| /dports/science/gromacs/gromacs-2021.4/src/gromacs/modularsimulator/ |
| H A D | energydata.cpp | 93 ObservablesHistory* observablesHistory, in EnergyData() argument
119 observablesHistory_(observablesHistory), in EnergyData()
447 ObservablesHistory* observablesHistory, in initializeEnergyHistory() argument
458 if (observablesHistory->energyHistory) in initializeEnergyHistory()
463 else if (observablesHistory->energyHistory) in initializeEnergyHistory()
469 observablesHistory->energyHistory = {}; in initializeEnergyHistory()
478 if (!observablesHistory->energyHistory) in initializeEnergyHistory()
480 observablesHistory->energyHistory = std::make_unique<energyhistory_t>(); in initializeEnergyHistory()
482 if (!observablesHistory->pullHistory) in initializeEnergyHistory()
484 observablesHistory->pullHistory = std::make_unique<PullHistory>(); in initializeEnergyHistory()
[all …]
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| H A D | checkpointhelper.cpp | 66 ObservablesHistory* observablesHistory, in CheckpointHelper() argument
78 observablesHistory_(observablesHistory), in CheckpointHelper()
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| H A D | energydata.h | 109 ObservablesHistory* observablesHistory,
213 ObservablesHistory* observablesHistory,
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| H A D | checkpointhelper.h | 105 ObservablesHistory* observablesHistory,
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/ |
| H A D | isimulator.h | 133 ObservablesHistory* observablesHistory, in LegacySimulatorData() argument
167 observablesHistory(observablesHistory), in LegacySimulatorData()
226 ObservablesHistory* observablesHistory; variable
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| H A D | simulationinput.cpp | 65 ObservablesHistory* observablesHistory, in applyLocalState() argument
72 observablesHistory, reproducibilityRequested, mdModulesNotifier, in applyLocalState()
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| H A D | simulationinput.h | 158 ObservablesHistory* observablesHistory,
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| H A D | simulatorbuilder.h | 121 ObservablesHistory* observablesHistory, in SimulatorStateData()
125 observablesHistory_p(observablesHistory), in SimulatorStateData()
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| H A D | minimize.cpp | 519 ObservablesHistory* observablesHistory) in write_em_traj() argument
541 … observablesHistory, state->f.view().force(), &checkpointDataHolder); in write_em_traj()
1258 state_global, observablesHistory); in do_cg()
1623 step, s_min, state_global, observablesHistory); in do_cg()
1868 … static_cast<real>(step), &ems.s, state_global, observablesHistory, in do_lbfgs()
2344 step, &ems, state_global, observablesHistory); in do_lbfgs()
2521 state_global, observablesHistory); in do_steep()
2577 top_global, inputrec, count, s_min, state_global, observablesHistory); in do_steep()
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| H A D | mimic.cpp | 188 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr) in do_mimic()
454 state_global, observablesHistory, top_global, fr, outf, in do_mimic()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
| H A D | trajectory_writing.cpp | 68 ObservablesHistory* observablesHistory, in do_md_trajectory_writing() argument
139 energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get()); in do_md_trajectory_writing()
150 … state_global, observablesHistory, f, &checkpointDataHolder); in do_md_trajectory_writing()
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| H A D | mdoutf.cpp | 299 ObservablesHistory* observablesHistory, in write_checkpoint() argument
354 edsamhistory_t* edsamhist = observablesHistory->edsamHistory.get(); in write_checkpoint()
357 swaphistory_t* swaphist = observablesHistory->swapHistory.get(); in write_checkpoint()
397 write_checkpoint_data(fp, headerContents, bExpanded, elamstats, state, observablesHistory, in write_checkpoint()
494 ObservablesHistory* observablesHistory, in mdoutf_write_checkpoint() argument
509 observablesHistory, *(of->mdModulesNotifier), modularSimulatorCheckpointData, in mdoutf_write_checkpoint()
522 ObservablesHistory* observablesHistory, in mdoutf_write_to_trajectory_files() argument
569 mdoutf_write_checkpoint(of, fplog, cr, step, t, state_global, observablesHistory, in mdoutf_write_to_trajectory_files()
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| H A D | mdoutf.h | 141 ObservablesHistory* observablesHistory,
169 ObservablesHistory* observablesHistory,
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| H A D | trajectory_writing.h | 73 ObservablesHistory* observablesHistory,
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/pulling/ |
| H A D | output.cpp | 556 void initPullHistory(pull_t* pull, ObservablesHistory* observablesHistory) in initPullHistory() argument
560 if (observablesHistory == nullptr) in initPullHistory()
566 if (observablesHistory->pullHistory == nullptr) in initPullHistory()
568 observablesHistory->pullHistory = std::make_unique<PullHistory>(); in initPullHistory()
569 pull->coordForceHistory = observablesHistory->pullHistory.get(); in initPullHistory()
577 pull->coordForceHistory = observablesHistory->pullHistory.get(); in initPullHistory()
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| H A D | output.h | 94 void initPullHistory(pull_t* pull, ObservablesHistory* observablesHistory);
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/ |
| H A D | checkpoint.h | 251 ObservablesHistory* observablesHistory,
269 ObservablesHistory* observablesHistory,
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| H A D | checkpoint.cpp | 2256 energyhistory_t* enerhist = observablesHistory->energyHistory.get(); in write_checkpoint_data()
2279 PullHistory* pullHist = observablesHistory->pullHistory.get(); in write_checkpoint_data()
2327 observablesHistory->edsamHistory.get(), nullptr) in write_checkpoint_data()
2331 observablesHistory->swapHistory.get(), nullptr) in write_checkpoint_data()
2518 ObservablesHistory* observablesHistory, in read_checkpoint() argument
2651 observablesHistory->energyHistory.get(), nullptr); in read_checkpoint()
2659 if (observablesHistory->pullHistory == nullptr) in read_checkpoint()
2661 observablesHistory->pullHistory = std::make_unique<PullHistory>(); in read_checkpoint()
2689 observablesHistory->edsamHistory.get(), nullptr); in read_checkpoint()
2710 observablesHistory->swapHistory.get(), nullptr); in read_checkpoint()
[all …]
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| /dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdrun/ |
| H A D | md.cpp | 261 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr) in do_md()
268 state_global, observablesHistory, in do_md()
379 if (observablesHistory->energyHistory) in do_md()
384 else if (observablesHistory->energyHistory) in do_md()
390 observablesHistory->energyHistory = {}; in do_md()
399 if (!observablesHistory->energyHistory) in do_md()
401 observablesHistory->energyHistory = compat::make_unique<energyhistory_t>(); in do_md()
403 if (!observablesHistory->pullHistory) in do_md()
405 observablesHistory->pullHistory = compat::make_unique<PullHistory>(); in do_md()
408 update_energyhistory(observablesHistory->energyHistory.get(), mdebin); in do_md()
[all …]
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| H A D | runner.cpp | 847 ObservablesHistory observablesHistory = {}; in mdrunner() local
871 &bReadEkin, &observablesHistory, in mdrunner()
1364 initPullHistory(inputrec->pull_work, &observablesHistory); in mdrunner()
1394 &mtop, globalState.get(), &observablesHistory, in mdrunner()
1402 || observablesHistory.edsamHistory); in mdrunner()
1451 &observablesHistory, in mdrunner()
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| H A D | md.cpp.preplumed | 244 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
251 state_global, observablesHistory,
362 if (observablesHistory->energyHistory)
367 else if (observablesHistory->energyHistory)
373 observablesHistory->energyHistory = {};
377 * This means that observablesHistory->pullHistory
382 if (!observablesHistory->energyHistory)
386 if (!observablesHistory->pullHistory)
388 observablesHistory->pullHistory = compat::make_unique<PullHistory>();
391 update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
[all …]
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| H A D | minimize.cpp | 577 ObservablesHistory *observablesHistory) in write_em_traj() argument
598 &state->s, state_global, observablesHistory, in write_em_traj()
1381 s_min, state_global, observablesHistory); in do_cg()
1763 s_min, state_global, observablesHistory); in do_cg()
2011 … top_global, step, static_cast<real>(step), &ems.s, state_global, observablesHistory, ems.f); in do_lbfgs()
2492 &ems, state_global, observablesHistory); in do_lbfgs()
2678 s_min, state_global, observablesHistory); in do_steep()
2741 s_min, state_global, observablesHistory); in do_steep()
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| /dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/ |
| H A D | runner.cpp | 1044 ObservablesHistory observablesHistory = {}; in mdrunner() local
1062 &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier()); in mdrunner()
1499 initPullHistory(pull_work, &observablesHistory); in mdrunner()
1522 &mtop, globalState.get(), &observablesHistory, cr, &atomSets, in mdrunner()
1617 pull_work, swap, &mtop, fcd, globalState.get(), &observablesHistory, mdAtoms.get(), in mdrunner()
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| H A D | minimize.cpp | 561 ObservablesHistory* observablesHistory) in write_em_traj() argument
582 observablesHistory, state->f); in write_em_traj()
1329 state_global, observablesHistory); in do_cg()
1690 step, s_min, state_global, observablesHistory); in do_cg()
1938 observablesHistory, ems.f); in do_lbfgs()
2411 step, &ems, state_global, observablesHistory); in do_lbfgs()
2588 state_global, observablesHistory); in do_steep()
2644 top_global, inputrec, count, s_min, state_global, observablesHistory); in do_steep()
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| /dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/ |
| H A D | minimize.cpp | 565 ObservablesHistory* observablesHistory) in write_em_traj() argument
587 … observablesHistory, state->f.view().force(), &checkpointDataHolder); in write_em_traj()
1335 state_global, observablesHistory); in do_cg()
1700 step, s_min, state_global, observablesHistory); in do_cg()
1945 … static_cast<real>(step), &ems.s, state_global, observablesHistory, in do_lbfgs()
2421 step, &ems, state_global, observablesHistory); in do_lbfgs()
2598 state_global, observablesHistory); in do_steep()
2654 top_global, inputrec, count, s_min, state_global, observablesHistory); in do_steep()
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