{
gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
}
- if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
- [](int i) { return i != eannNO; }))
+ if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](int i) {
+ return i != eannNO;
+ }))
{
gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
}
initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
const bool simulationsShareState = false;
- gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
- mdModulesNotifier, ir, top_global, oenv, wcycle,
- StartingBehavior::NewSimulation, simulationsShareState, ms);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
- mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
- simulationsShareState, mdModulesNotifier);
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifier,
+ ir,
+ top_global,
+ oenv,
+ wcycle,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ ms);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+ top_global,
+ ir,
+ pull_work,
+ mdoutf_get_fp_dhdl(outf),
+ true,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ mdModulesNotifier);
gstat = global_stat_init(ir);
/* Check for polarizable models and flexible constraints */
- shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
- ir->nstcalcenergy, DOMAINDECOMP(cr),
+ shellfc = init_shell_flexcon(fplog,
+ top_global,
+ constr ? constr->numFlexibleConstraints() : 0,
+ ir->nstcalcenergy,
+ DOMAINDECOMP(cr),
runScheduleWork->simulationWork.useGpuPme);
{
dd_init_local_state(cr->dd, state_global, state);
/* Distribute the charge groups over the nodes from the master node */
- dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
- imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
- nrnb, nullptr, FALSE);
+ dd_partition_system(fplog,
+ mdlog,
+ ir->init_step,
+ cr,
+ TRUE,
+ 1,
+ state_global,
+ *top_global,
+ ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ nullptr,
+ FALSE);
shouldCheckNumberOfBondedInteractions = true;
gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr->mpi_comm_mygroup);
}
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
bool bSumEkinhOld = false;
t_vcm* vcm = nullptr;
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
- force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
- &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ nullptr,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ constr,
+ &nullSignaller,
+ state->box,
+ &totalNumberOfBondedInteractions,
+ &bSumEkinhOld,
+ cglo_flags);
}
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
- makeConstArrayRef(state->x), state->box,
+ checkNumberOfBondedInteractions(mdlog,
+ cr,
+ totalNumberOfBondedInteractions,
+ top_global,
+ &top,
+ makeConstArrayRef(state->x),
+ state->box,
&shouldCheckNumberOfBondedInteractions);
if (MASTER(cr))
step_rel = 0;
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
- compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
- ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
- ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
+ compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
+ false,
+ MASTER(cr),
+ ir->nstlist,
+ mdrunOptions.reproducible,
+ nstglobalcomm,
+ mdrunOptions.maximumHoursToRun,
+ ir->nstlist == 0,
+ fplog,
+ step,
+ bNS,
+ walltime_accounting);
// we don't do counter resetting in rerun - finish will always be valid
walltime_accounting_set_valid_finish(walltime_accounting);
{
/* Repartition the domain decomposition */
const bool bMasterState = true;
- dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
- *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
- fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
+ dd_partition_system(fplog,
+ mdlog,
+ step,
+ cr,
+ bMasterState,
+ nstglobalcomm,
+ state_global,
+ *top_global,
+ ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle,
+ mdrunOptions.verbose);
shouldCheckNumberOfBondedInteractions = true;
}
if (shellfc)
{
/* Now is the time to relax the shells */
- relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
- imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
- state->natoms, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->box, state->lambda,
- &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
- fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
+ relax_shell_flexcon(fplog,
+ cr,
+ ms,
+ mdrunOptions.verbose,
+ enforcedRotation,
+ step,
+ ir,
+ imdSession,
+ pull_work,
+ bNS,
+ force_flags,
+ &top,
+ constr,
+ enerd,
+ state->natoms,
+ state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(),
+ state->box,
+ state->lambda,
+ &state->hist,
+ &f.view(),
+ force_vir,
+ mdatoms,
+ nrnb,
+ wcycle,
+ shellfc,
+ fr,
+ runScheduleWork,
+ t,
+ mu_tot,
+ vsite,
+ ddBalanceRegionHandler);
}
else
{
*/
Awh* awh = nullptr;
gmx_edsam* ed = nullptr;
- do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
- wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
- &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
- vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
+ do_force(fplog,
+ cr,
+ ms,
+ ir,
+ awh,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ step,
+ nrnb,
+ wcycle,
+ &top,
+ state->box,
+ state->x.arrayRefWithPadding(),
+ &state->hist,
+ &f.view(),
+ force_vir,
+ mdatoms,
+ enerd,
+ state->lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ ed,
+ GMX_FORCE_NS | force_flags,
+ ddBalanceRegionHandler);
}
/* Now we have the energies and forces corresponding to the
const bool isCheckpointingStep = false;
const bool doRerun = false;
const bool bSumEkinhOld = false;
- do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
- state_global, observablesHistory, top_global, fr, outf,
- energyOutput, ekind, f.view().force(), isCheckpointingStep,
- doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
+ do_md_trajectory_writing(fplog,
+ cr,
+ nfile,
+ fnm,
+ step,
+ step_rel,
+ t,
+ ir,
+ state,
+ state_global,
+ observablesHistory,
+ top_global,
+ fr,
+ outf,
+ energyOutput,
+ ekind,
+ f.view().force(),
+ isCheckpointingStep,
+ doRerun,
+ isLastStep,
+ mdrunOptions.writeConfout,
+ bSumEkinhOld);
}
stopHandler->setSignal();
t_vcm* vcm = nullptr;
SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
- enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
- state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ wcycle,
+ enerd,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ constr,
+ &signaller,
+ state->box,
+ &totalNumberOfBondedInteractions,
+ &bSumEkinhOld,
CGLO_GSTAT | CGLO_ENERGY
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
: 0));
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
- &top, makeConstArrayRef(state->x), state->box,
+ checkNumberOfBondedInteractions(mdlog,
+ cr,
+ totalNumberOfBondedInteractions,
+ top_global,
+ &top,
+ makeConstArrayRef(state->x),
+ state->box,
&shouldCheckNumberOfBondedInteractions);
}
if (DOMAINDECOMP(cr))
{
ftemp = gmx::makeArrayRef(fglobal);
- dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
- flocal, ftemp);
+ dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
}
else
{
if (MASTER(cr))
{
const bool bCalcEnerStep = true;
- energyOutput.addDataAtEnergyStep(
- doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
- ir->expandedvals, state->box,
- PTCouplingArrays({ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
- state->nhpres_xi, state->nhpres_vxi }),
- state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
+ bCalcEnerStep,
+ t,
+ mdatoms->tmass,
+ enerd,
+ ir->fepvals,
+ ir->expandedvals,
+ state->box,
+ PTCouplingArrays({ state->boxv,
+ state->nosehoover_xi,
+ state->nosehoover_vxi,
+ state->nhpres_xi,
+ state->nhpres_vxi }),
+ state->fep_state,
+ shake_vir,
+ force_vir,
+ total_vir,
+ pres,
+ ekind,
+ mu_tot,
+ constr);
const bool do_ene = true;
const bool do_log = true;
const bool do_or = ir->nstorireout != 0;
EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
- do_log ? fplog : nullptr, step, t, fr->fcdata.get(), awh);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ do_ene,
+ do_dr,
+ do_or,
+ do_log ? fplog : nullptr,
+ step,
+ t,
+ fr->fcdata.get(),
+ awh);
if (do_per_step(step, ir->nstlog))
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff