* \param[in] forceRec Force record, used for constructing vsites
* \param[in,out] graph The molecular graph, used for constructing vsites when != nullptr
*/
-static void prepareRerunState(const t_trxframe &rerunFrame,
- t_state *globalState,
+static void prepareRerunState(const t_trxframe& rerunFrame,
+ t_state* globalState,
bool constructVsites,
- const gmx_vsite_t *vsite,
- const t_idef &idef,
+ const gmx_vsite_t* vsite,
+ const t_idef& idef,
double timeStep,
- const t_forcerec &forceRec,
- t_graph *graph)
+ const t_forcerec& forceRec,
+ t_graph* graph)
{
auto x = makeArrayRef(globalState->x);
- auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec *>(rerunFrame.x), globalState->natoms);
+ auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
std::copy(rerunX.begin(), rerunX.end(), x.begin());
copy_mat(rerunFrame.box, globalState->box);
shift_self(graph, globalState->box, as_rvec_array(globalState->x.data()));
}
construct_vsites(vsite, globalState->x.rvec_array(), timeStep, globalState->v.rvec_array(),
- idef.iparams, idef.il,
- forceRec.ePBC, forceRec.bMolPBC, nullptr, globalState->box);
+ idef.iparams, idef.il, forceRec.ePBC, forceRec.bMolPBC, nullptr,
+ globalState->box);
if (graph)
{
unshift_self(graph, globalState->box, globalState->x.rvec_array());
// alias to avoid a large ripple of nearly useless changes.
// t_inputrec is being replaced by IMdpOptionsProvider, so this
// will go away eventually.
- t_inputrec *ir = inputrec;
+ t_inputrec* ir = inputrec;
int64_t step, step_rel;
double t, lam0[efptNR];
bool isLastStep = false;
bool doFreeEnergyPerturbation = false;
unsigned int force_flags;
tensor force_vir, shake_vir, total_vir, pres;
- t_trxstatus *status = nullptr;
+ t_trxstatus* status = nullptr;
rvec mu_tot;
t_trxframe rerun_fr;
gmx_localtop_t top;
- PaddedHostVector<gmx::RVec> f {};
+ PaddedHostVector<gmx::RVec> f{};
gmx_global_stat_t gstat;
- t_graph *graph = nullptr;
- gmx_shellfc_t *shellfc;
+ t_graph* graph = nullptr;
+ gmx_shellfc_t* shellfc;
- double cycles;
+ double cycles;
/* Domain decomposition could incorrectly miss a bonded
interaction, but checking for that requires a global
code. So we do that alongside the first global energy reduction
after a new DD is made. These variables handle whether the
check happens, and the result it returns. */
- bool shouldCheckNumberOfBondedInteractions = false;
- int totalNumberOfBondedInteractions = -1;
+ bool shouldCheckNumberOfBondedInteractions = false;
+ int totalNumberOfBondedInteractions = -1;
SimulationSignals signals;
// Most global communnication stages don't propagate mdrun
// signals, and will use this object to achieve that.
SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
- GMX_LOG(mdlog.info).asParagraph().
- appendText("Note that it is planned that the command gmx mdrun -rerun will "
- "be available in a different form in a future version of GROMACS, "
- "e.g. gmx rerun -f.");
+ GMX_LOG(mdlog.info)
+ .asParagraph()
+ .appendText(
+ "Note that it is planned that the command gmx mdrun -rerun will "
+ "be available in a different form in a future version of GROMACS, "
+ "e.g. gmx rerun -f.");
- if (ir->efep != efepNO && (mdAtoms->mdatoms()->nMassPerturbed > 0 ||
- (constr && constr->havePerturbedConstraints())))
+ if (ir->efep != efepNO
+ && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
{
- gmx_fatal(FARGS, "Perturbed masses or constraints are not supported by rerun. "
+ gmx_fatal(FARGS,
+ "Perturbed masses or constraints are not supported by rerun. "
"Either make a .tpr without mass and constraint perturbation, "
"or use GROMACS 2018.4, 2018.5 or later 2018 version.");
}
gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
}
if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
- [](int i){return i != eannNO; }))
+ [](int i) { return i != eannNO; }))
{
gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
}
/* Rerun can't work if an output file name is the same as the input file name.
* If this is the case, the user will get an error telling them what the issue is.
