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Searched refs:inputrec (Results 1 – 25 of 127) sorted by relevance

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/dports/science/gromacs/gromacs-2021.4/src/gromacs/modularsimulator/
H A Dmodularsimulator.cpp214 inputrec->eI == eiMD || inputrec->eI == eiVV, in isInputCompatible()
229 && conditionalAssert(inputrec->etc == etcNO || inputrec->etc == etcVRESCALE in isInputCompatible()
236 inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN, in isInputCompatible()
241 !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec) in isInputCompatible()
245 && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES in isInputCompatible()
254 && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0 in isInputCompatible()
265 inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0 in isInputCompatible()
266 && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0 in isInputCompatible()
267 && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0 in isInputCompatible()
268 && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0 in isInputCompatible()
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H A Dsimulatoralgorithm.cpp111 inputrec(inputrec), in ModularSimulatorAlgorithm()
205 if (inputrec->nsteps >= 0) in simulatorSetup()
217 gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf), timeString.c_str(), in simulatorSetup()
218 … gmx_step_str(inputrec->init_step, sbuf2), inputrec->init_step * inputrec->delta_t); in simulatorSetup()
232 step_ = inputrec->init_step; in simulatorSetup()
573 const auto* inputrec = legacySimulatorData_->inputrec; in build() local
575 inputrec->nstcalcenergy, inputrec->fepvals->nstdhdl, inputrec->nstpcouple)); in build()
577 inputrec->nstxout, inputrec->nstvout, inputrec->nstfout, in build()
581 addSignaller(loggingSignallerBuilder_.build(inputrec->nstlog, inputrec->init_step, in build()
583 addSignaller(lastStepSignallerBuilder_.build(inputrec->nsteps, inputrec->init_step, in build()
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H A Dcomputeglobalselement.cpp76 const t_inputrec* inputrec, in ComputeGlobalsElement() argument
86 doStopCM_(inputrec->comm_mode != ecmNO), in ComputeGlobalsElement()
87 nstcomm_(inputrec->nstcomm), in ComputeGlobalsElement()
89 lastStep_(inputrec->nsteps + inputrec->init_step), in ComputeGlobalsElement()
90 initStep_(inputrec->init_step), in ComputeGlobalsElement()
98 vcm_(global_top->groups, *inputrec), in ComputeGlobalsElement()
103 inputrec_(inputrec), in ComputeGlobalsElement()
364 legacySimulatorData->inputrec, legacySimulatorData->mdAtoms, in getElementPointerImpl()
402 simulator->cr, simulator->inputrec, simulator->mdAtoms, simulator->nrnb, in getElementPointerImpl()
H A Dparrinellorahmanbarostat.cpp73 const t_inputrec* inputrec, in ParrinelloRahmanBarostat() argument
85 inputrec_(inputrec),
288 legacySimulatorData->inputrec->nstpcouple, offset, in getElementPointerImpl()
289 legacySimulatorData->inputrec->delta_t * legacySimulatorData->inputrec->nstpcouple, in getElementPointerImpl()
290 legacySimulatorData->inputrec->init_step, statePropagatorData, energyData, in getElementPointerImpl()
291 … legacySimulatorData->fplog, legacySimulatorData->inputrec, legacySimulatorData->mdAtoms)); in getElementPointerImpl()
H A Dstatepropagatordata.cpp83 const t_inputrec* inputrec, in StatePropagatorData() argument
94 inputrec->nstxout,
95 inputrec->nstvout,
96 inputrec->nstfout,
97 inputrec->nstxout_compressed,
101 inputrec,
143 if (!inputrec->bContinuation)
167 if (inputrec->eI == eiVV)
665 systemHasPeriodicMolecules_(inputrec->bPeriodicMols), in Element()
666 pbcType_(inputrec->pbcType), in Element()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/taskassignment/
H A Ddecidegpuusage.cpp378 if (!pme_gpu_supports_input(inputrec, &message)) in decideWhetherToUseGpusForPme()
455 if (!EEL_PME(inputrec.coulombtype)) in determinePmeRunMode()
548 (EVDW_PME(inputrec.vdwtype) in decideWhetherToUseGpusForBonded()
605 if (inputrec.useMts) in decideWhetherToUseGpuForUpdate()
631 if (inputrec.eI != eiMD) in decideWhetherToUseGpuForUpdate()
635 if (inputrec.etc == etcNOSEHOOVER) in decideWhetherToUseGpuForUpdate()
639 if (!(inputrec.epc == epcNO || inputrec.epc == epcPARRINELLORAHMAN in decideWhetherToUseGpuForUpdate()
640 || inputrec.epc == epcBERENDSEN || inputrec.epc == epcCRESCALE)) in decideWhetherToUseGpuForUpdate()
646 if (EEL_PME_EWALD(inputrec.coulombtype) && inputrec.epsilon_surface != 0) in decideWhetherToUseGpuForUpdate()
659 if (inputrec.bPull && pull_have_constraint(*inputrec.pull)) in decideWhetherToUseGpuForUpdate()
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H A Ddecidesimulationworkload.cpp55 SimulationWorkload createSimulationWorkload(const t_inputrec& inputrec, in createSimulationWorkload() argument
67 simulationWorkload.computeNonbonded && inputrec.useMts in createSimulationWorkload()
68 && inputrec.mtsLevels.back().forceGroups[static_cast<int>(MtsForceGroups::Nonbonded)]; in createSimulationWorkload()
69 simulationWorkload.computeMuTot = inputrecNeedMutot(&inputrec); in createSimulationWorkload()
84 simulationWorkload.haveEwaldSurfaceContribution = haveEwaldSurfaceContribution(inputrec); in createSimulationWorkload()
H A Ddecidegpuusage.h157 const t_inputrec& inputrec,
230 const t_inputrec& inputrec,
247 …determinePmeRunMode(bool useGpuForPme, const TaskTarget& pmeFftTarget, const t_inputrec& inputrec);
266 const t_inputrec& inputrec,
301 const t_inputrec& inputrec,
H A Dresourcedivision.cpp348 const t_inputrec* inputrec, in get_nthreads_mpi() argument
361 GMX_RELEASE_ASSERT((EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)) in get_nthreads_mpi()
364 && pme_gpu_supports_input(*inputrec, nullptr), in get_nthreads_mpi()
381 checker.applyConstraint(inputrec->eI == eiLBFGS, "L-BFGS minimization"); in get_nthreads_mpi()
382 checker.applyConstraint(inputrec->coulombtype == eelEWALD, "Plain Ewald electrostatics"); in get_nthreads_mpi()
440 if (inputrec->eI == eiNM || EI_TPI(inputrec->eI)) in get_nthreads_mpi()
683 const t_inputrec* inputrec) in checkAndUpdateHardwareOptions() argument
729 GMX_RELEASE_ASSERT(inputrec, "Expect a valid inputrec"); in checkAndUpdateHardwareOptions()
730 if (EI_TPI(inputrec->eI) && hw_opt->nthreads_omp == 0) in checkAndUpdateHardwareOptions()
862 const t_inputrec& inputrec) in checkAndUpdateRequestedNumOpenmpThreads() argument
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/
H A Drunner.cpp874 EVDW_PME(inputrec->vdwtype), EEL_PME_EWALD(inputrec->coulombtype), in mdrunner()
943 if (inputrec->eI == eiNM || inputrec->eI == eiTPI) in mdrunner()
972 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI)) in mdrunner()
979 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))) in mdrunner()
1077 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step); in mdrunner()
1392 …if (!inputrec->bContinuation && MASTER(cr) && !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicM… in mdrunner()
1422 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol); in mdrunner()
1423 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj); in mdrunner()
1445 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)) in mdrunner()
1497 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage) in mdrunner()
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H A Dminimize.cpp821 t_inputrec* inputrec; member in __anon20dcc7fd0211::EnergyEvaluator
859 t = inputrec->init_t; in run()
869 if (inputrec->nstlist > 0) in run()
1176 number_steps = inputrec->nsteps; in do_cg()
1687 do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout)); in do_cg()
1753 nmaxcorr = inputrec->nbfgscorr; in do_lbfgs()
1806 number_steps = inputrec->nsteps; in do_lbfgs()
1931 if (inputrec->bIMD) in do_lbfgs()
2373 if (ems.fmax > inputrec->em_tol) in do_lbfgs()
2477 nsteps = inputrec->nsteps; in do_steep()
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H A Drunner.cpp.preplumed864 EVDW_PME(inputrec->vdwtype), EEL_PME_EWALD(inputrec->coulombtype),
933 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
962 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
969 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
1067 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step);
1382 …if (!inputrec->bContinuation && MASTER(cr) && !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicM…
1412 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1413 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1435 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1487 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdrun/
H A Drunner.cpp752 if (inputrec->eI == eiNM || inputrec->eI == eiTPI) in mdrunner()
782 (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI)) in mdrunner()
792 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))) in mdrunner()
827 fcRegisterSteps(inputrec->nsteps, inputrec->init_step); in mdrunner()
1265 !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols)) in mdrunner()
1294 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol); in mdrunner()
1295 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj); in mdrunner()
1305 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)) in mdrunner()
1360 init_pull(fplog, inputrec->pull, inputrec, in mdrunner()
1362 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage) in mdrunner()
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H A Dminimize.cpp881 t = inputrec->init_t; in run()
892 if (inputrec->nstlist > 0) in run()
1681 IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE); in do_cg()
1706 IMD_finalize(inputrec->bIMD, inputrec->imd); in do_cg()
1759 do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout)); in do_cg()
2005 if (inputrec->bIMD) in do_lbfgs()
2444 IMD_finalize(inputrec->bIMD, inputrec->imd); in do_lbfgs()
2559 nsteps = inputrec->nsteps; in do_steep()
2641 IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE); in do_steep()
2732 IMD_finalize(inputrec->bIMD, inputrec->imd); in do_steep()
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H A Drunner.cpp.preplumed752 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
782 (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
792 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
827 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1265 !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1294 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1295 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1305 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1360 init_pull(fplog, inputrec->pull, inputrec,
1362 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
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H A Dminimize.cpp.preplumed88 #include "gromacs/mdtypes/inputrec.h"
836 t = inputrec->init_t;
1606 IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE);
1631 IMD_finalize(inputrec->bIMD, inputrec->imd);
1684 do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
1930 if (inputrec->bIMD)
2369 IMD_finalize(inputrec->bIMD, inputrec->imd);
2484 nsteps = inputrec->nsteps;
2566 IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
2657 IMD_finalize(inputrec->bIMD, inputrec->imd);
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/
H A Drunner.cpp967 if (inputrec->eI == eiNM || inputrec->eI == eiTPI) in mdrunner()
997 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI)) in mdrunner()
1004 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))) in mdrunner()
1123 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step); in mdrunner()
1513 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols)) in mdrunner()
1543 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol); in mdrunner()
1544 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj); in mdrunner()
1571 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)) in mdrunner()
1642 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage) in mdrunner()
1653 if (inputrec->bRot) in mdrunner()
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H A Dminimize.cpp782 t_inputrec* inputrec; member in __anonb5f32c170111::EnergyEvaluator
816 t = inputrec->init_t; in run()
826 if (inputrec->nstlist > 0) in run()
911 if (inputrec->efep != efepNO) in run()
1107 number_steps = inputrec->nsteps; in do_cg()
1620 do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout)); in do_cg()
1685 nmaxcorr = inputrec->nbfgscorr; in do_lbfgs()
1739 number_steps = inputrec->nsteps; in do_lbfgs()
1861 if (inputrec->bIMD) in do_lbfgs()
2410 nsteps = inputrec->nsteps; in do_steep()
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H A Dtpi.cpp198 if (EVDW_PME(inputrec->vdwtype)) in do_tpi()
228 bCavity = (inputrec->eI == eiTPIC); in do_tpi()
263 temp = inputrec->opts.ref_t[0]; in do_tpi()
283 nsteps = inputrec->nsteps; in do_tpi()
289 drmax = inputrec->rtpi; in do_tpi()
369 const real maxCutoff = std::max(inputrec->rvdw, inputrec->rcoulomb); in do_tpi()
398 if (inputrec->nstlist > 1) in do_tpi()
434 inputrec->rlist = maxCutoff + 2 * inputrec->rtpi + 2 * molRadius; in do_tpi()
436 fr->nbv->changePairlistRadii(inputrec->rlist, inputrec->rlist); in do_tpi()
470 seed = inputrec->ld_seed; in do_tpi()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/
H A Drunner.cpp977 if (inputrec->eI == eiNM || inputrec->eI == eiTPI) in mdrunner()
1007 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI)) in mdrunner()
1014 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))) in mdrunner()
1133 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step); in mdrunner()
1509 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols)) in mdrunner()
1539 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol); in mdrunner()
1540 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj); in mdrunner()
1567 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)) in mdrunner()
1638 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage) in mdrunner()
1649 if (inputrec->bRot) in mdrunner()
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H A Dminimize.cpp828 t_inputrec* inputrec; member in __anon3b7ade1a0111::EnergyEvaluator
862 t = inputrec->init_t; in run()
872 if (inputrec->nstlist > 0) in run()
988 if (inputrec->efep != efepNO) in run()
1184 number_steps = inputrec->nsteps; in do_cg()
1697 do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout)); in do_cg()
1762 nmaxcorr = inputrec->nbfgscorr; in do_lbfgs()
1816 number_steps = inputrec->nsteps; in do_lbfgs()
1938 if (inputrec->bIMD) in do_lbfgs()
2487 nsteps = inputrec->nsteps; in do_steep()
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H A Drunner.cpp.preplumed967 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
997 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
1004 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
1123 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step);
1499 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
1529 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1530 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1557 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1628 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1639 if (inputrec->bRot)
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/
H A Dboxdeformation.cpp71 const t_inputrec& inputrec) in prepareBoxDeformation() argument
73 if (!inputrecDeform(&inputrec)) in prepareBoxDeformation()
77 if (!EI_DYNAMICS(inputrec.eI)) in prepareBoxDeformation()
97 …return std::make_unique<BoxDeformation>(inputrec.delta_t, inputrec.init_step, inputrec.deform, box… in prepareBoxDeformation()
H A Dsim_util.cpp517 if (step == inputrec.init_step && EI_DYNAMICS(inputrec.eI)) in checkPotentialEnergyValidity()
543 static bool haveSpecialForces(const t_inputrec& inputrec, in haveSpecialForces() argument
626 if (inputrec->bPull && pull_have_potential(*pull_work)) in computeSpecialForces()
660 if (inputrec->bRot) in computeSpecialForces()
678 if (inputrec->bIMD && stepWork.computeForces) in computeSpecialForces()
1128 const t_inputrec* inputrec, in do_force() argument
1611 if (inputrec->bRot) in do_force()
1649 if (inputrec->bPull && pull_have_constraint(*pull_work)) in do_force()
1729 if (inputrec->nwall && stepWork.computeNonbondedForces) in do_force()
1882 inputrec->mtsLevels[1].stepFactor); in do_force()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdlib/
H A Dsim_util.cpp523 if (step == inputrec.init_step && EI_DYNAMICS(inputrec.eI)) in checkPotentialEnergyValidity()
549 static bool haveSpecialForces(const t_inputrec& inputrec, in haveSpecialForces() argument
632 if (inputrec->bPull && pull_have_potential(*pull_work)) in computeSpecialForces()
666 if (inputrec->bRot) in computeSpecialForces()
684 if (inputrec->bIMD && stepWork.computeForces) in computeSpecialForces()
1134 const t_inputrec* inputrec, in do_force() argument
1610 if (inputrec->bRot) in do_force()
1648 if (inputrec->bPull && pull_have_constraint(*pull_work)) in do_force()
1728 if (inputrec->nwall && stepWork.computeNonbondedForces) in do_force()
1889 inputrec->mtsLevels[1].stepFactor); in do_force()
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