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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/mdrunutility/handlerestart.h"
63 #include "gromacs/mdtypes/commrec.h"
64 #include "gromacs/mdtypes/fcdata.h"
65 #include "gromacs/mdtypes/group.h"
66 #include "gromacs/mdtypes/inputrec.h"
67 #include "gromacs/mdtypes/mdatom.h"
68 #include "gromacs/mdtypes/state.h"
69 #include "gromacs/topology/topology.h"
70 #include "gromacs/utility/cstringutil.h"
71 #include "gromacs/utility/mdmodulenotification.h"
72 #include "gromacs/utility/stringutil.h"
73 #include "gromacs/utility/textreader.h"
74 #include "gromacs/utility/unique_cptr.h"
76 #include "testutils/refdata.h"
77 #include "testutils/setenv.h"
78 #include "testutils/testasserts.h"
79 #include "testutils/testfilemanager.h"
88 //! Wraps fclose to discard the return value to use it as a deleter with gmx::unique_cptr.
89 void fcloseWrapper(FILE* fp)
94 /*! \brief Test parameters space.
96 * The test will run on a set of combinations of this steucture parameters.
98 struct EnergyOutputTestParameters
100 //! Thermostat (enum)
101 int temperatureCouplingScheme;
103 int pressureCouplingScheme;
106 //! Number of saved energy frames (to test averages output).
108 //! If output should be initialized as a rerun.
110 //! Is box triclinic (off-diagonal elements will be printed).
114 /*! \brief Sets of parameters on which to run the tests.
116 * Only several combinations of the parameters are used. Using all possible combinations will
117 * require ~10 MB of test data and ~2 sec to run the tests.
119 const EnergyOutputTestParameters parametersSets[] = { { etcNO, epcNO, eiMD, 1, false, false },
120 { etcNO, epcNO, eiMD, 1, true, false },
121 { etcNO, epcNO, eiMD, 1, false, true },
122 { etcNO, epcNO, eiMD, 0, false, false },
123 { etcNO, epcNO, eiMD, 10, false, false },
124 { etcVRESCALE, epcNO, eiMD, 1, false, false },
125 { etcNOSEHOOVER, epcNO, eiMD, 1, false, false },
126 { etcNO, epcPARRINELLORAHMAN, eiMD, 1, false, false },
127 { etcNO, epcMTTK, eiMD, 1, false, false },
128 { etcNO, epcNO, eiVV, 1, false, false },
129 { etcNO, epcMTTK, eiVV, 1, false, false } };
131 /*! \brief Test fixture to test energy output.
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.
137 class EnergyOutputTest : public ::testing::TestWithParam<EnergyOutputTestParameters>
141 TestFileManager fileManager_;
142 //! Energy (.edr) file
143 ener_file_t energyFile_;
145 t_inputrec inputrec_;
152 //! Potential energy data
153 std::unique_ptr<gmx_enerdata_t> enerdata_;
154 //! Kinetic energy data (for temperatures output)
155 gmx_ekindata_t ekindata_;
160 //! Virial from constraints
161 tensor constraintsVirial_;
162 //! Virial from force computation
168 //! Names for the groups.
169 std::vector<std::string> groupNameStrings_ = { "Protein", "Water", "Lipid" };
170 //! Names for the groups as C strings.
171 std::vector<std::vector<char>> groupNameCStrings_;
172 //! Handles to the names as C strings in the way needed for SimulationGroups.
