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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  11  * as published by the Free Software Foundation; either version 2.1
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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 "config.h"
  57
  58 #include <cstdio>
  59 #include <cstdlib>
  60
  61 #include <gtest/gtest.h>
  62
  63 #include "gromacs/mdlib/ebin.h"
  64 #include "gromacs/mdlib/makeconstraints.h"
  65 #include "gromacs/mdtypes/commrec.h"
  66 #include "gromacs/mdtypes/fcdata.h"
  67 #include "gromacs/mdtypes/group.h"
  68 #include "gromacs/mdtypes/inputrec.h"
  69 #include "gromacs/mdtypes/mdatom.h"
  70 #include "gromacs/mdtypes/state.h"
  71 #include "gromacs/topology/topology.h"
  72 #include "gromacs/utility/cstringutil.h"
  73 #include "gromacs/utility/stringutil.h"
  74 #include "gromacs/utility/textreader.h"
  75 #include "gromacs/utility/unique_cptr.h"
  76
  77 #include "testutils/refdata.h"
  78 #include "testutils/testasserts.h"
  79 #include "testutils/testfilemanager.h"
  80
  81 namespace gmx
  82 {
  83 namespace test
  84 {
  85 namespace
  86 {
  87
  88 //! Wraps fclose to discard the return value to use it as a deleter with gmx::unique_cptr.
  89 void fcloseWrapper(FILE *fp)
  90 {
  91     fclose(fp);
  92 }
  93
  94 /*! \brief Test parameters space.
  95  *
  96  * The test will run on a set of combinations of this steucture parameters.
  97  */
  98 struct EnergyOutputTestParameters
  99 {
 100     //! If output should be initialized as a rerun.
 101     bool isRerun;
 102     //! Thermostat (enum)
 103     int  temperatureCouplingScheme;
 104     //! Barostat (enum)
 105     int  pressureCouplingScheme;
 106     //! Integrator
 107     int  integrator;
 108     //! Is box triclinic (off-diagonal elements will be printed).
 109     bool isBoxTriclinic;
 110     //! Number of saved energy frames (to test averages output).
 111     int  numFrames;
 112 };
 113
 114 /*! \brief Sets of parameters on which to run the tests.
 115  *
 116  * Only several combinations of the parameters are used. Using all possible combinations will require ~10 MB of
 117  * test data and ~2 sec to run the tests.
 118  */
 119 const EnergyOutputTestParameters parametersSets[] = {{false, etcNO,         epcNO,               eiMD, false, 1},
 120                                                      {true,  etcNO,         epcNO,               eiMD, false, 1},
 121                                                      {false, etcNO,         epcNO,               eiMD, true,  1},
 122                                                      {false, etcNO,         epcNO,               eiMD, false, 0},
 123                                                      {false, etcNO,         epcNO,               eiMD, false, 10},
 124                                                      {false, etcVRESCALE,   epcNO,               eiMD, false, 1},
 125                                                      {false, etcNOSEHOOVER, epcNO,               eiMD, false, 1},
 126                                                      {false, etcNO,         epcPARRINELLORAHMAN, eiMD, false, 1},
 127                                                      {false, etcNO,         epcMTTK,             eiMD, false, 1},
 128                                                      {false, etcNO,         epcNO,               eiVV, false, 1},
 129                                                      {false, etcNO,         epcMTTK,             eiVV, false, 1}};
 130
 131 /*! \brief Test fixture to test energy output.
 132  *
 133  * The class is initialized to maximize amount of energy terms printed.
 134  * The test is run for different combinations of temperature and pressure control
 135  * schemes. Different number of printed steps is also tested.