*/
- if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0 ||
- strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
+ if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
+ || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
{
- gmx_fatal(FARGS, "When using mdrun -rerun, the name of the input trajectory file "
+ gmx_fatal(FARGS,
+ "When using mdrun -rerun, the name of the input trajectory file "
"%s cannot be identical to the name of an output file (whether "
"given explicitly with -o or -x, or by default)",
opt2fn("-rerun", nfile, fnm));
}
/* Settings for rerun */
- ir->nstlist = 1;
- ir->nstcalcenergy = 1;
+ ir->nstlist = 1;
+ ir->nstcalcenergy = 1;
int nstglobalcomm = 1;
const bool bNS = true;
- ir->nstxout_compressed = 0;
- SimulationGroups *groups = &top_global->groups;
+ ir->nstxout_compressed = 0;
+ SimulationGroups* groups = &top_global->groups;
if (ir->eI == eiMimic)
{
top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
}
initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
- gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, ir, top_global, oenv, wcycle,
- StartingBehavior::NewSimulation);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true, mdModulesNotifier);
+ gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier,
+ ir, top_global, oenv, wcycle, StartingBehavior::NewSimulation);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
+ mdoutf_get_fp_dhdl(outf), true, mdModulesNotifier);
gstat = global_stat_init(ir);
/* Check for polarizable models and flexible constraints */
- shellfc = init_shell_flexcon(fplog,
- top_global, constr ? constr->numFlexibleConstraints() : 0,
+ shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
ir->nstcalcenergy, DOMAINDECOMP(cr));
{
double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
- fprintf(stderr,
- "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
- io);
+ fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
}
}
// Local state only becomes valid now.
std::unique_ptr<t_state> stateInstance;
- t_state * state;
+ t_state* state;
if (DOMAINDECOMP(cr))
{
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,
+ 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;
}
/* Copy the pointer to the global state */
state = state_global;
- mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
- &graph, mdAtoms, constr, vsite, shellfc);
+ mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &graph, mdAtoms, constr, vsite, shellfc);
}
auto mdatoms = mdAtoms->mdatoms();
}
{
- int cglo_flags = (CGLO_GSTAT |
- (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
+ int cglo_flags =
+ (CGLO_GSTAT
+ | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
bool bSumEkinhOld = false;
- t_vcm *vcm = nullptr;
- compute_globals(gstat, cr, ir, fr, ekind,
- state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
- mdatoms, nrnb, vcm,
- nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, &nullSignaller, state->box,
- &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
+ t_vcm* vcm = nullptr;
+ compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
+ state->box, state->lambda[efptVDW], mdatoms, nrnb, vcm, nullptr, enerd,
+ force_vir, shake_vir, total_vir, pres, mu_tot, constr, &nullSignaller,
+ state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
}
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, &top, state->x.rvec_array(), state->box,
+ checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
+ state->x.rvec_array(), state->box,
&shouldCheckNumberOfBondedInteractions);
if (MASTER(cr))
{
- fprintf(stderr, "starting md rerun '%s', reading coordinates from"
+ fprintf(stderr,
+ "starting md rerun '%s', reading coordinates from"
" input trajectory '%s'\n\n",
*(top_global->name), opt2fn("-rerun", nfile, fnm));
if (mdrunOptions.verbose)
{
- fprintf(stderr, "Calculated time to finish depends on nsteps from "
+ fprintf(stderr,
+ "Calculated time to finish depends on nsteps from "
"run input file,\nwhich may not correspond to the time "
"needed to process input trajectory.\n\n");
}
if (constr)
{
- GMX_LOG(mdlog.info).asParagraph().
- appendText("Simulations has constraints. Rerun does not recalculate constraints.");
+ GMX_LOG(mdlog.info)
+ .asParagraph()
+ .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
}
rerun_fr.natoms = 0;
if (MASTER(cr))
{
- isLastStep = !read_first_frame(oenv, &status,
- opt2fn("-rerun", nfile, fnm),
- &rerun_fr, TRX_NEED_X);
+ isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
if (rerun_fr.natoms != top_global->natoms)
{
gmx_fatal(FARGS,
{
if (!rerun_fr.bBox)
{
- gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
+ gmx_fatal(FARGS,
+ "Rerun trajectory frame step %" PRId64
+ " time %f "
"does not contain a box, while pbc is used",
rerun_fr.step, rerun_fr.time);
}
if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
{
- gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
- "has too small box dimensions", rerun_fr.step, rerun_fr.time);
+ gmx_fatal(FARGS,
+ "Rerun trajectory frame step %" PRId64
+ " time %f "
+ "has too small box dimensions",
+ rerun_fr.step, rerun_fr.time);
}
}
}
- GMX_LOG(mdlog.info).asParagraph().
- appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
+ GMX_LOG(mdlog.info)
+ .asParagraph()
+ .appendText(
+ "Rerun does not report kinetic energy, total energy, temperature, virial and "
+ "pressure.");
if (PAR(cr))
{
}
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);
const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
if (constructVsites && DOMAINDECOMP(cr))
{
- gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
+ gmx_fatal(FARGS,
+ "Vsite recalculation with -rerun is not implemented with domain "
+ "decomposition, "
"use a single rank");
}
- prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top.idef, ir->delta_t, *fr, graph);
+ prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top.idef, ir->delta_t,
+ *fr, graph);
}
isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
{
/* 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;
}
update_mdatoms(mdatoms, state->lambda[efptMASS]);
}
- force_flags = (GMX_FORCE_STATECHANGED |
- GMX_FORCE_DYNAMICBOX |
- GMX_FORCE_ALLFORCES |
- (GMX_GPU ? GMX_FORCE_VIRIAL : 0) | // TODO: Get rid of this once #2649 is solved
- GMX_FORCE_ENERGY |
- (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
+ force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
+ | (GMX_GPU ? GMX_FORCE_VIRIAL : 0) | // TODO: Get rid of this once #2649 is solved
+ GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
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, fcd,
- state->natoms,
- state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(),
- state->box,
- state->lambda,
- &state->hist,
- f.arrayRefWithPadding(), force_vir, mdatoms,
- nrnb, wcycle, graph,
- 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, fcd,
+ state->natoms, state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
+ f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
+ shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
}
else
{
* This is parallellized as well, and does communication too.
* Check comments in sim_util.c
*/
- 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.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
- state->lambda, graph,
- fr, runScheduleWork, vsite, mu_tot, t, ed,
- GMX_FORCE_NS | force_flags,
+ 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.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
+ fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
ddBalanceRegionHandler);
}
const bool isCheckpointingStep = false;
const bool doRerun = true;
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,
- 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, isCheckpointingStep, doRerun,
+ isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
}
stopHandler->setSignal();
{
shift_self(graph, state->box, as_rvec_array(state->x.data()));
}
- construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
- top.idef.iparams, top.idef.il,
+ construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t,
+ as_rvec_array(state->v.data()), top.idef.iparams, top.idef.il,
fr->ePBC, fr->bMolPBC, cr, state->box);
if (graph != nullptr)
const bool doInterSimSignal = false;
const bool doIntraSimSignal = true;
bool bSumEkinhOld = false;
- t_vcm *vcm = nullptr;
+ t_vcm* vcm = nullptr;
SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
- compute_globals(gstat, cr, ir, fr, ekind,
- state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
- mdatoms, nrnb, vcm,
- wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, &signaller,
- state->box,
- &totalNumberOfBondedInteractions, &bSumEkinhOld,
+ compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
+ state->box, state->lambda[efptVDW], mdatoms, nrnb, vcm, wcycle, enerd,
+ force_vir, shake_vir, total_vir, pres, mu_tot, 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, state->x.rvec_array(), state->box,
+ | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
+ : 0));
+ checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
+ &top, state->x.rvec_array(), state->box,
&shouldCheckNumberOfBondedInteractions);
}
if (MASTER(cr))
{
const bool bCalcEnerStep = true;
- energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
- t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, state->box,
- shake_vir, force_vir, total_vir, pres,
- ekind, mu_tot,
- constr);
+ energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep, t,
+ mdatoms->tmass, enerd, state, ir->fepvals,
+ ir->expandedvals, state->box, shake_vir, force_vir,
+ total_vir, pres, ekind, mu_tot, constr);
const bool do_ene = true;
const bool do_log = true;
- Awh *awh = nullptr;
+ Awh* awh = nullptr;
const bool do_dr = ir->nstdisreout != 0;
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,
- fcd, awh);
+ do_log ? fplog : nullptr, step, t, fcd, awh);
if (do_per_step(step, ir->nstlog))
{
}
/* Print the remaining wall clock time for the run */
- if (isMasterSimMasterRank(ms, MASTER(cr)) &&
- (mdrunOptions.verbose || gmx_got_usr_signal()))
+ if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
{
if (shellfc)
{
/* Ion/water position swapping.
* Not done in last step since trajectory writing happens before this call
* in the MD loop and exchanges would be lost anyway. */
- if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep &&
- do_per_step(step, ir->swap->nstswap))
+ if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep && do_per_step(step, ir->swap->nstswap))
{
const bool doRerun = true;
- do_swapcoords(cr, step, t, ir, swap, wcycle,
- rerun_fr.x,
- rerun_fr.box,
- MASTER(cr) && mdrunOptions.verbose,
- doRerun);
+ do_swapcoords(cr, step, t, ir, swap, wcycle, rerun_fr.x, rerun_fr.box,
+ MASTER(cr) && mdrunOptions.verbose, doRerun);
}
if (MASTER(cr))
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff