/dports/science/gromacs/gromacs-2021.4/src/gromacs/modularsimulator/ |
H A D | modularsimulator.cpp | 214 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() [all …]
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H A D | simulatoralgorithm.cpp | 111 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() [all …]
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H A D | computeglobalselement.cpp | 76 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()
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H A D | parrinellorahmanbarostat.cpp | 73 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()
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H A D | statepropagatordata.cpp | 83 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() [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/taskassignment/ |
H A D | decidegpuusage.cpp | 378 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() [all …]
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H A D | decidesimulationworkload.cpp | 55 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()
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H A D | decidegpuusage.h | 157 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,
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H A D | resourcedivision.cpp | 348 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 [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/ |
H A D | runner.cpp | 874 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() [all …]
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H A D | minimize.cpp | 821 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() [all …]
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H A D | runner.cpp.preplumed | 864 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) [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdrun/ |
H A D | runner.cpp | 752 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() [all …]
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H A D | minimize.cpp | 881 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() [all …]
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H A D | runner.cpp.preplumed | 752 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) [all …]
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H A D | minimize.cpp.preplumed | 88 #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); [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/ |
H A D | runner.cpp | 967 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() [all …]
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H A D | minimize.cpp | 782 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() [all …]
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H A D | tpi.cpp | 198 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() [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/ |
H A D | runner.cpp | 977 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() [all …]
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H A D | minimize.cpp | 828 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() [all …]
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H A D | runner.cpp.preplumed | 967 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) [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
H A D | boxdeformation.cpp | 71 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()
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H A D | sim_util.cpp | 517 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() [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 | 523 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() [all …]
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