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37 * Tests for energy output to log and .edr files.
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.
47 * \author Mark Abraham <mark.j.abraham@gmail.com>
48 * \author Artem Zhmurov <zhmurov@gmail.com>
50 * \ingroup module_mdlib
54 #include "gromacs/mdlib/energyoutput.h"
58 #include <gtest/gtest.h>
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"
75 #include "testutils/refdata.h"
76 #include "testutils/setenv.h"
77 #include "testutils/testasserts.h"
78 #include "testutils/testfilemanager.h"
87 //! Wraps fclose to discard the return value to use it as a deleter with gmx::unique_cptr.
88 void fcloseWrapper(FILE* fp)
93 /*! \brief Test parameters space.
95 * The test will run on a set of combinations of this steucture parameters.
97 struct EnergyOutputTestParameters
100 int temperatureCouplingScheme;
102 int pressureCouplingScheme;
105 //! Number of saved energy frames (to test averages output).
107 //! If output should be initialized as a rerun.
109 //! Is box triclinic (off-diagonal elements will be printed).
113 /*! \brief Sets of parameters on which to run the tests.
115 * Only several combinations of the parameters are used. Using all possible combinations will
116 * require ~10 MB of test data and ~2 sec to run the tests.
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 } };
130 /*! \brief Test fixture to test energy output.
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.
136 class EnergyOutputTest : public ::testing::TestWithParam<EnergyOutputTestParameters>
140 TestFileManager fileManager_;
141 //! Energy (.edr) file
142 ener_file_t energyFile_;
144 t_inputrec inputrec_;
153 //! Potential energy data
154 std::unique_ptr<gmx_enerdata_t> enerdata_;
155 //! Kinetic energy data (for temperatures output)
156 gmx_ekindata_t ekindata_;
161 //! Virial from constraints
162 tensor constraintsVirial_;
163 //! Virial from force computation
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
177 //! Distance and orientation restraints data
179 //! Communication record
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
190 unique_cptr<FILE, fcloseWrapper> logFileGuard_;
192 TestReferenceData refData_;
193 //! Checker for reference data
194 TestReferenceChecker checker_;
197 logFilename_(fileManager_.getTemporaryFilePath(".log")),
198 edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
199 log_(std::fopen(logFilename_.c_str(), "w")),
201 checker_(refData_.rootChecker())
204 inputrec_.delta_t = 0.001;
207 inputrec_.bQMMM = true;
208 // F_RF_EXCL will not be tested - group scheme is not supported any more
209 inputrec_.cutoff_scheme = ecutsVERLET;
211 inputrec_.coulombtype = eelPME;
213 inputrec_.vdwtype = evdwPME;
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;
225 // F_DISPCORR and F_PDISPCORR
226 inputrec_.eDispCorr = edispcEner;
227 inputrec_.bRot = true;
230 inputrec_.ref_p[YY][XX] = 0.0;
231 inputrec_.ref_p[ZZ][XX] = 0.0;
232 inputrec_.ref_p[ZZ][YY] = 0.0;
235 inputrec_.ewald_geometry = eewg3DC;
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;
243 mtop_.bIntermolecularInteractions = false;
245 // Constructing molecular topology
246 gmx_moltype_t molType;
248 molType.atoms.nr = 2;
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;
259 InteractionList interactionListEmpty;
260 interactionListEmpty.iatoms.resize(0);
261 molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
262 molType.ilist.at(F_SETTLE) = interactionListEmpty;
264 // F_LJ14 and F_COUL14
265 InteractionList interactionListLJ14;
266 interactionListLJ14.iatoms.resize(NRAL(F_LJ14) + 1);
267 molType.ilist.at(F_LJ14) = interactionListLJ14;
270 InteractionList interactionListLJC14Q;
