/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
H A D | makeconstraints.h | 100 pull_t* pull_work, in makeConstraints() argument 106 GMX_RELEASE_ASSERT(!ir.bPull || pull_work != nullptr, in makeConstraints() 109 bool doPullingWithConstraints = ir.bPull && pull_have_constraint(*pull_work); in makeConstraints() 116 mtop, ir, pull_work, std::forward<Args>(args)..., numConstraints, numSettles); in makeConstraints()
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H A D | constr.cpp | 102 pull_t* pull_work, 191 pull_t* pull_work = nullptr; member in gmx::Constraints::Impl 675 if (ir.bPull && pull_have_constraint(*pull_work)) in apply() 686 pull_constraint(pull_work, masses_, &pbc, cr, ir.delta_t, t, in apply() 994 pull_t* pull_work, in Constraints() argument 1003 …impl_(new Impl(mtop, ir, pull_work, log, cr, ms, nrnb, wcycle, pbcHandlingRequired, numConstraints… in Constraints() 1009 pull_t* pull_work, in Impl() argument 1024 pull_work(pull_work), in Impl()
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H A D | sim_util.cpp | 192 pull_t* pull_work, in pull_potential_wrapper() argument 207 pull_potential(pull_work, mdatoms->massT, &pbc, cr, t, lambda[efptRESTRAINT], in pull_potential_wrapper() 545 const pull_t* pull_work, in haveSpecialForces() argument 551 (inputrec.bPull && pull_have_potential(*pull_work)) || // pull in haveSpecialForces() 598 pull_t* pull_work, in computeSpecialForces() argument 626 if (inputrec->bPull && pull_have_potential(*pull_work)) in computeSpecialForces() 847 const pull_t* pull_work, in setupDomainLifetimeWorkload() argument 1132 pull_t* pull_work, in do_force() argument 1370 *inputrec, *fr, pull_work, ed, *mdatoms, simulationWork, stepWork); in do_force() 1649 if (inputrec->bPull && pull_have_constraint(*pull_work)) in do_force() [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/applied_forces/awh/ |
H A D | awh.cpp | 181 pull_t* pull_work, in Awh() argument 188 pull_(pull_work), in Awh() 196 GMX_RELEASE_ASSERT(pull_work != nullptr, in Awh() 469 void Awh::registerAwhWithPull(const AwhParams& awhParams, pull_t* pull_work) in registerAwhWithPull() argument 471 GMX_RELEASE_ASSERT(!anyDimUsesProvider(awhParams, eawhcoordproviderPULL) || pull_work, in registerAwhWithPull() 482 register_external_pull_potential(pull_work, biasParams.dimParams[d].coordIndex, in registerAwhWithPull() 568 pull_t* pull_work) in prepareAwhModule() argument 581 pull_work, inputRecord.fepvals->n_lambda, inputRecord.fepvals->init_fep_state); in prepareAwhModule()
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H A D | awh.h | 141 pull_t* pull_work, 255 static void registerAwhWithPull(const AwhParams& awhParams, pull_t* pull_work); 316 pull_t* pull_work);
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H A D | read_params.h | 100 pull_t* pull_work,
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H A D | read_params.cpp | 1055 pull_t* pull_work, in setStateDependentAwhPullDimParams() argument 1097 dimParams->coordValueInit = get_pull_coord_value(pull_work, dimParams->coordIndex, &pbc); in setStateDependentAwhPullDimParams() 1104 pull_t* pull_work, in setStateDependentAwhParams() argument 1142 setStateDependentAwhPullDimParams(dimParams, k, d, &pull_params, pull_work, pbc, in setStateDependentAwhParams() 1156 Awh::registerAwhWithPull(*awhParams, pull_work); in setStateDependentAwhParams()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/ |
H A D | isimulator.h | 129 pull_t* pull_work, in LegacySimulatorData() argument 163 pull_work(pull_work), in LegacySimulatorData() 218 pull_t* pull_work; variable
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H A D | minimize.cpp | 371 pull_t* pull_work, in init_em() argument 428 imdSession, pull_work, &ems->s, &ems->f, mdAtoms, top, fr, vsite, in init_em() 726 pull_t* pull_work, in em_dd_partition_system() argument 786 pull_t* pull_work; member in __anonb5f32c170111::EnergyEvaluator 848 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle, in run() 1093 init_em(fplog, mdlog, CG, cr, inputrec, imdSession, pull_work, state_global, top_global, s_min, in do_cg() 1099 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work, in do_cg() 1709 init_em(fplog, mdlog, LBFGS, cr, inputrec, imdSession, pull_work, state_global, top_global, in do_lbfgs() 1715 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work, in do_lbfgs() 2396 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work, in do_steep() [all …]
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H A D | rerun.cpp | 290 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, in do_rerun() 321 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr, in do_rerun() 518 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top, in do_rerun() 541 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, in do_rerun() 556 do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb, in do_rerun() 631 pull_print_output(pull_work, step, t); in do_rerun()
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H A D | mimic.cpp | 233 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, in do_mimic() 266 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr, in do_mimic() 402 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top, in do_mimic() 425 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, in do_mimic() 440 do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb, in do_mimic()
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H A D | simulatorbuilder.cpp | 139 … interactiveMD_->imdSession, centerOfMassPulling_->pull_work, ionSwapping_->ionSwap, in build() 157 legacyInput_->inputrec, interactiveMD_->imdSession, centerOfMassPulling_->pull_work, in build()
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H A D | md.cpp | 298 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, in do_md() 341 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr, in do_md() 456 preparePrevStepPullCom(ir, pull_work, mdatoms->massT, state, state_global, cr, in do_md() 462 shellfc != nullptr, opt2fn("-awh", nfile, fnm), pull_work); in do_md() 832 … *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top, in do_md() 919 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, in do_md() 945 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step, in do_md() 1338 updatePrevStepPullCom(pull_work, state); in do_md() 1577 pull_print_output(pull_work, step, t); in do_md() 1634 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr, in do_md()