 136  */
 137 class EnergyOutputTest : public ::testing::TestWithParam<EnergyOutputTestParameters>
 138 {
 139     public:
 140         //! File manager
 141         TestFileManager                     fileManager_;
 142         //! Energy (.edr) file
 143         ener_file_t                         energyFile_;
 144         //! Input data
 145         t_inputrec                          inputrec_;
 146         //! Topology
 147         gmx_mtop_t                          mtop_;
 148         //! Energy output object
 149         EnergyOutput                        energyOutput_;
 150         //! MD atoms
 151         t_mdatoms                           mdatoms_;
 152         //! Simulation time
 153         double                              time_;
 154         //! Total mass
 155         real                                tmass_;
 156         //! Potential energy data
 157         std::unique_ptr<gmx_enerdata_t>     enerdata_;
 158         //! Kinetic energy data (for temperatures output)
 159         gmx_ekindata_t                      ekindata_;
 160         //! System state
 161         t_state                             state_;
 162         //! PBC box
 163         matrix                              box_;
 164         //! Virial from constraints
 165         tensor                              constraintsVirial_;
 166         //! Virial from force computation
 167         tensor                              forceVirial_;
 168         //! Total virial
 169         tensor                              totalVirial_;
 170         //! Pressure
 171         tensor                              pressure_;
 172         //! Names for the groups.
 173         std::vector<std::string>            groupNameStrings_ = { "Protein", "Water", "Lipid" };
 174         //! Names for the groups as C strings.
 175         std::vector < std::vector < char>>  groupNameCStrings_;
 176         //! Handles to the names as C strings in the way needed for SimulationGroups.
 177         std::vector<char *>                 groupNameHandles_;
 178         //! Total dipole momentum
 179         rvec                                muTotal_;
 180         //! Distance and orientation restraints data
 181         t_fcdata                            fcd_;
 182         //! Communication record
 183         t_commrec                           cr_;
 184         //! Constraints object (for constraints RMSD output in case of LINCS)
 185         std::unique_ptr<Constraints>        constraints_;
 186         //! \brief Temporary output filename
 187         std::string                         logFilename_;
 188         //! Temporary energy output filename
 189         std::string                         edrFilename_;
 190         //! Pointer to a temporary output file
 191         FILE                               *log_;
 192         //! Log file wrapper
 193         unique_cptr<FILE, fcloseWrapper>    logFileGuard_;
 194         //! Reference data
 195         TestReferenceData                   refData_;
 196         //! Checker for reference data
 197         TestReferenceChecker                checker_;
 198
 199         EnergyOutputTest() :
 200             logFilename_(fileManager_.getTemporaryFilePath(".log")),
 201             edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
 202             log_(std::fopen(logFilename_.c_str(), "w")),
 203             logFileGuard_(log_),
 204             checker_(refData_.rootChecker())
 205         {
 206             // Input record
 207             inputrec_.delta_t = 0.001;
 208
 209             // F_EQM
 210             inputrec_.bQMMM          = true;
 211             // F_RF_EXCL will not be tested - group scheme is not supported any more
 212             inputrec_.cutoff_scheme  = ecutsVERLET;
 213             // F_COUL_RECIP
 214             inputrec_.coulombtype    = eelPME;
 215             // F_LJ_RECIP
 216             inputrec_.vdwtype        = evdwPME;
 217
 218             // F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED, F_DVDL_RESTRAINT, F_DKDL and F_DVDL
 219             inputrec_.efep = efepYES;
 220             inputrec_.fepvals->separate_dvdl[efptCOUL]      = true;
 221             inputrec_.fepvals->separate_dvdl[efptVDW]       = true;
 222             inputrec_.fepvals->separate_dvdl[efptBONDED]    = true;
 223             inputrec_.fepvals->separate_dvdl[efptRESTRAINT] = true;
 224             inputrec_.fepvals->separate_dvdl[efptMASS]      = true;
 225             inputrec_.fepvals->separate_dvdl[efptCOUL]      = true;
 226             inputrec_.fepvals->separate_dvdl[efptFEP]       = true;
 227
 228             // F_DISPCORR and F_PDISPCORR
 229             inputrec_.eDispCorr       = edispcEner;
 230             inputrec_.bRot            = true;
 231
 232             // F_ECONSERVED
 233             inputrec_.ref_p[YY][XX]   = 0.0;
 234             inputrec_.ref_p[ZZ][XX]   = 0.0;
 235             inputrec_.ref_p[ZZ][YY]   = 0.0;
 236
 237             // Dipole (mu)
 238             inputrec_.ewald_geometry  = eewg3DC;
 239
 240             // GMX_CONSTRAINTVIR environment variable should also be
 241             // set to print constraints and force virials separately.
 242             //
 243             // TODO extract a helper function if we ever need to do
 244             // this kind of thing again.
 245 #if GMX_NATIVE_WINDOWS
 246             _putenv_s("GMX_CONSTRAINTVIR", "true");
 247 #else
 248             setenv("GMX_CONSTRAINTVIR", "true", 1);
 249 #endif
 250             // To print constrain RMSD, constraints algorithm should be set to LINCS.
 251             inputrec_.eConstrAlg = econtLINCS;
 252
 253             mtop_.bIntermolecularInteractions = false;
 254
 255             // Constructing molecular topology
 256             gmx_moltype_t molType;
 257
 258             molType.atoms.nr = 2;
 259
 260             // F_CONSTR
 261             // This must be initialized so that Constraints object can be created below.
 262             InteractionList interactionListConstr;
 263             interactionListConstr.iatoms.resize(NRAL(F_CONSTR) + 1);
 264             interactionListConstr.iatoms[0] = 0;
 265             interactionListConstr.iatoms[1] = 0;
 266             interactionListConstr.iatoms[2] = 1;
 267             molType.ilist.at(F_CONSTR)      = interactionListConstr;
 268
 269             InteractionList interactionListEmpty;
 270             interactionListEmpty.iatoms.resize(0);
 271             molType.ilist.at(F_CONSTRNC)   = interactionListEmpty;
 272             molType.ilist.at(F_SETTLE)     = interactionListEmpty;
 273
 274             // F_LJ14 and F_COUL14
 275             InteractionList interactionListLJ14;
 276             interactionListLJ14.iatoms.resize(NRAL(F_LJ14) + 1);
 277             molType.ilist.at(F_LJ14)     = interactionListLJ14;
 278
 279             // F_LJC14_Q
 280             InteractionList interactionListLJC14Q;
 281             interactionListLJC14Q.iatoms.resize(NRAL(F_LJC14_Q) + 1);
 282             molType.ilist.at(F_LJC14_Q)  = interactionListLJC14Q;
 283
 284             // TODO Do proper initialization for distance and orientation
 285             //      restraints and remove comments to enable their output
 286             // F_DISRES
 287             //InteractionList interactionListDISRES;
 288             //interactionListDISRES.iatoms.resize(NRAL(F_DISRES) + 1);
 289             //molType.ilist.at(F_DISRES)   = interactionListDISRES;
 290             //
 291             // F_ORIRES
 292             //InteractionList interactionListORIRES;
 293             //interactionListORIRES.iatoms.resize(NRAL(F_ORIRES) + 1);
 294             //molType.ilist.at(F_ORIRES)   = interactionListORIRES;
 295
 296             mtop_.moltype.push_back(molType);
 297
 298             gmx_molblock_t molBlock;
 299             molBlock.type = 0;
 300             molBlock.nmol = 1;
 301             mtop_.molblock.push_back(molBlock);
 302
 303             // This is to keep constraints initialization happy
 304             mtop_.natoms = 2;
 305             mtop_.ffparams.iparams.resize(F_NRE);
 306             mtop_.ffparams.functype.resize(F_NRE);
 307             mtop_.ffparams.iparams.at(F_CONSTR).constr.dA   = 1.0;
 308             mtop_.ffparams.iparams.at(F_CONSTR).constr.dB   = 1.0;
 309             mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dA = 1.0;
 310             mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dB = 1.0;
 311
 312             // Groups for energy output, temperature coupling and acceleration
 313             for (const auto &string : groupNameStrings_)
 314             {
 315                 std::vector<char> cString(string.begin(), string.end());
 316                 // Need to add null termination
 317                 cString.push_back('\0');
 318                 groupNameCStrings_.emplace_back(cString);
 319                 groupNameHandles_.emplace_back(groupNameCStrings_.back().data());
 320             }
 321             for (auto &handle : groupNameHandles_)
 322             {
 323                 mtop_.groups.groupNames.emplace_back(&handle);
 324             }
 325
 326             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(3);
 327             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][0] = 0;
 328             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][1] = 1;
 329             mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][2] = 2;
 330
 331             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(3);
 332             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][0] = 0;
 333             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][1] = 1;
 334             mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][2] = 2;
 335
 336             mtop_.groups.groups[SimulationAtomGroupType::Acceleration].resize(2);
 337             mtop_.groups.groups[SimulationAtomGroupType::Acceleration][0] = 0;
 338             mtop_.groups.groups[SimulationAtomGroupType::Acceleration][1] = 2;
 339
 340             // Nose-Hoover chains
 341             inputrec_.bPrintNHChains     = true;
 342             inputrec_.opts.nhchainlength = 2;
 343             state_.nosehoover_xi.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()*inputrec_.opts.nhchainlength);
 344             state_.nosehoover_vxi.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()*inputrec_.opts.nhchainlength);
 345
 346             // This will be needed only with MTTK barostat
 347             state_.nhpres_xi.resize(1*inputrec_.opts.nhchainlength);
 348             state_.nhpres_vxi.resize(1*inputrec_.opts.nhchainlength);
 349
 350             // Group pairs
 351             enerdata_ = std::make_unique<gmx_enerdata_t>(mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].size(), 0);
 352
 353             // Kinetic energy and related data
 354             ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size());
 355             ekindata_.grpstat.resize(mtop_.groups.groups[SimulationAtomGroupType::Acceleration].size());
 356
 357             // This is needed so that the ebin space will be allocated
 358             inputrec_.cos_accel = 1.0;
 359             // This is to keep the destructor happy (otherwise sfree() segfaults)
 360             ekindata_.nthreads = 0;
 361             snew(ekindata_.ekin_work_alloc, 1);
 362             snew(ekindata_.ekin_work, 1);
 363             snew(ekindata_.dekindl_work, 1);
 364
 365             // Group options for annealing output
 366             inputrec_.opts.ngtc = 3;
 367             snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
 368             snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
 369             inputrec_.opts.annealing[0] = eannNO;
 370             inputrec_.opts.annealing[1] = eannSINGLE;
 371             inputrec_.opts.annealing[2] = eannPERIODIC;
 372
 373             // This is to keep done_inputrec happy (otherwise sfree() segfaults)
 374             snew(inputrec_.opts.anneal_time, inputrec_.opts.ngtc);
 375             snew(inputrec_.opts.anneal_temp, inputrec_.opts.ngtc);
 376
 377             // Communication record (for Constraints constructor)
 378             cr_.nnodes = 1;
 379             cr_.dd     = nullptr;
 380
 381             // Constraints object (to get constraints RMSD from)
 382             // TODO EnergyOutput should not take Constraints object
 383             // TODO This object will always return zero as RMSD value.
 384             //      It is more relevant to have non-zero value for testing.
 385             constraints_ = makeConstraints(mtop_, inputrec_, nullptr, false, nullptr, mdatoms_, &cr_,
 386                                            nullptr, nullptr, nullptr, false);
 387
 388             // No position/orientation restraints
 389             fcd_.disres.npair  = 0;
 390             fcd_.orires.nr     = 0;
 391
 392         }
 393
 394         /*! \brief Helper function to generate synthetic data to output
 395          *
 396          * \param[in,out] testValue    Base value fr energy data.
