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Searched refs:pull_work (Results 1 – 25 of 51) sorted by relevance

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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/
H A Dmakeconstraints.h100 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()
H A Dconstr.cpp102 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()
H A Dsim_util.cpp192 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 …]
/dports/science/gromacs/gromacs-2021.4/src/gromacs/applied_forces/awh/
H A Dawh.cpp181 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()
H A Dawh.h141 pull_t* pull_work,
255 static void registerAwhWithPull(const AwhParams& awhParams, pull_t* pull_work);
316 pull_t* pull_work);
H A Dread_params.h100 pull_t* pull_work,
H A Dread_params.cpp1055 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()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/
H A Disimulator.h129 pull_t* pull_work, in LegacySimulatorData() argument
163 pull_work(pull_work), in LegacySimulatorData()
218 pull_t* pull_work; variable
H A Dminimize.cpp371 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 …]
H A Drerun.cpp290 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()
H A Dmimic.cpp233 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()
H A Dsimulatorbuilder.cpp139 … interactiveMD_->imdSession, centerOfMassPulling_->pull_work, ionSwapping_->ionSwap, in build()
157 legacyInput_->inputrec, interactiveMD_->imdSession, centerOfMassPulling_->pull_work, in build()
H A Dmd.cpp298 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()
H A Dsimulatorbuilder.h279 explicit CenterOfMassPulling(pull_t* pullWork) : pull_work(pullWork) {} in CenterOfMassPulling()
281 pull_t* pull_work; variable
H A Dshellfc.h102 pull_t* pull_work,
/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxpreprocess/
H A Dreadpull.cpp518 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()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/modularsimulator/
H A Dforceelement.cpp89 pull_t* pull_work, in ForceElement() argument
122 pull_work_(pull_work), in ForceElement()
269 … legacySimulatorData->imdSession, legacySimulatorData->pull_work, legacySimulatorData->constr, in getElementPointerImpl()
H A Ddomdechelper.cpp77 pull_t* pull_work) : in DomDecHelper() argument
97 pull_work_(pull_work) in DomDecHelper()
H A Ddomdechelper.h109 pull_t* pull_work);
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/
H A Dminimize.cpp378 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 …]
H A Dmd.cpp317 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 …]
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/
H A Dminimize.cpp368 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 …]
H A Dmd.cpp311 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 …]
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdlib/
H A Dsim_util.cpp198 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 …]
/dports/science/gromacs/gromacs-2021.4/src/gromacs/domdec/
H A Dpartition.h123 pull_t* pull_work,

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