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