 397          */
 398         void setStepData(double *testValue)
 399         {
 400
 401             time_                             = (*testValue += 0.1);
 402             tmass_                            = (*testValue += 0.1);
 403
 404             enerdata_->term[F_LJ]             = (*testValue += 0.1);
 405             enerdata_->term[F_COUL_SR]        = (*testValue += 0.1);
 406             enerdata_->term[F_EPOT]           = (*testValue += 0.1);
 407             enerdata_->term[F_EKIN]           = (*testValue += 0.1);
 408             enerdata_->term[F_ETOT]           = (*testValue += 0.1);
 409             enerdata_->term[F_TEMP]           = (*testValue += 0.1);
 410             enerdata_->term[F_PRES]           = (*testValue += 0.1);
 411
 412             enerdata_->term[F_BHAM]           = (*testValue += 0.1);
 413             enerdata_->term[F_EQM]            = (*testValue += 0.1);
 414             enerdata_->term[F_RF_EXCL]        = (*testValue += 0.1);
 415             enerdata_->term[F_COUL_RECIP]     = (*testValue += 0.1);
 416             enerdata_->term[F_LJ_RECIP]       = (*testValue += 0.1);
 417             enerdata_->term[F_LJ14]           = (*testValue += 0.1);
 418             enerdata_->term[F_COUL14]         = (*testValue += 0.1);
 419             enerdata_->term[F_LJC14_Q]        = (*testValue += 0.1);
 420             enerdata_->term[F_LJC_PAIRS_NB]   = (*testValue += 0.1);
 421
 422             enerdata_->term[F_DVDL_COUL]      = (*testValue += 0.1);
 423             enerdata_->term[F_DVDL_VDW]       = (*testValue += 0.1);
 424             enerdata_->term[F_DVDL_BONDED]    = (*testValue += 0.1);
 425             enerdata_->term[F_DVDL_RESTRAINT] = (*testValue += 0.1);
 426             enerdata_->term[F_DKDL]           = (*testValue += 0.1);
 427             enerdata_->term[F_DVDL]           = (*testValue += 0.1);
 428
 429             enerdata_->term[F_DISPCORR]       = (*testValue += 0.1);
 430             enerdata_->term[F_PDISPCORR]      = (*testValue += 0.1);
 431             enerdata_->term[F_DISRESVIOL]     = (*testValue += 0.1);
 432             enerdata_->term[F_ORIRESDEV]      = (*testValue += 0.1);
 433             enerdata_->term[F_COM_PULL]       = (*testValue += 0.1);
 434             enerdata_->term[F_ECONSERVED]     = (*testValue += 0.1);
 435
 436             // Group pairs
 437             for (int i = 0; i < enerdata_->grpp.nener; i++)
 438             {
 439                 for (int k = 0; k < egNR; k++)
 440                 {
 441                     enerdata_->grpp.ener[k][i] = (*testValue += 0.1);
 442                 }
 443             }
 444
 445             // Kinetic energy and related data
 446             for (int i = 0; i < gmx::ssize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
 447             {
 448                 ekindata_.tcstat[i].T      = (*testValue += 0.1);
 449                 ekindata_.tcstat[i].lambda = (*testValue += 0.1);
 450             }
 451             for (int i = 0; i < gmx::ssize(mtop_.groups.groups[SimulationAtomGroupType::Acceleration]); i++)
 452             {
 453                 ekindata_.grpstat[i].u[XX] = (*testValue += 0.1);
 454                 ekindata_.grpstat[i].u[YY] = (*testValue += 0.1);
 455                 ekindata_.grpstat[i].u[ZZ] = (*testValue += 0.1);
 456             }
 457
 458             // This conditional is to check whether the ebin was allocated.
 459             // Otherwise it will print cosacc data into the first bin.
 460             if (inputrec_.cos_accel != 0)
 461             {
 462                 ekindata_.cosacc.cos_accel = (*testValue += 0.1);
 463                 ekindata_.cosacc.vcos      = (*testValue += 0.1);
 464             }
 465
 466             state_.box[XX][XX]         = (*testValue += 0.1);
 467             state_.box[XX][YY]         = (*testValue += 0.1);
 468             state_.box[XX][ZZ]         = (*testValue += 0.1);
 469             state_.box[YY][XX]         = (*testValue += 0.1);
 470             state_.box[YY][YY]         = (*testValue += 0.1);
 471             state_.box[YY][ZZ]         = (*testValue += 0.1);
 472             state_.box[ZZ][XX]         = (*testValue += 0.1);
 473             state_.box[ZZ][YY]         = (*testValue += 0.1);
 474             state_.box[ZZ][ZZ]         = (*testValue += 0.1);
 475
 476             box_[XX][XX]               = (*testValue += 0.1);
 477             box_[XX][YY]               = (*testValue += 0.1);
 478             box_[XX][ZZ]               = (*testValue += 0.1);
 479             box_[YY][XX]               = (*testValue += 0.1);
 480             box_[YY][YY]               = (*testValue += 0.1);
 481             box_[YY][ZZ]               = (*testValue += 0.1);
 482             box_[ZZ][XX]               = (*testValue += 0.1);
 483             box_[ZZ][YY]               = (*testValue += 0.1);
 484             box_[ZZ][ZZ]               = (*testValue += 0.1);
 485
 486             constraintsVirial_[XX][XX] = (*testValue += 0.1);
 487             constraintsVirial_[XX][YY] = (*testValue += 0.1);
 488             constraintsVirial_[XX][ZZ] = (*testValue += 0.1);
 489             constraintsVirial_[YY][XX] = (*testValue += 0.1);
 490             constraintsVirial_[YY][YY] = (*testValue += 0.1);
 491             constraintsVirial_[YY][ZZ] = (*testValue += 0.1);
 492             constraintsVirial_[ZZ][XX] = (*testValue += 0.1);
 493             constraintsVirial_[ZZ][YY] = (*testValue += 0.1);
 494             constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1);
 495
 496             forceVirial_[XX][XX]       = (*testValue += 0.1);
 497             forceVirial_[XX][YY]       = (*testValue += 0.1);
 498             forceVirial_[XX][ZZ]       = (*testValue += 0.1);
 499             forceVirial_[YY][XX]       = (*testValue += 0.1);
 500             forceVirial_[YY][YY]       = (*testValue += 0.1);
 501             forceVirial_[YY][ZZ]       = (*testValue += 0.1);
 502             forceVirial_[ZZ][XX]       = (*testValue += 0.1);
 503             forceVirial_[ZZ][YY]       = (*testValue += 0.1);
 504             forceVirial_[ZZ][ZZ]       = (*testValue += 0.1);
 505
 506             totalVirial_[XX][XX]       = (*testValue += 0.1);
 507             totalVirial_[XX][YY]       = (*testValue += 0.1);
 508             totalVirial_[XX][ZZ]       = (*testValue += 0.1);
 509             totalVirial_[YY][XX]       = (*testValue += 0.1);
 510             totalVirial_[YY][YY]       = (*testValue += 0.1);
 511             totalVirial_[YY][ZZ]       = (*testValue += 0.1);
 512             totalVirial_[ZZ][XX]       = (*testValue += 0.1);
 513             totalVirial_[ZZ][YY]       = (*testValue += 0.1);
 514             totalVirial_[ZZ][ZZ]       = (*testValue += 0.1);
 515
 516             pressure_[XX][XX]          = (*testValue += 0.1);
 517             pressure_[XX][YY]          = (*testValue += 0.1);
 518             pressure_[XX][ZZ]          = (*testValue += 0.1);
 519             pressure_[YY][XX]          = (*testValue += 0.1);
 520             pressure_[YY][YY]          = (*testValue += 0.1);
 521             pressure_[YY][ZZ]          = (*testValue += 0.1);
 522             pressure_[ZZ][XX]          = (*testValue += 0.1);
 523             pressure_[ZZ][YY]          = (*testValue += 0.1);