271 interactionListLJC14Q.iatoms.resize(NRAL(F_LJC14_Q) + 1);
272 molType.ilist.at(F_LJC14_Q) = interactionListLJC14Q;
274 // TODO Do proper initialization for distance and orientation
275 // restraints and remove comments to enable their output
277 // InteractionList interactionListDISRES;
278 // interactionListDISRES.iatoms.resize(NRAL(F_DISRES) + 1);
279 // molType.ilist.at(F_DISRES) = interactionListDISRES;
282 // InteractionList interactionListORIRES;
283 // interactionListORIRES.iatoms.resize(NRAL(F_ORIRES) + 1);
284 // molType.ilist.at(F_ORIRES) = interactionListORIRES;
286 mtop_.moltype.push_back(molType);
288 gmx_molblock_t molBlock;
291 mtop_.molblock.push_back(molBlock);
293 // This is to keep constraints initialization happy
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;
302 // Groups for energy output, temperature coupling and acceleration
303 for (const auto& string : groupNameStrings_)
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());
311 for (auto& handle : groupNameHandles_)
313 mtop_.groups.groupNames.emplace_back(&handle);
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;
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;
326 mtop_.groups.groups[SimulationAtomGroupType::Acceleration].resize(2);
327 mtop_.groups.groups[SimulationAtomGroupType::Acceleration][0] = 0;
328 mtop_.groups.groups[SimulationAtomGroupType::Acceleration][1] = 2;
330 // Nose-Hoover chains
331 inputrec_.bPrintNHChains = true;
332 inputrec_.opts.nhchainlength = 2;
333 state_.nosehoover_xi.resize(
334 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()
335 * inputrec_.opts.nhchainlength);
336 state_.nosehoover_vxi.resize(
337 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()
338 * inputrec_.opts.nhchainlength);
340 // This will be needed only with MTTK barostat
341 state_.nhpres_xi.resize(1 * inputrec_.opts.nhchainlength);
342 state_.nhpres_vxi.resize(1 * inputrec_.opts.nhchainlength);
345 enerdata_ = std::make_unique<gmx_enerdata_t>(
346 mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].size(), 0);
348 // Kinetic energy and related data
349 ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size());
350 ekindata_.grpstat.resize(mtop_.groups.groups[SimulationAtomGroupType::Acceleration].size());
352 // This is needed so that the ebin space will be allocated
353 inputrec_.cos_accel = 1.0;
354 // This is to keep the destructor happy (otherwise sfree() segfaults)
355 ekindata_.nthreads = 0;
356 snew(ekindata_.ekin_work_alloc, 1);
357 snew(ekindata_.ekin_work, 1);
358 snew(ekindata_.dekindl_work, 1);
360 // Group options for annealing output
361 inputrec_.opts.ngtc = 3;
362 snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
363 snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
364 inputrec_.opts.annealing[0] = eannNO;
365 inputrec_.opts.annealing[1] = eannSINGLE;
366 inputrec_.opts.annealing[2] = eannPERIODIC;
368 // This is to keep done_inputrec happy (otherwise sfree() segfaults)
369 snew(inputrec_.opts.anneal_time, inputrec_.opts.ngtc);
370 snew(inputrec_.opts.anneal_temp, inputrec_.opts.ngtc);
372 // Communication record (for Constraints constructor)
376 // Constraints object (to get constraints RMSD from)
377 // TODO EnergyOutput should not take Constraints object
378 // TODO This object will always return zero as RMSD value.
379 // It is more relevant to have non-zero value for testing.
380 constraints_ = makeConstraints(mtop_, inputrec_, nullptr, false, nullptr, mdatoms_, &cr_,
381 nullptr, nullptr, nullptr, false);
383 // No position/orientation restraints
384 fcd_.disres.npair = 0;
388 /*! \brief Helper function to generate synthetic data to output
390 * \param[in,out] testValue Base value fr energy data.