173 std::vector<char*> groupNameHandles_;
174 //! Total dipole momentum
176 //! Communication record
178 //! Constraints object (for constraints RMSD output in case of LINCS)
179 std::unique_ptr<Constraints> constraints_;
180 //! Temporary output filename
181 std::string logFilename_;
182 //! Temporary energy output filename
183 std::string edrFilename_;
184 //! Pointer to a temporary output file
187 unique_cptr<FILE, fcloseWrapper> logFileGuard_;
189 TestReferenceData refData_;
190 //! Checker for reference data
191 TestReferenceChecker checker_;
194 logFilename_(fileManager_.getTemporaryFilePath(".log")),
195 edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
196 log_(std::fopen(logFilename_.c_str(), "w")),
198 checker_(refData_.rootChecker())
201 inputrec_.delta_t = 0.001;
204 inputrec_.bQMMM = true;
205 // F_RF_EXCL will not be tested - group scheme is not supported any more
206 inputrec_.cutoff_scheme = ecutsVERLET;
208 inputrec_.coulombtype = eelPME;
210 inputrec_.vdwtype = evdwPME;
212 // F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED, F_DVDL_RESTRAINT, F_DKDL and F_DVDL
213 inputrec_.efep = efepYES;
214 inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
215 inputrec_.fepvals->separate_dvdl[efptVDW] = true;
216 inputrec_.fepvals->separate_dvdl[efptBONDED] = true;
217 inputrec_.fepvals->separate_dvdl[efptRESTRAINT] = true;
218 inputrec_.fepvals->separate_dvdl[efptMASS] = true;
219 inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
220 inputrec_.fepvals->separate_dvdl[efptFEP] = true;
222 // F_DISPCORR and F_PDISPCORR
223 inputrec_.eDispCorr = edispcEner;
224 inputrec_.bRot = true;
227 inputrec_.ref_p[YY][XX] = 0.0;
228 inputrec_.ref_p[ZZ][XX] = 0.0;
229 inputrec_.ref_p[ZZ][YY] = 0.0;
232 inputrec_.ewald_geometry = eewg3DC;
234 // GMX_CONSTRAINTVIR environment variable should also be
235 // set to print constraints and force virials separately.
236 gmxSetenv("GMX_CONSTRAINTVIR", "true", 1);
237 // To print constrain RMSD, constraints algorithm should be set to LINCS.
238 inputrec_.eConstrAlg = econtLINCS;
240 mtop_.bIntermolecularInteractions = false;
242 // Constructing molecular topology
243 gmx_moltype_t molType;
245 molType.atoms.nr = 2;
248 // This must be initialized so that Constraints object can be created below.
249 InteractionList interactionListConstr;
250 interactionListConstr.iatoms.resize(NRAL(F_CONSTR) + 1);
251 interactionListConstr.iatoms[0] = 0;
252 interactionListConstr.iatoms[1] = 0;
253 interactionListConstr.iatoms[2] = 1;
254 molType.ilist.at(F_CONSTR) = interactionListConstr;
256 InteractionList interactionListEmpty;
257 interactionListEmpty.iatoms.resize(0);
258 molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
259 molType.ilist.at(F_SETTLE) = interactionListEmpty;
261 // F_LJ14 and F_COUL14
262 InteractionList interactionListLJ14;
263 interactionListLJ14.iatoms.resize(NRAL(F_LJ14) + 1);
264 molType.ilist.at(F_LJ14) = interactionListLJ14;
267 InteractionList interactionListLJC14Q;
268 interactionListLJC14Q.iatoms.resize(NRAL(F_LJC14_Q) + 1);
269 molType.ilist.at(F_LJC14_Q) = interactionListLJC14Q;
271 // TODO Do proper initialization for distance and orientation
272 // restraints and remove comments to enable their output
274 // InteractionList interactionListDISRES;
275 // interactionListDISRES.iatoms.resize(NRAL(F_DISRES) + 1);
276 // molType.ilist.at(F_DISRES) = interactionListDISRES;
279 // InteractionList interactionListORIRES;
280 // interactionListORIRES.iatoms.resize(NRAL(F_ORIRES) + 1);
281 // molType.ilist.at(F_ORIRES) = interactionListORIRES;
283 mtop_.moltype.push_back(molType);
285 gmx_molblock_t molBlock;
288 mtop_.molblock.push_back(molBlock);
290 // This is to keep constraints initialization happy
292 mtop_.ffparams.iparams.resize(F_NRE);
293 mtop_.ffparams.functype.resize(F_NRE);
294 mtop_.ffparams.iparams.at(F_CONSTR).constr.dA = 1.0;
295 mtop_.ffparams.iparams.at(F_CONSTR).constr.dB = 1.0;
296 mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dA = 1.0;
297 mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dB = 1.0;
299 // Groups for energy output, temperature coupling and acceleration
300 for (const auto& string : groupNameStrings_)
302 std::vector<char> cString(string.begin(), string.end());
303 // Need to add null termination
304 cString.push_back('\0');
305 groupNameCStrings_.emplace_back(cString);
306 groupNameHandles_.emplace_back(groupNameCStrings_.back().data());
308 for (auto& handle : groupNameHandles_)
310 mtop_.groups.groupNames.emplace_back(&handle);
313 mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(3);
314 mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][0] = 0;
315 mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][1] = 1;
316 mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][2] = 2;
318 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(3);
319 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][0] = 0;
320 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][1] = 1;
321 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][2] = 2;
323 // Nose-Hoover chains
324 inputrec_.bPrintNHChains = true;
325 inputrec_.opts.nhchainlength = 2;
326 state_.nosehoover_xi.resize(
327 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()
328 * inputrec_.opts.nhchainlength);
329 state_.nosehoover_vxi.resize(
330 mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()
331 * inputrec_.opts.nhchainlength);
333 // This will be needed only with MTTK barostat
334 state_.nhpres_xi.resize(1 * inputrec_.opts.nhchainlength);
335 state_.nhpres_vxi.resize(1 * inputrec_.opts.nhchainlength);
338 enerdata_ = std::make_unique<gmx_enerdata_t>(
339 mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].size(), 0);
341 // Kinetic energy and related data
342 ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size());
344 // This is needed so that the ebin space will be allocated
345 inputrec_.cos_accel = 1.0;
346 // This is to keep the destructor happy (otherwise sfree() segfaults)
347 ekindata_.nthreads = 0;
348 snew(ekindata_.ekin_work_alloc, 1);
349 snew(ekindata_.ekin_work, 1);
350 snew(ekindata_.dekindl_work, 1);
352 // Group options for annealing output
353 inputrec_.opts.ngtc = 3;
354 snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
355 snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
356 inputrec_.opts.annealing[0] = eannNO;
357 inputrec_.opts.annealing[1] = eannSINGLE;
358 inputrec_.opts.annealing[2] = eannPERIODIC;
360 // This is to keep done_inputrec happy (otherwise sfree() segfaults)
361 snew(inputrec_.opts.anneal_time, inputrec_.opts.ngtc);
362 snew(inputrec_.opts.anneal_temp, inputrec_.opts.ngtc);
364 // Communication record (for Constraints constructor)
368 // Constraints object (to get constraints RMSD from)
369 // TODO EnergyOutput should not take Constraints object
370 // TODO This object will always return zero as RMSD value.
371 // It is more relevant to have non-zero value for testing.
372 constraints_ = makeConstraints(
373 mtop_, inputrec_, nullptr, false, nullptr, &cr_, nullptr, nullptr, nullptr, false);
376 /*! \brief Helper function to generate synthetic data to output
378 * \param[in,out] testValue Base value fr energy data.
380 void setStepData(double* testValue)
383 time_ = (*testValue += 0.1);
384 tmass_ = (*testValue += 0.1);
386 enerdata_->term[F_LJ] = (*testValue += 0.1);
387 enerdata_->term[F_COUL_SR] = (*testValue += 0.1);
388 enerdata_->term[F_EPOT] = (*testValue += 0.1);
389 enerdata_->term[F_EKIN] = (*testValue += 0.1);
390 enerdata_->term[F_ETOT] = (*testValue += 0.1);
391 enerdata_->term[F_TEMP] = (*testValue += 0.1);
392 enerdata_->term[F_PRES] = (*testValue += 0.1);
394 enerdata_->term[F_BHAM] = (*testValue += 0.1);
395 enerdata_->term[F_EQM] = (*testValue += 0.1);
396 enerdata_->term[F_RF_EXCL] = (*testValue += 0.1);
397 enerdata_->term[F_COUL_RECIP] = (*testValue += 0.1);
398 enerdata_->term[F_LJ_RECIP] = (*testValue += 0.1);
399 enerdata_->term[F_LJ14] = (*testValue += 0.1);
400 enerdata_->term[F_COUL14] = (*testValue += 0.1);
401 enerdata_->term[F_LJC14_Q] = (*testValue += 0.1);
402 enerdata_->term[F_LJC_PAIRS_NB] = (*testValue += 0.1);
404 enerdata_->term[F_DVDL_COUL] = (*testValue += 0.1);
405 enerdata_->term[F_DVDL_VDW] = (*testValue += 0.1);
406 enerdata_->term[F_DVDL_BONDED] = (*testValue += 0.1);
407 enerdata_->term[F_DVDL_RESTRAINT] = (*testValue += 0.1);
408 enerdata_->term[F_DKDL] = (*testValue += 0.1);
409 enerdata_->term[F_DVDL] = (*testValue += 0.1);
411 enerdata_->term[F_DISPCORR] = (*testValue += 0.1);
412 enerdata_->term[F_PDISPCORR] = (*testValue += 0.1);
413 enerdata_->term[F_DISRESVIOL] = (*testValue += 0.1);
414 enerdata_->term[F_ORIRESDEV] = (*testValue += 0.1);
415 enerdata_->term[F_COM_PULL] = (*testValue += 0.1);
416 enerdata_->term[F_ECONSERVED] = (*testValue += 0.1);
419 for (int i = 0; i < enerdata_->grpp.nener; i++)
421 for (int k = 0; k < egNR; k++)
423 enerdata_->grpp.ener[k][i] = (*testValue += 0.1);
427 // Kinetic energy and related data
428 for (auto& tcstat : ekindata_.tcstat)
430 tcstat.T = (*testValue += 0.1);
431 tcstat.lambda = (*testValue += 0.1);
433 // Removing constant acceleration removed a total increment of 0.6
434 // To avoid unnecessary changes in reference data, we keep the increment
437 // This conditional is to check whether the ebin was allocated.
438 // Otherwise it will print cosacc data into the first bin.
439 if (inputrec_.cos_accel != 0)
441 ekindata_.cosacc.cos_accel = (*testValue += 0.1);
442 ekindata_.cosacc.vcos = (*testValue += 0.1);
445 state_.box[XX][XX] = (*testValue += 0.1);
446 state_.box[XX][YY] = (*testValue += 0.1);
447 state_.box[XX][ZZ] = (*testValue += 0.1);
448 state_.box[YY][XX] = (*testValue += 0.1);
449 state_.box[YY][YY] = (*testValue += 0.1);
450 state_.box[YY][ZZ] = (*testValue += 0.1);
451 state_.box[ZZ][XX] = (*testValue += 0.1);
452 state_.box[ZZ][YY] = (*testValue += 0.1);
453 state_.box[ZZ][ZZ] = (*testValue += 0.1);
455 box_[XX][XX] = (*testValue += 0.1);
456 box_[XX][YY] = (*testValue += 0.1);
457 box_[XX][ZZ] = (*testValue += 0.1);
458 box_[YY][XX] = (*testValue += 0.1);
459 box_[YY][YY] = (*testValue += 0.1);
460 box_[YY][ZZ] = (*testValue += 0.1);
461 box_[ZZ][XX] = (*testValue += 0.1);
462 box_[ZZ][YY] = (*testValue += 0.1);