 524             pressure_[ZZ][ZZ]          = (*testValue += 0.1);
 525
 526             muTotal_[XX]               = (*testValue += 0.1);
 527             muTotal_[YY]               = (*testValue += 0.1);
 528             muTotal_[ZZ]               = (*testValue += 0.1);
 529
 530             state_.boxv[XX][XX]        = (*testValue += 0.1);
 531             state_.boxv[XX][YY]        = (*testValue += 0.1);
 532             state_.boxv[XX][ZZ]        = (*testValue += 0.1);
 533             state_.boxv[YY][XX]        = (*testValue += 0.1);
 534             state_.boxv[YY][YY]        = (*testValue += 0.1);
 535             state_.boxv[YY][ZZ]        = (*testValue += 0.1);
 536             state_.boxv[ZZ][XX]        = (*testValue += 0.1);
 537             state_.boxv[ZZ][YY]        = (*testValue += 0.1);
 538             state_.boxv[ZZ][ZZ]        = (*testValue += 0.1);
 539
 540             for (int i = 0; i < inputrec_.opts.ngtc; i++)
 541             {
 542                 inputrec_.opts.ref_t[i] = (*testValue += 0.1);
 543             }
 544
 545             for (int k = 0; k < gmx::ssize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling])*inputrec_.opts.nhchainlength; k++)
 546             {
 547                 state_.nosehoover_xi[k]  = (*testValue += 0.1);
 548                 state_.nosehoover_vxi[k] = (*testValue += 0.1);
 549             }
 550             for (int k = 0; k < inputrec_.opts.nhchainlength; k++)
 551             {
 552                 state_.nhpres_xi[k]  = (*testValue += 0.1);
 553                 state_.nhpres_vxi[k] = (*testValue += 0.1);
 554             }
 555         }
 556
 557         /*! \brief Check if the contents of the .edr file correspond to the reference data.
 558          *
 559          * The code below is based on the 'gmx dump' tool.
 560          *
 561          * \param[in] fileName    Name of the file to check.
 562          * \param[in] frameCount  Number of frames to check.
 563          */
 564         void checkEdrFile(const char *fileName, int frameCount)
 565         {
 566             ener_file_t    edrFile;
 567             gmx_enxnm_t   *energyTermsEdr = nullptr;
 568             int            numEnergyTermsEdr;
 569
 570             edrFile = open_enx(fileName, "r");
 571             do_enxnms(edrFile, &numEnergyTermsEdr, &energyTermsEdr);
 572             assert(energyTermsEdr);
 573
 574             // Check header
 575             TestReferenceChecker edrFileRef(checker_.checkCompound("File", "EnergyFile"));
 576             TestReferenceChecker energyTermsRef(edrFileRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
 577             for (int i = 0; i < numEnergyTermsEdr; i++)
 578             {
 579                 TestReferenceChecker energyTermRef(energyTermsRef.checkCompound("EnergyTerm", nullptr));
 580                 energyTermRef.checkString(energyTermsEdr[i].name, "Name");
 581                 energyTermRef.checkString(energyTermsEdr[i].unit, "Units");
 582             }
 583
 584             // Check frames
 585             TestReferenceChecker framesRef(edrFileRef.checkSequenceCompound("Frames", frameCount));
 586             t_enxframe          *frameEdr;
 587             snew(frameEdr, 1);
 588             char                 buffer[22];
 589             for (int frameId = 0; frameId < frameCount; frameId++)
 590             {
 591                 bool bCont = do_enx(edrFile, frameEdr);
 592                 EXPECT_TRUE(bCont) << gmx::formatString("Cant read frame %d from .edr file.", frameId);
 593
 594                 TestReferenceChecker frameRef(framesRef.checkCompound("Frame", nullptr));
 595                 frameRef.checkReal(frameEdr->t, "Time");
 596                 frameRef.checkReal(frameEdr->dt, "Timestep");
 597                 frameRef.checkString(gmx_step_str(frameEdr->step, buffer), "Step");
 598                 frameRef.checkString(gmx_step_str(frameEdr->nsum, buffer), "NumSteps");
 599
 600                 EXPECT_EQ(frameEdr->nre, numEnergyTermsEdr) << gmx::formatString("Wrong number of energy terms in frame %d.", frameId);
 601                 TestReferenceChecker energyValuesRef(frameRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
 602                 for (int i = 0; i < numEnergyTermsEdr; i++)
 603                 {
 604                     TestReferenceChecker energyValueRef(energyValuesRef.checkCompound("EnergyTerm", nullptr));
 605                     energyValueRef.checkString(energyTermsEdr[i].name, "Name");
 606                     energyValueRef.checkReal(frameEdr->ener[i].e, "Value");
 607                 }
 608             }
 609
 610             free_enxnms(numEnergyTermsEdr, energyTermsEdr);
 611             done_ener_file(edrFile);
 612
 613             free_enxframe(frameEdr);
 614             sfree(frameEdr);
 615         }
 616
 617 };
 618
 619 TEST_P(EnergyOutputTest, CheckOutput)
 620 {
 621     ASSERT_NE(log_, nullptr);
 622     // Binary output will be written to the temporary location
 623     energyFile_ = open_enx(edrFilename_.c_str(), "w");
 624     ASSERT_NE(energyFile_, nullptr);
 625
 626     EnergyOutputTestParameters parameters = GetParam();
 627     inputrec_.etc = parameters.temperatureCouplingScheme;
 628     inputrec_.epc = parameters.pressureCouplingScheme;
 629     inputrec_.eI  = parameters.integrator;
 630
 631     if (parameters.isBoxTriclinic)
 632     {
 633         inputrec_.ref_p[YY][XX]   = 1.0;
 634     }
 635
 636     energyOutput_.prepare(energyFile_, &mtop_, &inputrec_, nullptr, nullptr, parameters.isRerun);
 637
 638     // Add synthetic data for a single step
 639     double testValue = 10.0;
 640     for (int frame = 0; frame < parameters.numFrames; frame++)
 641     {
 642         setStepData(&testValue);
 643         energyOutput_.addDataAtEnergyStep(false, true, time_, tmass_, enerdata_.get(),
 644                                           &state_, nullptr, nullptr, box_,
 645                                           constraintsVirial_, forceVirial_, totalVirial_, pressure_,
 646                                           &ekindata_, muTotal_, constraints_.get());
 647
 648         energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
 649                                             100*frame, time_, eprNORMAL,
 650                                             nullptr,  &mtop_.groups, &inputrec_.opts, nullptr);
 651         time_ += 1.0;
 652     }
 653
 654     energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
 655                                         100, time_, eprAVER,
 656                                         nullptr,  &mtop_.groups, &inputrec_.opts, nullptr);
 657
 658     // We need to close the file before the contents are available.
 659     logFileGuard_.reset(nullptr);
 660
 661     done_ener_file(energyFile_);
 662
 663     // Set tolerance
 664     checker_.setDefaultTolerance(relativeToleranceAsFloatingPoint(testValue, 1.0e-5));
 665
 666     if (parameters.numFrames > 0)
 667     {
 668         // Test binary output
 669         checkEdrFile(edrFilename_.c_str(), parameters.numFrames);
 670     }
 671
 672     // Test printed values
 673     checker_.checkInteger(energyOutput_.numEnergyTerms(), "Number of Energy Terms");
 674     checker_.checkString(TextReader::readFileToString(logFilename_), "log");
 675 }
 676
 677 INSTANTIATE_TEST_CASE_P(WithParameters, EnergyOutputTest,
 678                             ::testing::ValuesIn(parametersSets));
 679
 680 }  // namespace
 681 }  // namespace test
 682 }  // namespace gmx