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H A D | simulatorbuilder.h | 279 explicit CenterOfMassPulling(pull_t* pullWork) : pull_work(pullWork) {} in CenterOfMassPulling() 281 pull_t* pull_work; variable
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H A D | shellfc.h | 102 pull_t* pull_work,
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxpreprocess/ |
H A D | readpull.cpp | 518 pull_t* pull_work; in set_pull_init() local 525 pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda); in set_pull_init() 540 initPullComFromPrevStep(nullptr, pull_work, md->massT, &pbc, x); in set_pull_init() 542 pull_calc_coms(nullptr, pull_work, md->massT, &pbc, t_start, x, nullptr); in set_pull_init() 547 *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms), in set_pull_init() 578 … *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms), in set_pull_init() 616 value = get_pull_coord_value(pull_work, c, &pbc); in set_pull_init() 669 return pull_work; in set_pull_init()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/modularsimulator/ |
H A D | forceelement.cpp | 89 pull_t* pull_work, in ForceElement() argument 122 pull_work_(pull_work), in ForceElement() 269 … legacySimulatorData->imdSession, legacySimulatorData->pull_work, legacySimulatorData->constr, in getElementPointerImpl()
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H A D | domdechelper.cpp | 77 pull_t* pull_work) : in DomDecHelper() argument 97 pull_work_(pull_work) in DomDecHelper()
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H A D | domdechelper.h | 109 pull_t* pull_work);
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/ |
H A D | minimize.cpp | 378 pull_t* pull_work, in init_em() argument 435 imdSession, pull_work, &ems->s, &ems->f, mdAtoms, top, fr, vsite, in init_em() 772 pull_t* pull_work, in em_dd_partition_system() argument 832 pull_t* pull_work; member in __anon3b7ade1a0111::EnergyEvaluator 886 em_dd_partition_system(fplog, mdlog, count, cr, top_global, inputrec, imdSession, pull_work, in run() 911 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle, in run() 1176 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work, in do_cg() 1196 inputrec, imdSession, pull_work, nrnb, wcycle, gstat, in do_cg() 1792 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work, in do_lbfgs() 1851 inputrec, imdSession, pull_work, nrnb, wcycle, gstat, in do_lbfgs() [all …]
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H A D | md.cpp | 317 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, in do_md() 360 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr, in do_md() 475 preparePrevStepPullCom(ir, pull_work, mdatoms->massT, state, state_global, cr, in do_md() 481 shellfc != nullptr, opt2fn("-awh", nfile, fnm), pull_work); in do_md() 986 imdSession, pull_work, in do_md() 991 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step, in do_md() 1028 imdSession, pull_work, in do_md() 1083 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, in do_md() 1131 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step, in do_md() 1540 updatePrevStepPullCom(pull_work, state); in do_md() [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/ |
H A D | minimize.cpp | 368 pull_t* pull_work, in init_em() argument 427 imdSession, pull_work, &ems->s, &ems->f, mdAtoms, top, fr, vsite, in init_em() 765 pull_t* pull_work, in em_dd_partition_system() argument 825 pull_t* pull_work; member in __anon20dcc7fd0211::EnergyEvaluator 884 em_dd_partition_system(fplog, mdlog, count, cr, top_global, inputrec, imdSession, pull_work, in run() 909 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle, in run() 1169 … gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work, nullptr, in do_cg() 1189 imdSession, pull_work, nrnb, wcycle, gstat, vsite, constr, in do_cg() 1843 imdSession, pull_work, nrnb, wcycle, gstat, vsite, constr, in do_lbfgs() 2490 imdSession, pull_work, nrnb, wcycle, gstat, vsite, constr, in do_steep() [all …]
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H A D | md.cpp | 311 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, in do_md() 347 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr, in do_md() 459 preparePrevStepPullCom(ir, pull_work, mdatoms, state, state_global, cr, in do_md() 465 shellfc != nullptr, opt2fn("-awh", nfile, fnm), pull_work); in do_md() 990 imdSession, pull_work, in do_md() 995 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step, in do_md() 1032 imdSession, pull_work, in do_md() 1083 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd, in do_md() 1131 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step, in do_md() 1513 updatePrevStepPullCom(pull_work, state); in do_md() [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdlib/ |
H A D | sim_util.cpp | 198 pull_t* pull_work, in pull_potential_wrapper() argument 213 pull_potential(pull_work, mdatoms->massT, &pbc, cr, t, lambda[efptRESTRAINT], in pull_potential_wrapper() 551 const pull_t* pull_work, in haveSpecialForces() argument 557 (inputrec.bPull && pull_have_potential(*pull_work)) || // pull in haveSpecialForces() 604 pull_t* pull_work, in computeSpecialForces() argument 632 if (inputrec->bPull && pull_have_potential(*pull_work)) in computeSpecialForces() 853 const pull_t* pull_work, in setupDomainLifetimeWorkload() argument 1138 pull_t* pull_work, in do_force() argument 1376 *inputrec, *fr, pull_work, ed, *mdatoms, simulationWork, stepWork); in do_force() 1648 if (inputrec->bPull && pull_have_constraint(*pull_work)) in do_force() [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/domdec/ |
H A D | partition.h | 123 pull_t* pull_work,
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