constraint-flatbottom",
 111         { { "pull-ngroups", "3" },
 112           { "pull-ncoords", "2" },
 113           { "pull-nstxout", "0" },
 114           { "pull-nstfout", "0" },
 115           { "pull-group1-name", "r_1" },
 116           { "pull-group2-name", "r_2" },
 117           { "pull-group3-name", "r_3" },
 118           { "pull-coord1-groups", "1 2" },
 119           { "pull-coord1-type", "constraint" },
 120           { "pull-coord1-geometry", "distance" },
 121           { "pull-coord1-dim", "Y Y Y" },
 122           { "pull-coord1-init", "0.5" },
 123           { "pull-coord2-groups", "1 3" },
 124           { "pull-coord2-type", "flat-bottom" },
 125           { "pull-coord2-geometry", "distance" },
 126           { "pull-coord2-dim", "Y Y Y" },
 127           { "pull-coord2-init", "0.4" },
 128           { "pull-coord2-k", "100" } } } }
 129 };
 130
 131 //! Helper type
 132 using MdpField = MdpFieldValues::value_type;
 133
 134 /*! \brief Test fixture base for simple mdrun systems
 135  *
 136  * This test ensures mdrun can run a simulation, reaching
 137  * reproducible energies.
 138  *
 139  * The choices for tolerance are arbitrary but sufficient. */
 140 class PullIntegrationTest :
 141     public MdrunTestFixture,
 142     public ::testing::WithParamInterface<std::tuple<std::string, std::string>>
 143 {
 144 };
 145
 146 //! Adds integrator and nonbonded parameter setup
 147 void addBasicMdpValues(MdpFieldValues* mdpFieldValues)
 148 {
 149     (*mdpFieldValues)["nsteps"]        = "20";
 150     (*mdpFieldValues)["nstcomm"]       = "10";
 151     (*mdpFieldValues)["nstlist"]       = "10";
 152     (*mdpFieldValues)["nstcalcenergy"] = "5";
 153     (*mdpFieldValues)["nstenergy"]     = "5";
 154     (*mdpFieldValues)["coulombtype"]   = "Reaction-field";
 155     (*mdpFieldValues)["vdwtype"]       = "Cut-off";
 156 }
 157
 158 TEST_P(PullIntegrationTest, WithinTolerances)
 159 {
 160     auto params         = GetParam();
 161     auto simulationName = std::get<0>(params);
 162     auto pullSetup      = std::get<1>(params);
 163     SCOPED_TRACE(formatString("Comparing simple mdrun for '%s'", simulationName.c_str()));
 164
 165     // TODO At some point we should also test PME-only ranks.
 166     int numRanksAvailable = getNumberOfTestMpiRanks();
 167     if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
 168     {
 169         fprintf(stdout,
 170                 "Test system '%s' cannot run with %d ranks.\n"
 171                 "The supported numbers are: %s\n",
 172                 simulationName.c_str(),
 173                 numRanksAvailable,
 174                 reportNumbersOfPpRanksSupported(simulationName).c_str());
 175         return;
 176     }
 177     auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(), "md", "no", "no");
 178     addBasicMdpValues(&mdpFieldValues);
 179
 180     // Add the pull parameters
 181     mdpFieldValues["pull"]    = "yes";
 182     const auto& mdpPullParams = c_mdpPullParams.at(pullSetup);
 183     for (const auto& param : mdpPullParams)
 184     {
 185         mdpFieldValues[param.first] = param.second;
 186     }
 187
 188     // Prepare the .tpr file
 189     {
 190         CommandLine caller;
 191         runner_.useTopGroAndNdxFromDatabase(simulationName);
 192         runner_.useNdxFromDatabase(simulationName + "_pull");
 193         runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
 194         EXPECT_EQ(0, runner_.callGrompp(caller));
 195     }
 196     // Do mdrun
 197     {
 198         CommandLine mdrunCaller;
 199         ASSERT_EQ(0, runner_.callMdrun(mdrunCaller));
 200         EnergyTermsToCompare energyTermsToCompare{ {
 201                 { interaction_function[F_COM_PULL].longname, energyToleranceForSystem_g.at(simulationName) },
 202                 { interaction_function[F_EPOT].longname, energyToleranceForSystem_g.at(simulationName) },
 203                 { interaction_function[F_EKIN].longname, energyToleranceForSystem_g.at(simulationName) },
 204                 { interaction_function[F_PRES].longname, pressureToleranceForSystem_g.at(simulationName) },
 205         } };
 206         TestReferenceData    refData;
 207         auto                 checker = refData.rootChecker()
 208                                .checkCompound("Simulation", simulationName)
 209                                .checkCompound("PullSetup", pullSetup);
 210         checkEnergiesAgainstReferenceData(runner_.edrFileName_, energyTermsToCompare, &checker);
 211     }
 212 }
 213
 214 INSTANTIATE_TEST_SUITE_P(PullTest,
 215                          PullIntegrationTest,
 216                          ::testing::Combine(::testing::Values("spc216"),
 217                                             ::testing::Values("umbrella-3D",
 218                                                               "umbrella-2D",
 219                                                               "constraint-flatbottom")));
 220
 221 } // namespace
 222 } // namespace test
 223 } // namespace gmx