463 box_[ZZ][ZZ] = (*testValue += 0.1);
465 constraintsVirial_[XX][XX] = (*testValue += 0.1);
466 constraintsVirial_[XX][YY] = (*testValue += 0.1);
467 constraintsVirial_[XX][ZZ] = (*testValue += 0.1);
468 constraintsVirial_[YY][XX] = (*testValue += 0.1);
469 constraintsVirial_[YY][YY] = (*testValue += 0.1);
470 constraintsVirial_[YY][ZZ] = (*testValue += 0.1);
471 constraintsVirial_[ZZ][XX] = (*testValue += 0.1);
472 constraintsVirial_[ZZ][YY] = (*testValue += 0.1);
473 constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1);
475 forceVirial_[XX][XX] = (*testValue += 0.1);
476 forceVirial_[XX][YY] = (*testValue += 0.1);
477 forceVirial_[XX][ZZ] = (*testValue += 0.1);
478 forceVirial_[YY][XX] = (*testValue += 0.1);
479 forceVirial_[YY][YY] = (*testValue += 0.1);
480 forceVirial_[YY][ZZ] = (*testValue += 0.1);
481 forceVirial_[ZZ][XX] = (*testValue += 0.1);
482 forceVirial_[ZZ][YY] = (*testValue += 0.1);
483 forceVirial_[ZZ][ZZ] = (*testValue += 0.1);
485 totalVirial_[XX][XX] = (*testValue += 0.1);
486 totalVirial_[XX][YY] = (*testValue += 0.1);
487 totalVirial_[XX][ZZ] = (*testValue += 0.1);
488 totalVirial_[YY][XX] = (*testValue += 0.1);
489 totalVirial_[YY][YY] = (*testValue += 0.1);
490 totalVirial_[YY][ZZ] = (*testValue += 0.1);
491 totalVirial_[ZZ][XX] = (*testValue += 0.1);
492 totalVirial_[ZZ][YY] = (*testValue += 0.1);
493 totalVirial_[ZZ][ZZ] = (*testValue += 0.1);
495 pressure_[XX][XX] = (*testValue += 0.1);
496 pressure_[XX][YY] = (*testValue += 0.1);
497 pressure_[XX][ZZ] = (*testValue += 0.1);
498 pressure_[YY][XX] = (*testValue += 0.1);
499 pressure_[YY][YY] = (*testValue += 0.1);
500 pressure_[YY][ZZ] = (*testValue += 0.1);
501 pressure_[ZZ][XX] = (*testValue += 0.1);
502 pressure_[ZZ][YY] = (*testValue += 0.1);
503 pressure_[ZZ][ZZ] = (*testValue += 0.1);
505 muTotal_[XX] = (*testValue += 0.1);
506 muTotal_[YY] = (*testValue += 0.1);
507 muTotal_[ZZ] = (*testValue += 0.1);
509 state_.boxv[XX][XX] = (*testValue += 0.1);
510 state_.boxv[XX][YY] = (*testValue += 0.1);
511 state_.boxv[XX][ZZ] = (*testValue += 0.1);
512 state_.boxv[YY][XX] = (*testValue += 0.1);
513 state_.boxv[YY][YY] = (*testValue += 0.1);
514 state_.boxv[YY][ZZ] = (*testValue += 0.1);
515 state_.boxv[ZZ][XX] = (*testValue += 0.1);
516 state_.boxv[ZZ][YY] = (*testValue += 0.1);
517 state_.boxv[ZZ][ZZ] = (*testValue += 0.1);
519 for (int i = 0; i < inputrec_.opts.ngtc; i++)
521 inputrec_.opts.ref_t[i] = (*testValue += 0.1);
524 for (index k = 0; k < ssize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling])
525 * inputrec_.opts.nhchainlength;
528 state_.nosehoover_xi[k] = (*testValue += 0.1);
529 state_.nosehoover_vxi[k] = (*testValue += 0.1);
531 for (int k = 0; k < inputrec_.opts.nhchainlength; k++)
533 state_.nhpres_xi[k] = (*testValue += 0.1);
534 state_.nhpres_vxi[k] = (*testValue += 0.1);
538 /*! \brief Check if the contents of the .edr file correspond to the reference data.
540 * The code below is based on the 'gmx dump' tool.
542 * \param[in] fileName Name of the file to check.
543 * \param[in] frameCount Number of frames to check.
545 void checkEdrFile(const char* fileName, int frameCount)
548 gmx_enxnm_t* energyTermsEdr = nullptr;
549 int numEnergyTermsEdr;
551 edrFile = open_enx(fileName, "r");
552 do_enxnms(edrFile, &numEnergyTermsEdr, &energyTermsEdr);
553 assert(energyTermsEdr);
556 TestReferenceChecker edrFileRef(checker_.checkCompound("File", "EnergyFile"));
557 TestReferenceChecker energyTermsRef(
558 edrFileRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
559 for (int i = 0; i < numEnergyTermsEdr; i++)
561 TestReferenceChecker energyTermRef(energyTermsRef.checkCompound("EnergyTerm", nullptr));
562 energyTermRef.checkString(energyTermsEdr[i].name, "Name");
563 energyTermRef.checkString(energyTermsEdr[i].unit, "Units");
567 TestReferenceChecker framesRef(edrFileRef.checkSequenceCompound("Frames", frameCount));
568 t_enxframe* frameEdr;
571 for (int frameId = 0; frameId < frameCount; frameId++)
573 bool bCont = do_enx(edrFile, frameEdr);
574 EXPECT_TRUE(bCont) << gmx::formatString("Cant read frame %d from .edr file.", frameId);
576 TestReferenceChecker frameRef(framesRef.checkCompound("Frame", nullptr));
577 frameRef.checkReal(frameEdr->t, "Time");
578 frameRef.checkReal(frameEdr->dt, "Timestep");
579 frameRef.checkString(gmx_step_str(frameEdr->step, buffer), "Step");
580 frameRef.checkString(gmx_step_str(frameEdr->nsum, buffer), "NumSteps");
582 EXPECT_EQ(frameEdr->nre, numEnergyTermsEdr)
583 << gmx::formatString("Wrong number of energy terms in frame %d.", frameId);
584 TestReferenceChecker energyValuesRef(
585 frameRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
586 for (int i = 0; i < numEnergyTermsEdr; i++)
588 TestReferenceChecker energyValueRef(energyValuesRef.checkCompound("EnergyTerm", nullptr));
589 energyValueRef.checkString(energyTermsEdr[i].name, "Name");
590 energyValueRef.checkReal(frameEdr->ener[i].e, "Value");
594 free_enxnms(numEnergyTermsEdr, energyTermsEdr);
595 done_ener_file(edrFile);
597 free_enxframe(frameEdr);
602 TEST_P(EnergyOutputTest, CheckOutput)
604 ASSERT_NE(log_, nullptr);
605 // Binary output will be written to the temporary location
606 energyFile_ = open_enx(edrFilename_.c_str(), "w");
607 ASSERT_NE(energyFile_, nullptr);
609 EnergyOutputTestParameters parameters = GetParam();
610 inputrec_.etc = parameters.temperatureCouplingScheme;
611 inputrec_.epc = parameters.pressureCouplingScheme;
612 inputrec_.eI = parameters.integrator;
614 if (parameters.isBoxTriclinic)
616 inputrec_.ref_p[YY][XX] = 1.0;
619 MdModulesNotifier mdModulesNotifier;
620 std::unique_ptr<EnergyOutput> energyOutput =
621 std::make_unique<EnergyOutput>(energyFile_,
627 StartingBehavior::NewSimulation,
631 // Add synthetic data for a single step
632 double testValue = 10.0;
633 for (int frame = 0; frame < parameters.numFrames; frame++)
635 setStepData(&testValue);
636 energyOutput->addDataAtEnergyStep(false,
644 PTCouplingArrays({ state_.boxv,
645 state_.nosehoover_xi,
646 state_.nosehoover_vxi,
648 state_.nhpres_vxi }),
658 energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
659 energyOutput->printStepToEnergyFile(
660 energyFile_, true, false, false, log_, 100 * frame, time_, nullptr, nullptr);
664 energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
665 energyOutput->printAverages(log_, &mtop_.groups);
667 // We need to close the file before the contents are available.
668 logFileGuard_.reset(nullptr);
670 done_ener_file(energyFile_);
673 checker_.setDefaultTolerance(relativeToleranceAsFloatingPoint(testValue, 1.0e-5));
675 if (parameters.numFrames > 0)
677 // Test binary output
678 checkEdrFile(edrFilename_.c_str(), parameters.numFrames);
681 // Test printed values
682 checker_.checkInteger(energyOutput->numEnergyTerms(), "Number of Energy Terms");
683 checker_.checkString(TextReader::readFileToString(logFilename_), "log");
686 INSTANTIATE_TEST_CASE_P(WithParameters, EnergyOutputTest, ::testing::ValuesIn(parametersSets));