392 void setStepData(double* testValue)
395 time_ = (*testValue += 0.1);
396 tmass_ = (*testValue += 0.1);
398 enerdata_->term[F_LJ] = (*testValue += 0.1);
399 enerdata_->term[F_COUL_SR] = (*testValue += 0.1);
400 enerdata_->term[F_EPOT] = (*testValue += 0.1);
401 enerdata_->term[F_EKIN] = (*testValue += 0.1);
402 enerdata_->term[F_ETOT] = (*testValue += 0.1);
403 enerdata_->term[F_TEMP] = (*testValue += 0.1);
404 enerdata_->term[F_PRES] = (*testValue += 0.1);
406 enerdata_->term[F_BHAM] = (*testValue += 0.1);
407 enerdata_->term[F_EQM] = (*testValue += 0.1);
408 enerdata_->term[F_RF_EXCL] = (*testValue += 0.1);
409 enerdata_->term[F_COUL_RECIP] = (*testValue += 0.1);
410 enerdata_->term[F_LJ_RECIP] = (*testValue += 0.1);
411 enerdata_->term[F_LJ14] = (*testValue += 0.1);
412 enerdata_->term[F_COUL14] = (*testValue += 0.1);
413 enerdata_->term[F_LJC14_Q] = (*testValue += 0.1);
414 enerdata_->term[F_LJC_PAIRS_NB] = (*testValue += 0.1);
416 enerdata_->term[F_DVDL_COUL] = (*testValue += 0.1);
417 enerdata_->term[F_DVDL_VDW] = (*testValue += 0.1);
418 enerdata_->term[F_DVDL_BONDED] = (*testValue += 0.1);
419 enerdata_->term[F_DVDL_RESTRAINT] = (*testValue += 0.1);
420 enerdata_->term[F_DKDL] = (*testValue += 0.1);
421 enerdata_->term[F_DVDL] = (*testValue += 0.1);
423 enerdata_->term[F_DISPCORR] = (*testValue += 0.1);
424 enerdata_->term[F_PDISPCORR] = (*testValue += 0.1);
425 enerdata_->term[F_DISRESVIOL] = (*testValue += 0.1);
426 enerdata_->term[F_ORIRESDEV] = (*testValue += 0.1);
427 enerdata_->term[F_COM_PULL] = (*testValue += 0.1);
428 enerdata_->term[F_ECONSERVED] = (*testValue += 0.1);
431 for (int i = 0; i < enerdata_->grpp.nener; i++)
433 for (int k = 0; k < egNR; k++)
435 enerdata_->grpp.ener[k][i] = (*testValue += 0.1);
439 // Kinetic energy and related data
440 for (auto& tcstat : ekindata_.tcstat)
442 tcstat.T = (*testValue += 0.1);
443 tcstat.lambda = (*testValue += 0.1);
445 for (auto& grpstat : ekindata_.grpstat)
447 grpstat.u[XX] = (*testValue += 0.1);
448 grpstat.u[YY] = (*testValue += 0.1);
449 grpstat.u[ZZ] = (*testValue += 0.1);
452 // This conditional is to check whether the ebin was allocated.
453 // Otherwise it will print cosacc data into the first bin.
454 if (inputrec_.cos_accel != 0)
456 ekindata_.cosacc.cos_accel = (*testValue += 0.1);
457 ekindata_.cosacc.vcos = (*testValue += 0.1);
460 state_.box[XX][XX] = (*testValue += 0.1);
461 state_.box[XX][YY] = (*testValue += 0.1);
462 state_.box[XX][ZZ] = (*testValue += 0.1);
463 state_.box[YY][XX] = (*testValue += 0.1);
464 state_.box[YY][YY] = (*testValue += 0.1);
465 state_.box[YY][ZZ] = (*testValue += 0.1);
466 state_.box[ZZ][XX] = (*testValue += 0.1);
467 state_.box[ZZ][YY] = (*testValue += 0.1);
468 state_.box[ZZ][ZZ] = (*testValue += 0.1);
470 box_[XX][XX] = (*testValue += 0.1);
471 box_[XX][YY] = (*testValue += 0.1);
472 box_[XX][ZZ] = (*testValue += 0.1);
473 box_[YY][XX] = (*testValue += 0.1);
474 box_[YY][YY] = (*testValue += 0.1);
475 box_[YY][ZZ] = (*testValue += 0.1);
476 box_[ZZ][XX] = (*testValue += 0.1);
477 box_[ZZ][YY] = (*testValue += 0.1);
478 box_[ZZ][ZZ] = (*testValue += 0.1);
480 constraintsVirial_[XX][XX] = (*testValue += 0.1);
481 constraintsVirial_[XX][YY] = (*testValue += 0.1);
482 constraintsVirial_[XX][ZZ] = (*testValue += 0.1);
483 constraintsVirial_[YY][XX] = (*testValue += 0.1);
484 constraintsVirial_[YY][YY] = (*testValue += 0.1);
485 constraintsVirial_[YY][ZZ] = (*testValue += 0.1);
486 constraintsVirial_[ZZ][XX] = (*testValue += 0.1);
487 constraintsVirial_[ZZ][YY] = (*testValue += 0.1);
488 constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1);
490 forceVirial_[XX][XX] = (*testValue += 0.1);
491 forceVirial_[XX][YY] = (*testValue += 0.1);
492 forceVirial_[XX][ZZ] = (*testValue += 0.1);
493 forceVirial_[YY][XX] = (*testValue += 0.1);
494 forceVirial_[YY][YY] = (*testValue += 0.1);
495 forceVirial_[YY][ZZ] = (*testValue += 0.1);
496 forceVirial_[ZZ][XX] = (*testValue += 0.1);
497 forceVirial_[ZZ][YY] = (*testValue += 0.1);
498 forceVirial_[ZZ][ZZ] = (*testValue += 0.1);
500 totalVirial_[XX][XX] = (*testValue += 0.1);
501 totalVirial_[XX][YY] = (*testValue += 0.1);
502 totalVirial_[XX][ZZ] = (*testValue += 0.1);
503 totalVirial_[YY][XX] = (*testValue += 0.1);
504 totalVirial_[YY][YY] = (*testValue += 0.1);
505 totalVirial_[YY][ZZ] = (*testValue += 0.1);
506 totalVirial_[ZZ][XX] = (*testValue += 0.1);
507 totalVirial_[ZZ][YY] = (*testValue += 0.1);
508 totalVirial_[ZZ][ZZ] = (*testValue += 0.1);
510 pressure_[XX][XX] = (*testValue += 0.1);
511 pressure_[XX][YY] = (*testValue += 0.1);
512 pressure_[XX][ZZ] = (*testValue += 0.1);
513 pressure_[YY][XX] = (*testValue += 0.1);
514 pressure_[YY][YY] = (*testValue += 0.1);
515 pressure_[YY][ZZ] = (*testValue += 0.1);
516 pressure_[ZZ][XX] = (*testValue += 0.1);
517 pressure_[ZZ][YY] = (*testValue += 0.1);
518 pressure_[ZZ][ZZ] = (*testValue += 0.1);
520 muTotal_[XX] = (*testValue += 0.1);
521 muTotal_[YY] = (*testValue += 0.1);
522 muTotal_[ZZ] = (*testValue += 0.1);
524 state_.boxv[XX][XX] = (*testValue += 0.1);
525 state_.boxv[XX][YY] = (*testValue += 0.1);
526 state_.boxv[XX][ZZ] = (*testValue += 0.1);
527 state_.boxv[YY][XX] = (*testValue += 0.1);
528 state_.boxv[YY][YY] = (*testValue += 0.1);
529 state_.boxv[YY][ZZ] = (*testValue += 0.1);
530 state_.boxv[ZZ][XX] = (*testValue += 0.1);
531 state_.boxv[ZZ][YY] = (*testValue += 0.1);
532 state_.boxv[ZZ][ZZ] = (*testValue += 0.1);
534 for (int i = 0; i < inputrec_.opts.ngtc; i++)
536 inputrec_.opts.ref_t[i] = (*testValue += 0.1);
539 for (index k = 0; k < ssize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling])
540 * inputrec_.opts.nhchainlength;
543 state_.nosehoover_xi[k] = (*testValue += 0.1);
544 state_.nosehoover_vxi[k] = (*testValue += 0.1);
546 for (int k = 0; k < inputrec_.opts.nhchainlength; k++)
548 state_.nhpres_xi[k] = (*testValue += 0.1);
549 state_.nhpres_vxi[k] = (*testValue += 0.1);
553 /*! \brief Check if the contents of the .edr file correspond to the reference data.
555 * The code below is based on the 'gmx dump' tool.
557 * \param[in] fileName Name of the file to check.
558 * \param[in] frameCount Number of frames to check.
560 void checkEdrFile(const char* fileName, int frameCount)
563 gmx_enxnm_t* energyTermsEdr = nullptr;
564 int numEnergyTermsEdr;
566 edrFile = open_enx(fileName, "r");
567 do_enxnms(edrFile, &numEnergyTermsEdr, &energyTermsEdr);
568 assert(energyTermsEdr);
571 TestReferenceChecker edrFileRef(checker_.checkCompound("File", "EnergyFile"));
572 TestReferenceChecker energyTermsRef(
573 edrFileRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
574 for (int i = 0; i < numEnergyTermsEdr; i++)
576 TestReferenceChecker energyTermRef(energyTermsRef.checkCompound("EnergyTerm", nullptr));
577 energyTermRef.checkString(energyTermsEdr[i].name, "Name");
578 energyTermRef.checkString(energyTermsEdr[i].unit, "Units");
582 TestReferenceChecker framesRef(edrFileRef.checkSequenceCompound("Frames", frameCount));
583 t_enxframe* frameEdr;
586 for (int frameId = 0; frameId < frameCount; frameId++)
588 bool bCont = do_enx(edrFile, frameEdr);
589 EXPECT_TRUE(bCont) << gmx::formatString("Cant read frame %d from .edr file.", frameId);
591 TestReferenceChecker frameRef(framesRef.checkCompound("Frame", nullptr));
592 frameRef.checkReal(frameEdr->t, "Time");
593 frameRef.checkReal(frameEdr->dt, "Timestep");
594 frameRef.checkString(gmx_step_str(frameEdr->step, buffer), "Step");
595 frameRef.checkString(gmx_step_str(frameEdr->nsum, buffer), "NumSteps");
597 EXPECT_EQ(frameEdr->nre, numEnergyTermsEdr)
598 << gmx::formatString("Wrong number of energy terms in frame %d.", frameId);
599 TestReferenceChecker energyValuesRef(
600 frameRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
601 for (int i = 0; i < numEnergyTermsEdr; i++)
603 TestReferenceChecker energyValueRef(energyValuesRef.checkCompound("EnergyTerm", nullptr));
604 energyValueRef.checkString(energyTermsEdr[i].name, "Name");
605 energyValueRef.checkReal(frameEdr->ener[i].e, "Value");
609 free_enxnms(numEnergyTermsEdr, energyTermsEdr);
610 done_ener_file(edrFile);
612 free_enxframe(frameEdr);
617 TEST_P(EnergyOutputTest, CheckOutput)
619 ASSERT_NE(log_, nullptr);
620 // Binary output will be written to the temporary location
621 energyFile_ = open_enx(edrFilename_.c_str(), "w");
622 ASSERT_NE(energyFile_, nullptr);
624 EnergyOutputTestParameters parameters = GetParam();
625 inputrec_.etc = parameters.temperatureCouplingScheme;
626 inputrec_.epc = parameters.pressureCouplingScheme;
627 inputrec_.eI = parameters.integrator;
629 if (parameters.isBoxTriclinic)
631 inputrec_.ref_p[YY][XX] = 1.0;
634 MdModulesNotifier mdModulesNotifier;
635 std::unique_ptr<EnergyOutput> energyOutput = std::make_unique<EnergyOutput>(
636 energyFile_, &mtop_, &inputrec_, nullptr, nullptr, parameters.isRerun, mdModulesNotifier);
638 // Add synthetic data for a single step
639 double testValue = 10.0;
640 for (int frame = 0; frame < parameters.numFrames; frame++)
642 setStepData(&testValue);
643 energyOutput->addDataAtEnergyStep(false, true, time_, tmass_, enerdata_.get(), &state_, nullptr,
644 nullptr, box_, constraintsVirial_, forceVirial_, totalVirial_,
645 pressure_, &ekindata_, muTotal_, constraints_.get());
647 energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
648 energyOutput->printStepToEnergyFile(energyFile_, true, false, false, log_, 100 * frame,
649 time_, nullptr, nullptr);
653 energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
654 energyOutput->printAverages(log_, &mtop_.groups);
656 // We need to close the file before the contents are available.
657 logFileGuard_.reset(nullptr);
659 done_ener_file(energyFile_);
662 checker_.setDefaultTolerance(relativeToleranceAsFloatingPoint(testValue, 1.0e-5));
664 if (parameters.numFrames > 0)
666 // Test binary output
667 checkEdrFile(edrFilename_.c_str(), parameters.numFrames);
670 // Test printed values
671 checker_.checkInteger(energyOutput->numEnergyTerms(), "Number of Energy Terms");
672 checker_.checkString(TextReader::readFileToString(logFilename_), "log");
675 INSTANTIATE_TEST_CASE_P(WithParameters, EnergyOutputTest, ::testing::ValuesIn(parametersSets));