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