/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
#include "gromacs/mdtypes/state.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
#include "gromacs/utility/unique_cptr.h"
struct EnergyOutputTestParameters
{
//! Thermostat (enum)
- int temperatureCouplingScheme;
+ TemperatureCoupling temperatureCouplingScheme;
//! Barostat (enum)
- int pressureCouplingScheme;
+ PressureCoupling pressureCouplingScheme;
//! Integrator
- int integrator;
+ IntegrationAlgorithm integrator;
//! Number of saved energy frames (to test averages output).
int numFrames;
//! If output should be initialized as a rerun.
* Only several combinations of the parameters are used. Using all possible combinations will
* require ~10 MB of test data and ~2 sec to run the tests.
*/
-const EnergyOutputTestParameters parametersSets[] = { { etcNO, epcNO, eiMD, 1, false, false },
- { etcNO, epcNO, eiMD, 1, true, false },
- { etcNO, epcNO, eiMD, 1, false, true },
- { etcNO, epcNO, eiMD, 0, false, false },
- { etcNO, epcNO, eiMD, 10, false, false },
- { etcVRESCALE, epcNO, eiMD, 1, false, false },
- { etcNOSEHOOVER, epcNO, eiMD, 1, false, false },
- { etcNO, epcPARRINELLORAHMAN, eiMD, 1, false, false },
- { etcNO, epcMTTK, eiMD, 1, false, false },
- { etcNO, epcNO, eiVV, 1, false, false },
- { etcNO, epcMTTK, eiVV, 1, false, false } };
+const EnergyOutputTestParameters parametersSets[] = {
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 1, true, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, true },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 0, false, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 10, false, false },
+ { TemperatureCoupling::VRescale, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::NoseHoover, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::ParrinelloRahman, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::Mttk, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::VV, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::Mttk, IntegrationAlgorithm::VV, 1, false, false }
+};
/*! \brief Test fixture to test energy output.
*
*/
class EnergyOutputTest : public ::testing::TestWithParam<EnergyOutputTestParameters>
{
+ int numTempCouplingGroups_ = 3;
+ real cosAccel_ = 1.0;
+
public:
//! File manager
TestFileManager fileManager_;
t_inputrec inputrec_;
//! Topology
gmx_mtop_t mtop_;
- //! MD atoms
- t_mdatoms mdatoms_;
//! Simulation time
double time_;
//! Total mass
t_state state_;
//! PBC box
matrix box_;
- //! Virial from constraints
- tensor constraintsVirial_;
- //! Virial from force computation
- tensor forceVirial_;
//! Total virial
tensor totalVirial_;
//! Pressure
std::vector<char*> groupNameHandles_;
//! Total dipole momentum
rvec muTotal_;
- //! Distance and orientation restraints data
- t_fcdata fcd_;
//! Communication record
t_commrec cr_;
//! Constraints object (for constraints RMSD output in case of LINCS)
TestReferenceChecker checker_;
EnergyOutputTest() :
+ ekindata_(numTempCouplingGroups_, cosAccel_, 1),
logFilename_(fileManager_.getTemporaryFilePath(".log")),
edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
log_(std::fopen(logFilename_.c_str(), "w")),
// Input record
inputrec_.delta_t = 0.001;
- // F_EQM
- inputrec_.bQMMM = true;
// F_RF_EXCL will not be tested - group scheme is not supported any more
- inputrec_.cutoff_scheme = ecutsVERLET;
+ inputrec_.cutoff_scheme = CutoffScheme::Verlet;
// F_COUL_RECIP
- inputrec_.coulombtype = eelPME;
+ inputrec_.coulombtype = CoulombInteractionType::Pme;
// F_LJ_RECIP
- inputrec_.vdwtype = evdwPME;
+ inputrec_.vdwtype = VanDerWaalsType::Pme;
// F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED, F_DVDL_RESTRAINT, F_DKDL and F_DVDL
- inputrec_.efep = efepYES;
- inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
- inputrec_.fepvals->separate_dvdl[efptVDW] = true;
- inputrec_.fepvals->separate_dvdl[efptBONDED] = true;
- inputrec_.fepvals->separate_dvdl[efptRESTRAINT] = true;
- inputrec_.fepvals->separate_dvdl[efptMASS] = true;
- inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
- inputrec_.fepvals->separate_dvdl[efptFEP] = true;
+ inputrec_.efep = FreeEnergyPerturbationType::Yes;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Coul] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Vdw] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Bonded] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Restraint] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Mass] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Coul] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = true;
// F_DISPCORR and F_PDISPCORR
- inputrec_.eDispCorr = edispcEner;
+ inputrec_.eDispCorr = DispersionCorrectionType::Ener;
inputrec_.bRot = true;
// F_ECONSERVED
inputrec_.ref_p[ZZ][YY] = 0.0;
// Dipole (mu)
- inputrec_.ewald_geometry = eewg3DC;
+ inputrec_.ewald_geometry = EwaldGeometry::ThreeDC;
- // GMX_CONSTRAINTVIR environment variable should also be
- // set to print constraints and force virials separately.
- gmxSetenv("GMX_CONSTRAINTVIR", "true", 1);
// To print constrain RMSD, constraints algorithm should be set to LINCS.
- inputrec_.eConstrAlg = econtLINCS;
+ inputrec_.eConstrAlg = ConstraintAlgorithm::Lincs;
mtop_.bIntermolecularInteractions = false;
mtop_.groups.groupNames.emplace_back(&handle);
}
- mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(3);
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(numTempCouplingGroups_);
mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][0] = 0;
mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][1] = 1;
mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][2] = 2;
- mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(3);
+ mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(numTempCouplingGroups_);
mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][0] = 0;
mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][1] = 1;
mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][2] = 2;
- mtop_.groups.groups[SimulationAtomGroupType::Acceleration].resize(2);
- mtop_.groups.groups[SimulationAtomGroupType::Acceleration][0] = 0;
- mtop_.groups.groups[SimulationAtomGroupType::Acceleration][1] = 2;
-
// Nose-Hoover chains
inputrec_.bPrintNHChains = true;
inputrec_.opts.nhchainlength = 2;
// Kinetic energy and related data
ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size());
- ekindata_.grpstat.resize(mtop_.groups.groups[SimulationAtomGroupType::Acceleration].size());
// This is needed so that the ebin space will be allocated
- inputrec_.cos_accel = 1.0;
- // This is to keep the destructor happy (otherwise sfree() segfaults)
- ekindata_.nthreads = 0;
- snew(ekindata_.ekin_work_alloc, 1);
- snew(ekindata_.ekin_work, 1);
- snew(ekindata_.dekindl_work, 1);
+ inputrec_.cos_accel = cosAccel_;
// Group options for annealing output
- inputrec_.opts.ngtc = 3;
+ inputrec_.opts.ngtc = numTempCouplingGroups_;
snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
- inputrec_.opts.annealing[0] = eannNO;
- inputrec_.opts.annealing[1] = eannSINGLE;
- inputrec_.opts.annealing[2] = eannPERIODIC;
+ inputrec_.opts.annealing[0] = SimulatedAnnealing::No;
+ inputrec_.opts.annealing[1] = SimulatedAnnealing::Single;
+ inputrec_.opts.annealing[2] = SimulatedAnnealing::Periodic;
// This is to keep done_inputrec happy (otherwise sfree() segfaults)
snew(inputrec_.opts.anneal_time, inputrec_.opts.ngtc);
// TODO EnergyOutput should not take Constraints object
// TODO This object will always return zero as RMSD value.
// It is more relevant to have non-zero value for testing.
- constraints_ = makeConstraints(mtop_, inputrec_, nullptr, false, nullptr, mdatoms_, &cr_,
- nullptr, nullptr, nullptr, false);
-
- // No position/orientation restraints
- fcd_.disres.npair = 0;
- fcd_.orires.nr = 0;
+ constraints_ = makeConstraints(
+ mtop_, inputrec_, nullptr, false, nullptr, &cr_, false, nullptr, nullptr, nullptr, false, nullptr);
}
/*! \brief Helper function to generate synthetic data to output
// Group pairs
for (int i = 0; i < enerdata_->grpp.nener; i++)
{
- for (int k = 0; k < egNR; k++)
+ for (int k = 0; k < static_cast<int>(NonBondedEnergyTerms::Count); k++)
{
- enerdata_->grpp.ener[k][i] = (*testValue += 0.1);
+ enerdata_->grpp.energyGroupPairTerms[k][i] = (*testValue += 0.1);
}
}
tcstat.T = (*testValue += 0.1);
tcstat.lambda = (*testValue += 0.1);
}
- for (auto& grpstat : ekindata_.grpstat)
- {
- grpstat.u[XX] = (*testValue += 0.1);
- grpstat.u[YY] = (*testValue += 0.1);
- grpstat.u[ZZ] = (*testValue += 0.1);
- }
+ // Removing constant acceleration removed a total increment of 0.6
+ // To avoid unnecessary changes in reference data, we keep the increment
+ (*testValue += 0.6);
// This conditional is to check whether the ebin was allocated.
// Otherwise it will print cosacc data into the first bin.
box_[ZZ][YY] = (*testValue += 0.1);
box_[ZZ][ZZ] = (*testValue += 0.1);
- constraintsVirial_[XX][XX] = (*testValue += 0.1);
- constraintsVirial_[XX][YY] = (*testValue += 0.1);
- constraintsVirial_[XX][ZZ] = (*testValue += 0.1);
- constraintsVirial_[YY][XX] = (*testValue += 0.1);
- constraintsVirial_[YY][YY] = (*testValue += 0.1);
- constraintsVirial_[YY][ZZ] = (*testValue += 0.1);
- constraintsVirial_[ZZ][XX] = (*testValue += 0.1);
- constraintsVirial_[ZZ][YY] = (*testValue += 0.1);
- constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1);
-
- forceVirial_[XX][XX] = (*testValue += 0.1);
- forceVirial_[XX][YY] = (*testValue += 0.1);
- forceVirial_[XX][ZZ] = (*testValue += 0.1);
- forceVirial_[YY][XX] = (*testValue += 0.1);
- forceVirial_[YY][YY] = (*testValue += 0.1);
- forceVirial_[YY][ZZ] = (*testValue += 0.1);
- forceVirial_[ZZ][XX] = (*testValue += 0.1);
- forceVirial_[ZZ][YY] = (*testValue += 0.1);
- forceVirial_[ZZ][ZZ] = (*testValue += 0.1);
+ // Removing GMX_CONSTRVIR removed a total increment of 1.8
+ // To avoid unnecessary changes in reference data, we keep the increment
+ (*testValue += 1.8);
totalVirial_[XX][XX] = (*testValue += 0.1);
totalVirial_[XX][YY] = (*testValue += 0.1);
inputrec_.ref_p[YY][XX] = 1.0;
}
- MdModulesNotifier mdModulesNotifier;
- std::unique_ptr<EnergyOutput> energyOutput = std::make_unique<EnergyOutput>(
- energyFile_, &mtop_, &inputrec_, nullptr, nullptr, parameters.isRerun,
- StartingBehavior::NewSimulation, mdModulesNotifier);
+ MDModulesNotifiers mdModulesNotifiers;
+ std::unique_ptr<EnergyOutput> energyOutput =
+ std::make_unique<EnergyOutput>(energyFile_,
+ mtop_,
+ inputrec_,
+ nullptr,
+ nullptr,
+ parameters.isRerun,
+ StartingBehavior::NewSimulation,
+ false,
+ mdModulesNotifiers);
// Add synthetic data for a single step
double testValue = 10.0;
for (int frame = 0; frame < parameters.numFrames; frame++)
{
setStepData(&testValue);
- energyOutput->addDataAtEnergyStep(false, true, time_, tmass_, enerdata_.get(), &state_, nullptr,
- nullptr, box_, constraintsVirial_, forceVirial_, totalVirial_,
- pressure_, &ekindata_, muTotal_, constraints_.get());
+ energyOutput->addDataAtEnergyStep(false,
+ true,
+ time_,
+ tmass_,
+ enerdata_.get(),
+ nullptr,
+ box_,
+ PTCouplingArrays({ state_.boxv,
+ state_.nosehoover_xi,
+ state_.nosehoover_vxi,
+ state_.nhpres_xi,
+ state_.nhpres_vxi }),
+ state_.fep_state,
+ totalVirial_,
+ pressure_,
+ &ekindata_,
+ muTotal_,
+ constraints_.get());
energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
- energyOutput->printStepToEnergyFile(energyFile_, true, false, false, log_, 100 * frame,
- time_, nullptr, nullptr);
+ energyOutput->printStepToEnergyFile(
+ energyFile_, true, false, false, log_, 100 * frame, time_, nullptr, nullptr);
time_ += 1.0;
}
checker_.checkString(TextReader::readFileToString(logFilename_), "log");
}
-INSTANTIATE_TEST_CASE_P(WithParameters, EnergyOutputTest, ::testing::ValuesIn(parametersSets));
+INSTANTIATE_TEST_SUITE_P(WithParameters, EnergyOutputTest, ::testing::ValuesIn(parametersSets));
} // namespace
} // namespace test
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff