src/gromacs/mdlib/tests/energyoutput.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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   8  *
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  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
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  35 /*! \internal \file
  36  * \brief
  37  * Tests for energy output to log and .edr files.
  38  *
  39  * \todo Position and orientation restraints tests.
  40  * \todo Average and sum in edr file test.
  41  * \todo AWH output tests.
  42  * \todo The log and edr outputs are currently saved to the file on the disk and then read
  43  *       to compare with the reference data. This will be more elegant (and run faster) when we
  44  *       refactor the output routines to write to a stream interface, which can already be handled
  45  *       in-memory when running tests.
  46  *
  47  * \author Mark Abraham <mark.j.abraham@gmail.com>
  48  * \author Artem Zhmurov <zhmurov@gmail.com>
  49  *
  50  * \ingroup module_mdlib
  51  */
  52 #include "gmxpre.h"
  53
  54 #include "gromacs/mdlib/energyoutput.h"
  55
  56 #include <cstdio>
  57
  58 #include <gtest/gtest.h>
  59
  60 #include "gromacs/mdlib/ebin.h"
  61 #include "gromacs/mdlib/makeconstraints.h"
  62 #include "gromacs/mdtypes/commrec.h"
  63 #include "gromacs/mdtypes/fcdata.h"
  64 #include "gromacs/mdtypes/group.h"
  65 #include "gromacs/mdtypes/inputrec.h"
  66 #include "gromacs/mdtypes/mdatom.h"
  67 #include "gromacs/mdtypes/state.h"
  68 #include "gromacs/topology/topology.h"
  69 #include "gromacs/utility/cstringutil.h"
  70 #include "gromacs/utility/stringutil.h"
  71 #include "gromacs/utility/textreader.h"
  72 #include "gromacs/utility/unique_cptr.h"
  73
  74 #include "testutils/refdata.h"
  75 #include "testutils/setenv.h"
  76 #include "testutils/testasserts.h"
  77 #include "testutils/testfilemanager.h"
  78
  79 namespace gmx
  80 {
  81 namespace test
  82 {
  83 namespace
  84 {
  85
  86 //! Wraps fclose to discard the return value to use it as a deleter with gmx::unique_cptr.
  87 void fcloseWrapper(FILE *fp)
  88 {
  89     fclose(fp);
  90 }
  91
  92 /*! \brief Test parameters space.
  93  *
  94  * The test will run on a set of combinations of this steucture parameters.
  95  */
  96 struct EnergyOutputTestParameters
  97 {
  98     //! Thermostat (enum)
  99     int  temperatureCouplingScheme;
 100     //! Barostat (enum)
 101     int  pressureCouplingScheme;
 102     //! Integrator
 103     int  integrator;
 104     //! Number of saved energy frames (to test averages output).
 105     int  numFrames;
 106     //! If output should be initialized as a rerun.
 107     bool isRerun;
 108     //! Is box triclinic (off-diagonal elements will be printed).
 109     bool isBoxTriclinic;
 110 };
 111
 112 /*! \brief Sets of parameters on which to run the tests.
 113  *
 114  * Only several combinations of the parameters are used. Using all possible combinations will require ~10 MB of
 115  * test data and ~2 sec to run the tests.
 116  */
 117 const EnergyOutputTestParameters parametersSets[] = {{etcNO,         epcNO,               eiMD, 1,  false, false},
 118                                                      {etcNO,         epcNO,               eiMD, 1,  true,  false},
 119                                                      {etcNO,         epcNO,               eiMD, 1,  false, true},
 120                                                      {etcNO,         epcNO,               eiMD, 0,  false, false},
 121                                                      {etcNO,         epcNO,               eiMD, 10, false, false},
 122                                                      {etcVRESCALE,   epcNO,               eiMD, 1,  false, false},
 123                                                      {etcNOSEHOOVER, epcNO,               eiMD, 1,  false, false},
 124                                                      {etcNO,         epcPARRINELLORAHMAN, eiMD, 1,  false, false},
 125                                                      {etcNO,         epcMTTK,             eiMD, 1,  false, false},
 126                                                      {etcNO,         epcNO,               eiVV, 1,  false, false},
 127                                                      {etcNO,         epcMTTK,             eiVV, 1,  false, false}};
 128
 129 /*! \brief Test fixture to test energy output.
 130  *
 131  * The class is initialized to maximize amount of energy terms printed.
 132  * The test is run for different combinations of temperature and pressure control
 133  * schemes. Different number of printed steps is also tested.
 134  */
 135 class EnergyOutputTest : public ::testing::TestWithParam<EnergyOutputTestParameters>
 136 {
 137     public:
 138         //! File manager
 139         TestFileManager                     fileManager_;
 140         //! Energy (.edr) file
 141         ener_file_t                         energyFile_;
 142         //! Input data
 143         t_inputrec                          inputrec_;
 144         //! Topology
 145         gmx_mtop_t                          mtop_;
 146         //! MD atoms
 147         t_mdatoms                           mdatoms_;
 148         //! Simulation time
 149         double                              time_;
 150         //! Total mass
 151         real                                tmass_;
 152         //! Potential energy data
 153         std::unique_ptr<gmx_enerdata_t>     enerdata_;
 154         //! Kinetic energy data (for temperatures output)
 155         gmx_ekindata_t                      ekindata_;
 156         //! System state
 157         t_state                             state_;
 158         //! PBC box
 159         matrix                              box_;
 160         //! Virial from constraints
 161         tensor                              constraintsVirial_;
 162         //! Virial from force computation
 163         tensor                              forceVirial_;
 164         //! Total virial
 165         tensor                              totalVirial_;
 166         //! Pressure
 167         tensor                              pressure_;
 168         //! Names for the groups.
 169         std::vector<std::string>            groupNameStrings_ = { "Protein", "Water", "Lipid" };
 170         //! Names for the groups as C strings.
 171         std::vector < std::vector < char>>  groupNameCStrings_;
 172         //! Handles to the names as C strings in the way needed for SimulationGroups.
 173         std::vector<char *>                 groupNameHandles_;
 174         //! Total dipole momentum
 175         rvec                                muTotal_;
 176         //! Distance and orientation restraints data
 177         t_fcdata                            fcd_;
 178         //! Communication record
 179         t_commrec                           cr_;
 180         //! Constraints object (for constraints RMSD output in case of LINCS)
 181         std::unique_ptr<Constraints>        constraints_;
 182         //! Temporary output filename
 183         std::string                         logFilename_;
 184         //! Temporary energy output filename
 185         std::string                         edrFilename_;
 186         //! Pointer to a temporary output file
 187         FILE                               *log_;
 188         //! Log file wrapper
 189         unique_cptr<FILE, fcloseWrapper>    logFileGuard_;
 190         //! Reference data
 191         TestReferenceData                   refData_;
 192         //! Checker for reference data
 193         TestReferenceChecker                checker_;
 194
 195         EnergyOutputTest() :
 196             logFilename_(fileManager_.getTemporaryFilePath(".log")),
 197             edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
 198             log_(std::fopen(logFilename_.c_str(), "w")),
 199             logFileGuard_(log_),
 200             checker_(refData_.rootChecker())
 201         {
 202             // Input record
 203             inputrec_.delta_t = 0.001;
 204
 205             // F_EQM
 206             inputrec_.bQMMM          = true;
 207             // F_RF_EXCL will not be tested - group scheme is not supported any more
 208             inputrec_.cutoff_scheme  = ecutsVERLET;
 209             // F_COUL_RECIP
 210             inputrec_.coulombtype    = eelPME;
 211             // F_LJ_RECIP
 212             inputrec_.vdwtype        = evdwPME;
 213
 214             // F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED, F_DVDL_RESTRAINT, F_DKDL and F_DVDL
 215             inputrec_.efep = efepYES;
 216             inputrec_.fepvals->separate_dvdl[efptCOUL]      = true;
 217             inputrec_.fepvals->separate_dvdl[efptVDW]       = true;
 218             inputrec_.fepvals->separate_dvdl[efptBONDED]    = true;
 219             inputrec_.fepvals->separate_dvdl[efptRESTRAINT] = true;
 220             inputrec_.fepvals->separate_dvdl[efptMASS]      = true;
 221             inputrec_.fepvals->separate_dvdl[efptCOUL]      = true;
 222             inputrec_.fepvals->separate_dvdl[efptFEP]       = true;
 223
 224             // F_DISPCORR and F_PDISPCORR
 225             inputrec_.eDispCorr       = edispcEner;
 226             inputrec_.bRot            = true;
 227
 228             // F_ECONSERVED
 229             inputrec_.ref_p[YY][XX]   = 0.0;
 230             inputrec_.ref_p[ZZ][XX]   = 0.0;
 231             inputrec_.ref_p[ZZ][YY]   = 0.0;
 232
 233             // Dipole (mu)
 234             inputrec_.ewald_geometry  = eewg3DC;
 235
 236             // GMX_CONSTRAINTVIR environment variable should also be
 237             // set to print constraints and force virials separately.
 238             gmxSetenv("GMX_CONSTRAINTVIR", "true", 1);
 239             // To print constrain RMSD, constraints algorithm should be set to LINCS.
 240             inputrec_.eConstrAlg = econtLINCS;
 241
 242             mtop_.bIntermolecularInteractions = false;
 243
 244             // Constructing molecular topology
 245             gmx_moltype_t molType;
 246
 247             molType.atoms.nr = 2;
 248
 249             // F_CONSTR
 250             // This must be initialized so that Constraints object can be created below.
 251             InteractionList interactionListConstr;
 252             interactionListConstr.iatoms.resize(NRAL(F_CONSTR) + 1);
 253             interactionListConstr.iatoms[0] = 0;
 254             interactionListConstr.iatoms[1] = 0;
 255             interactionListConstr.iatoms[2] = 1;
 256             molType.ilist.at(F_CONSTR)      = interactionListConstr;
 257
 258             InteractionList interactionListEmpty;
 259             interactionListEmpty.iatoms.resize(0);
 260             molType.ilist.at(F_CONSTRNC)   = interactionListEmpty;
 261             molType.ilist.at(F_SETTLE)     = interactionListEmpty;
 262
 263             // F_LJ14 and F_COUL14
 264             InteractionList interactionListLJ14;
 265             interactionListLJ14.iatoms.resize(NRAL(F_LJ14) + 1);
 266             molType.ilist.at(F_LJ14)     = interactionListLJ14;
 267
 268             // F_LJC14_Q
 269             InteractionList interactionListLJC14Q;
 270             interactionListLJC14Q.iatoms.resize(NRAL(F_LJC14_Q) + 1);
 271             molType.ilist.at(F_LJC14_Q)  = interactionListLJC14Q;
 272
 273             // TODO Do proper initialization for distance and orientation
 274             //      restraints and remove comments to enable their output
 275             // F_DISRES
 276             //InteractionList interactionListDISRES;
 277             //interactionListDISRES.iatoms.resize(NRAL(F_DISRES) + 1);
 278             //molType.ilist.at(F_DISRES)   = interactionListDISRES;
 279             //
 280             // F_ORIRES
 281             //InteractionList interactionListORIRES;
 282             //interactionListORIRES.iatoms.resize(NRAL(F_ORIRES) + 1);
 283             //molType.ilist.at(F_ORIRES)   = interactionListORIRES;
 284
 285             mtop_.moltype.push_back(molType);
 286
 287             gmx_molblock_t molBlock;
 288             molBlock.type = 0;
 289             molBlock.nmol = 1;
 290             mtop_.molblock.push_back(molBlock);
 291
 292             // This is to keep constraints initialization happy
 293             mtop_.natoms = 2;
 294             mtop_.ffparams.iparams.resize(F_NRE);
 295             mtop_.ffparams.functype.resize(F_NRE);
 296             mtop_.ffparams.iparams.at(F_CONSTR).constr.dA   = 1.0;
 297             mtop_.ffparams.iparams.at(F_CONSTR).constr.dB   = 1.0;
 298             mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dA = 1.0;
 299             mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dB = 1.0;
 300
 301             // Groups for energy output, temperature coupling and acceleration
 302             for (const auto &string : groupNameStrings_)
 303             {
 304                 std::vector<char> cString(string.begin(), string.end());
 305                 // Need to add null termination
 306                 cString.push_back('\0');
 307                 groupNameCStrings_.emplace_back(cString);
 308                 groupNameHandles_.emplace_back(groupNameCStrings_.back().data());
 309             }
 310             for (auto &handle : groupNameHandles_)
 311             {
 312                 mtop_.groups.groupNames.emplace_back(&handle);
 313             }
 314
 315             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(3);
 316             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][0] = 0;
 317             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][1] = 1;
 318             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][2] = 2;
 319
 320             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(3);
 321             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][0] = 0;
 322             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][1] = 1;
 323             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][2] = 2;
 324
 325             mtop_.groups.groups[SimulationAtomGroupType::Acceleration].resize(2);
 326             mtop_.groups.groups[SimulationAtomGroupType::Acceleration][0] = 0;
 327             mtop_.groups.groups[SimulationAtomGroupType::Acceleration][1] = 2;
 328
 329             // Nose-Hoover chains
 330             inputrec_.bPrintNHChains     = true;
 331             inputrec_.opts.nhchainlength = 2;
 332             state_.nosehoover_xi.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()*inputrec_.opts.nhchainlength);
 333             state_.nosehoover_vxi.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()*inputrec_.opts.nhchainlength);
 334
 335             // This will be needed only with MTTK barostat
 336             state_.nhpres_xi.resize(1*inputrec_.opts.nhchainlength);
 337             state_.nhpres_vxi.resize(1*inputrec_.opts.nhchainlength);
 338
 339             // Group pairs
 340             enerdata_ = std::make_unique<gmx_enerdata_t>(mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].size(), 0);
 341
 342             // Kinetic energy and related data
 343             ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size());
 344             ekindata_.grpstat.resize(mtop_.groups.groups[SimulationAtomGroupType::Acceleration].size());
 345
 346             // This is needed so that the ebin space will be allocated
 347             inputrec_.cos_accel = 1.0;
 348             // This is to keep the destructor happy (otherwise sfree() segfaults)
 349             ekindata_.nthreads = 0;
 350             snew(ekindata_.ekin_work_alloc, 1);
 351             snew(ekindata_.ekin_work, 1);
 352             snew(ekindata_.dekindl_work, 1);
 353
 354             // Group options for annealing output
 355             inputrec_.opts.ngtc = 3;
 356             snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
 357             snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
 358             inputrec_.opts.annealing[0] = eannNO;
 359             inputrec_.opts.annealing[1] = eannSINGLE;
 360             inputrec_.opts.annealing[2] = eannPERIODIC;
 361
 362             // This is to keep done_inputrec happy (otherwise sfree() segfaults)
 363             snew(inputrec_.opts.anneal_time, inputrec_.opts.ngtc);
 364             snew(inputrec_.opts.anneal_temp, inputrec_.opts.ngtc);
 365
 366             // Communication record (for Constraints constructor)
 367             cr_.nnodes = 1;
 368             cr_.dd     = nullptr;
 369
 370             // Constraints object (to get constraints RMSD from)
 371             // TODO EnergyOutput should not take Constraints object
 372             // TODO This object will always return zero as RMSD value.
 373             //      It is more relevant to have non-zero value for testing.
 374             constraints_ = makeConstraints(mtop_, inputrec_, nullptr, false, nullptr, mdatoms_, &cr_,
 375                                            nullptr, nullptr, nullptr, false);
 376
 377             // No position/orientation restraints
 378             fcd_.disres.npair  = 0;
 379             fcd_.orires.nr     = 0;
 380
 381         }
 382
 383         /*! \brief Helper function to generate synthetic data to output
 384          *
 385          * \param[in,out] testValue    Base value fr energy data.
 386          */
 387         void setStepData(double *testValue)
 388         {
 389
 390             time_                             = (*testValue += 0.1);
 391             tmass_                            = (*testValue += 0.1);
 392
 393             enerdata_->term[F_LJ]             = (*testValue += 0.1);
 394             enerdata_->term[F_COUL_SR]        = (*testValue += 0.1);
 395             enerdata_->term[F_EPOT]           = (*testValue += 0.1);
 396             enerdata_->term[F_EKIN]           = (*testValue += 0.1);
 397             enerdata_->term[F_ETOT]           = (*testValue += 0.1);
 398             enerdata_->term[F_TEMP]           = (*testValue += 0.1);
 399             enerdata_->term[F_PRES]           = (*testValue += 0.1);
 400
 401             enerdata_->term[F_BHAM]           = (*testValue += 0.1);
 402             enerdata_->term[F_EQM]            = (*testValue += 0.1);
 403             enerdata_->term[F_RF_EXCL]        = (*testValue += 0.1);
 404             enerdata_->term[F_COUL_RECIP]     = (*testValue += 0.1);
 405             enerdata_->term[F_LJ_RECIP]       = (*testValue += 0.1);
 406             enerdata_->term[F_LJ14]           = (*testValue += 0.1);
 407             enerdata_->term[F_COUL14]         = (*testValue += 0.1);
 408             enerdata_->term[F_LJC14_Q]        = (*testValue += 0.1);
 409             enerdata_->term[F_LJC_PAIRS_NB]   = (*testValue += 0.1);
 410
 411             enerdata_->term[F_DVDL_COUL]      = (*testValue += 0.1);
 412             enerdata_->term[F_DVDL_VDW]       = (*testValue += 0.1);
 413             enerdata_->term[F_DVDL_BONDED]    = (*testValue += 0.1);
 414             enerdata_->term[F_DVDL_RESTRAINT] = (*testValue += 0.1);
 415             enerdata_->term[F_DKDL]           = (*testValue += 0.1);
 416             enerdata_->term[F_DVDL]           = (*testValue += 0.1);
 417
 418             enerdata_->term[F_DISPCORR]       = (*testValue += 0.1);
 419             enerdata_->term[F_PDISPCORR]      = (*testValue += 0.1);
 420             enerdata_->term[F_DISRESVIOL]     = (*testValue += 0.1);
 421             enerdata_->term[F_ORIRESDEV]      = (*testValue += 0.1);
 422             enerdata_->term[F_COM_PULL]       = (*testValue += 0.1);
 423             enerdata_->term[F_ECONSERVED]     = (*testValue += 0.1);
 424
 425             // Group pairs
 426             for (int i = 0; i < enerdata_->grpp.nener; i++)
 427             {
 428                 for (int k = 0; k < egNR; k++)
 429                 {
 430                     enerdata_->grpp.ener[k][i] = (*testValue += 0.1);
 431                 }
 432             }
 433
 434             // Kinetic energy and related data
 435             for (auto &tcstat : ekindata_.tcstat)
 436             {
 437                 tcstat.T      = (*testValue += 0.1);
 438                 tcstat.lambda = (*testValue += 0.1);
 439             }
 440             for (auto &grpstat : ekindata_.grpstat)
 441             {
 442                 grpstat.u[XX] = (*testValue += 0.1);
 443                 grpstat.u[YY] = (*testValue += 0.1);
 444                 grpstat.u[ZZ] = (*testValue += 0.1);
 445             }
 446
 447             // This conditional is to check whether the ebin was allocated.
 448             // Otherwise it will print cosacc data into the first bin.
 449             if (inputrec_.cos_accel != 0)
 450             {
 451                 ekindata_.cosacc.cos_accel = (*testValue += 0.1);
 452                 ekindata_.cosacc.vcos      = (*testValue += 0.1);
 453             }
 454
 455             state_.box[XX][XX]         = (*testValue += 0.1);
 456             state_.box[XX][YY]         = (*testValue += 0.1);
 457             state_.box[XX][ZZ]         = (*testValue += 0.1);
 458             state_.box[YY][XX]         = (*testValue += 0.1);
 459             state_.box[YY][YY]         = (*testValue += 0.1);
 460             state_.box[YY][ZZ]         = (*testValue += 0.1);
 461             state_.box[ZZ][XX]         = (*testValue += 0.1);
 462             state_.box[ZZ][YY]         = (*testValue += 0.1);
 463             state_.box[ZZ][ZZ]         = (*testValue += 0.1);
 464
 465             box_[XX][XX]               = (*testValue += 0.1);
 466             box_[XX][YY]               = (*testValue += 0.1);
 467             box_[XX][ZZ]               = (*testValue += 0.1);
 468             box_[YY][XX]               = (*testValue += 0.1);
 469             box_[YY][YY]               = (*testValue += 0.1);
 470             box_[YY][ZZ]               = (*testValue += 0.1);
 471             box_[ZZ][XX]               = (*testValue += 0.1);
 472             box_[ZZ][YY]               = (*testValue += 0.1);
 473             box_[ZZ][ZZ]               = (*testValue += 0.1);
 474
 475             constraintsVirial_[XX][XX] = (*testValue += 0.1);
 476             constraintsVirial_[XX][YY] = (*testValue += 0.1);
 477             constraintsVirial_[XX][ZZ] = (*testValue += 0.1);
 478             constraintsVirial_[YY][XX] = (*testValue += 0.1);
 479             constraintsVirial_[YY][YY] = (*testValue += 0.1);
 480             constraintsVirial_[YY][ZZ] = (*testValue += 0.1);
 481             constraintsVirial_[ZZ][XX] = (*testValue += 0.1);
 482             constraintsVirial_[ZZ][YY] = (*testValue += 0.1);
 483             constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1);
 484
 485             forceVirial_[XX][XX]       = (*testValue += 0.1);
 486             forceVirial_[XX][YY]       = (*testValue += 0.1);
 487             forceVirial_[XX][ZZ]       = (*testValue += 0.1);
 488             forceVirial_[YY][XX]       = (*testValue += 0.1);
 489             forceVirial_[YY][YY]       = (*testValue += 0.1);
 490             forceVirial_[YY][ZZ]       = (*testValue += 0.1);
 491             forceVirial_[ZZ][XX]       = (*testValue += 0.1);
 492             forceVirial_[ZZ][YY]       = (*testValue += 0.1);
 493             forceVirial_[ZZ][ZZ]       = (*testValue += 0.1);
 494
 495             totalVirial_[XX][XX]       = (*testValue += 0.1);
 496             totalVirial_[XX][YY]       = (*testValue += 0.1);
 497             totalVirial_[XX][ZZ]       = (*testValue += 0.1);
 498             totalVirial_[YY][XX]       = (*testValue += 0.1);
 499             totalVirial_[YY][YY]       = (*testValue += 0.1);
 500             totalVirial_[YY][ZZ]       = (*testValue += 0.1);
 501             totalVirial_[ZZ][XX]       = (*testValue += 0.1);
 502             totalVirial_[ZZ][YY]       = (*testValue += 0.1);
 503             totalVirial_[ZZ][ZZ]       = (*testValue += 0.1);
 504
 505             pressure_[XX][XX]          = (*testValue += 0.1);
 506             pressure_[XX][YY]          = (*testValue += 0.1);
 507             pressure_[XX][ZZ]          = (*testValue += 0.1);
 508             pressure_[YY][XX]          = (*testValue += 0.1);
 509             pressure_[YY][YY]          = (*testValue += 0.1);
 510             pressure_[YY][ZZ]          = (*testValue += 0.1);
 511             pressure_[ZZ][XX]          = (*testValue += 0.1);
 512             pressure_[ZZ][YY]          = (*testValue += 0.1);
 513             pressure_[ZZ][ZZ]          = (*testValue += 0.1);
 514
 515             muTotal_[XX]               = (*testValue += 0.1);
 516             muTotal_[YY]               = (*testValue += 0.1);
 517             muTotal_[ZZ]               = (*testValue += 0.1);
 518
 519             state_.boxv[XX][XX]        = (*testValue += 0.1);
 520             state_.boxv[XX][YY]        = (*testValue += 0.1);
 521             state_.boxv[XX][ZZ]        = (*testValue += 0.1);
 522             state_.boxv[YY][XX]        = (*testValue += 0.1);
 523             state_.boxv[YY][YY]        = (*testValue += 0.1);
 524             state_.boxv[YY][ZZ]        = (*testValue += 0.1);
 525             state_.boxv[ZZ][XX]        = (*testValue += 0.1);
 526             state_.boxv[ZZ][YY]        = (*testValue += 0.1);
 527             state_.boxv[ZZ][ZZ]        = (*testValue += 0.1);
 528
 529             for (int i = 0; i < inputrec_.opts.ngtc; i++)
 530             {
 531                 inputrec_.opts.ref_t[i] = (*testValue += 0.1);
 532             }
 533
 534             for (index k = 0; k < ssize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling])*inputrec_.opts.nhchainlength; k++)
 535             {
 536                 state_.nosehoover_xi[k]  = (*testValue += 0.1);
 537                 state_.nosehoover_vxi[k] = (*testValue += 0.1);
 538             }
 539             for (int k = 0; k < inputrec_.opts.nhchainlength; k++)
 540             {
 541                 state_.nhpres_xi[k]  = (*testValue += 0.1);
 542                 state_.nhpres_vxi[k] = (*testValue += 0.1);
 543             }
 544
 545         }
 546
 547         /*! \brief Check if the contents of the .edr file correspond to the reference data.
 548          *
 549          * The code below is based on the 'gmx dump' tool.
 550          *
 551          * \param[in] fileName    Name of the file to check.
 552          * \param[in] frameCount  Number of frames to check.
 553          */
 554         void checkEdrFile(const char *fileName, int frameCount)
 555         {
 556             ener_file_t    edrFile;
 557             gmx_enxnm_t   *energyTermsEdr = nullptr;
 558             int            numEnergyTermsEdr;
 559
 560             edrFile = open_enx(fileName, "r");
 561             do_enxnms(edrFile, &numEnergyTermsEdr, &energyTermsEdr);
 562             assert(energyTermsEdr);
 563
 564             // Check header
 565             TestReferenceChecker edrFileRef(checker_.checkCompound("File", "EnergyFile"));
 566             TestReferenceChecker energyTermsRef(edrFileRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
 567             for (int i = 0; i < numEnergyTermsEdr; i++)
 568             {
 569                 TestReferenceChecker energyTermRef(energyTermsRef.checkCompound("EnergyTerm", nullptr));
 570                 energyTermRef.checkString(energyTermsEdr[i].name, "Name");
 571                 energyTermRef.checkString(energyTermsEdr[i].unit, "Units");
 572             }
 573
 574             // Check frames
 575             TestReferenceChecker framesRef(edrFileRef.checkSequenceCompound("Frames", frameCount));
 576             t_enxframe          *frameEdr;
 577             snew(frameEdr, 1);
 578             char                 buffer[22];
 579             for (int frameId = 0; frameId < frameCount; frameId++)
 580             {
 581                 bool bCont = do_enx(edrFile, frameEdr);
 582                 EXPECT_TRUE(bCont) << gmx::formatString("Cant read frame %d from .edr file.", frameId);
 583
 584                 TestReferenceChecker frameRef(framesRef.checkCompound("Frame", nullptr));
 585                 frameRef.checkReal(frameEdr->t, "Time");
 586                 frameRef.checkReal(frameEdr->dt, "Timestep");
 587                 frameRef.checkString(gmx_step_str(frameEdr->step, buffer), "Step");
 588                 frameRef.checkString(gmx_step_str(frameEdr->nsum, buffer), "NumSteps");
 589
 590                 EXPECT_EQ(frameEdr->nre, numEnergyTermsEdr) << gmx::formatString("Wrong number of energy terms in frame %d.", frameId);
 591                 TestReferenceChecker energyValuesRef(frameRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
 592                 for (int i = 0; i < numEnergyTermsEdr; i++)
 593                 {
 594                     TestReferenceChecker energyValueRef(energyValuesRef.checkCompound("EnergyTerm", nullptr));
 595                     energyValueRef.checkString(energyTermsEdr[i].name, "Name");
 596                     energyValueRef.checkReal(frameEdr->ener[i].e, "Value");
 597                 }
 598             }
 599
 600             free_enxnms(numEnergyTermsEdr, energyTermsEdr);
 601             done_ener_file(edrFile);
 602
 603             free_enxframe(frameEdr);
 604             sfree(frameEdr);
 605         }
 606
 607 };
 608
 609 TEST_P(EnergyOutputTest, CheckOutput)
 610 {
 611     ASSERT_NE(log_, nullptr);
 612     // Binary output will be written to the temporary location
 613     energyFile_ = open_enx(edrFilename_.c_str(), "w");
 614     ASSERT_NE(energyFile_, nullptr);
 615
 616     EnergyOutputTestParameters parameters = GetParam();
 617     inputrec_.etc = parameters.temperatureCouplingScheme;
 618     inputrec_.epc = parameters.pressureCouplingScheme;
 619     inputrec_.eI  = parameters.integrator;
 620
 621     if (parameters.isBoxTriclinic)
 622     {
 623         inputrec_.ref_p[YY][XX]   = 1.0;
 624     }
 625
 626     std::unique_ptr<EnergyOutput> energyOutput = std::make_unique<EnergyOutput>(energyFile_, &mtop_, &inputrec_, nullptr, nullptr, parameters.isRerun);
 627
 628     // Add synthetic data for a single step
 629     double testValue = 10.0;
 630     for (int frame = 0; frame < parameters.numFrames; frame++)
 631     {
 632         setStepData(&testValue);
 633         energyOutput->addDataAtEnergyStep(false, true, time_, tmass_, enerdata_.get(),
 634                                           &state_, nullptr, nullptr, box_,
 635                                           constraintsVirial_, forceVirial_, totalVirial_, pressure_,
 636                                           &ekindata_, muTotal_, constraints_.get());
 637
 638         energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
 639         energyOutput->printStepToEnergyFile(energyFile_, true, false, false, log_,
 640                                             100*frame, time_,
 641                                             nullptr, nullptr);
 642         time_ += 1.0;
 643     }
 644
 645     energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
 646     energyOutput->printAverages(log_, &mtop_.groups);
 647
 648     // We need to close the file before the contents are available.
 649     logFileGuard_.reset(nullptr);
 650
 651     done_ener_file(energyFile_);
 652
 653     // Set tolerance
 654     checker_.setDefaultTolerance(relativeToleranceAsFloatingPoint(testValue, 1.0e-5));
 655
 656     if (parameters.numFrames > 0)
 657     {
 658         // Test binary output
 659         checkEdrFile(edrFilename_.c_str(), parameters.numFrames);
 660     }
 661
 662     // Test printed values
 663     checker_.checkInteger(energyOutput->numEnergyTerms(), "Number of Energy Terms");
 664     checker_.checkString(TextReader::readFileToString(logFilename_), "log");
 665 }
 666
 667 INSTANTIATE_TEST_CASE_P(WithParameters, EnergyOutputTest,
 668                             ::testing::ValuesIn(parametersSets));
 669
 670 }  // namespace
 671 }  // namespace test
 672 }  // namespace gmx