#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/domdec/mdsetup.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/mdrunoptions.h"
#include "gromacs/mdtypes/observableshistory.h"
+#include "gromacs/mdtypes/observablesreducer.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/mimic/utilities.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/output.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/swap/swapcoords.h"
#include "gromacs/timing/wallcycle.h"
// t_inputrec is being replaced by IMdpOptionsProvider, so this
// will go away eventually.
const t_inputrec* ir = inputrec;
- int64_t step, step_rel;
double t;
bool isLastStep = false;
bool doFreeEnergyPerturbation = false;
t_trxstatus* status = nullptr;
rvec mu_tot;
t_trxframe rerun_fr;
- gmx_localtop_t top(top_global.ffparams);
ForceBuffers f;
gmx_global_stat_t gstat;
gmx_shellfc_t* shellfc;
int nstglobalcomm = 1;
const bool bNS = true;
+ ObservablesReducer observablesReducer = observablesReducerBuilder->build();
+
const SimulationGroups* groups = &top_global.groups;
if (ir->eI == IntegrationAlgorithm::Mimic)
{
- auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
+ auto* nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
}
int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
top_global,
constr ? constr->numFlexibleConstraints() : 0,
ir->nstcalcenergy,
- DOMAINDECOMP(cr),
+ haveDDAtomOrdering(*cr),
runScheduleWork->simulationWork.useGpuPme);
{
}
}
- // Local state only becomes valid now.
- std::unique_ptr<t_state> stateInstance;
- t_state* state;
-
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
- stateInstance = std::make_unique<t_state>();
- state = stateInstance.get();
+ // Local state only becomes valid now.
dd_init_local_state(*cr->dd, state_global, state);
/* Distribute the charge groups over the nodes from the master node */
state,
&f,
mdAtoms,
- &top,
+ top,
fr,
vsite,
constr,
/* Copy the pointer to the global state */
state = state_global;
- mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
+ mdAlgorithmsSetupAtomData(cr, *ir, top_global, top, fr, &f, mdAtoms, constr, vsite, shellfc);
}
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
+ fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
// NOTE: The global state is no longer used at this point.
// But state_global is still used as temporary storage space for writing
doFreeEnergyPerturbation = true;
}
+ int64_t step = ir->init_step;
+ int64_t step_rel = 0;
+
{
- int cglo_flags = CGLO_GSTAT;
- if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
- {
- cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
- }
+ int cglo_flags = CGLO_GSTAT;
bool bSumEkinhOld = false;
t_vcm* vcm = nullptr;
compute_globals(gstat,
shake_vir,
total_vir,
pres,
- gmx::ArrayRef<real>{},
&nullSignaller,
state->box,
&bSumEkinhOld,
- cglo_flags);
- if (DOMAINDECOMP(cr))
- {
- checkNumberOfBondedInteractions(
- mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
- }
+ cglo_flags,
+ step,
+ &observablesReducer);
+ // Clean up after pre-step use of compute_globals()
+ observablesReducer.markAsReadyToReduce();
}
if (MASTER(cr))
calc_shifts(rerun_fr.box, fr->shift_vec);
}
- step = ir->init_step;
- step_rel = 0;
-
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
false,
if (MASTER(cr))
{
const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
- if (constructVsites && DOMAINDECOMP(cr))
+ if (constructVsites && haveDDAtomOrdering(*cr))
{
gmx_fatal(FARGS,
"Vsite recalculation with -rerun is not implemented with domain "
isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
/* Repartition the domain decomposition */
const bool bMasterState = true;
state,
&f,
mdAtoms,
- &top,
+ top,
fr,
vsite,
constr,
update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
}
+ fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
+
force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
| GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
pull_work,
bNS,
force_flags,
- &top,
+ top,
constr,
enerd,
state->natoms,
&f.view(),
force_vir,
*mdatoms,
+ fr->longRangeNonbondeds.get(),
nrnb,
wcycle,
shellfc,
step,
nrnb,
wcycle,
- &top,
+ top,
state->box,
state->x.arrayRefWithPadding(),
&state->hist,
mu_tot,
t,
ed,
+ fr->longRangeNonbondeds.get(),
GMX_FORCE_NS | force_flags,
ddBalanceRegionHandler);
}
SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
- if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
- {
- cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
- }
compute_globals(gstat,
cr,
ir,
shake_vir,
total_vir,
pres,
- constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
&signaller,
state->box,
&bSumEkinhOld,
- cglo_flags);
- if (DOMAINDECOMP(cr))
- {
- checkNumberOfBondedInteractions(
- mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
- }
+ cglo_flags,
+ step,
+ &observablesReducer);
+ // Clean up after pre-step use of compute_globals()
+ observablesReducer.markAsReadyToReduce();
}
/* Note: this is OK, but there are some numerical precision issues with using the convergence of
mdatoms->tmass,
enerd,
ir->fepvals.get(),
- ir->expandedvals.get(),
state->box,
PTCouplingArrays({ state->boxv,
state->nosehoover_xi,
state->nhpres_xi,
state->nhpres_vxi }),
state->fep_state,
- shake_vir,
- force_vir,
total_vir,
pres,
ekind,
fr->fcdata.get(),
awh);
+ if (ir->bPull)
+ {
+ pull_print_output(pull_work, step, t);
+ }
+
if (do_per_step(step, ir->nstlog))
{
if (fflush(fplog) != 0)
}
cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
- if (DOMAINDECOMP(cr) && wcycle)
+ if (haveDDAtomOrdering(*cr) && wcycle)
{
dd_cycles_add(cr->dd, cycles, ddCyclStep);
}
step++;
step_rel++;
}
+ observablesReducer.markAsReadyToReduce();
}
/* End of main MD loop */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff