{
class Awh;
-EnergyElement::EnergyElement(
- StatePropagatorData *statePropagatorData,
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement,
- const gmx_mtop_t *globalTopology,
- const t_inputrec *inputrec,
- const MDAtoms *mdAtoms,
- gmx_enerdata_t *enerd,
- gmx_ekindata_t *ekind,
- const Constraints *constr,
- FILE *fplog,
- t_fcdata *fcd,
- const MdModulesNotifier &mdModulesNotifier,
- bool isMasterRank,
- ObservablesHistory *observablesHistory,
- StartingBehavior startingBehavior) :
+EnergyElement::EnergyElement(StatePropagatorData* statePropagatorData,
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement,
+ const gmx_mtop_t* globalTopology,
+ const t_inputrec* inputrec,
+ const MDAtoms* mdAtoms,
+ gmx_enerdata_t* enerd,
+ gmx_ekindata_t* ekind,
+ const Constraints* constr,
+ FILE* fplog,
+ t_fcdata* fcd,
+ const MdModulesNotifier& mdModulesNotifier,
+ bool isMasterRank,
+ ObservablesHistory* observablesHistory,
+ StartingBehavior startingBehavior) :
isMasterRank_(isMasterRank),
energyWritingStep_(-1),
energyCalculationStep_(-1),
pressureStep_(-1),
needToSumEkinhOld_(false),
startingBehavior_(startingBehavior),
- dummyLegacyState_(),
statePropagatorData_(statePropagatorData),
freeEnergyPerturbationElement_(freeEnergyPerturbationElement),
vRescaleThermostat_(nullptr),
if (freeEnergyPerturbationElement_)
{
- dummyLegacyState_.flags = (1u << estFEPSTATE);
+ dummyLegacyState_.flags = (1U << estFEPSTATE);
}
}
-void EnergyElement::scheduleTask(
- Step step, Time time, const RegisterRunFunctionPtr ®isterRunFunction)
+void EnergyElement::scheduleTask(Step step, Time time, const RegisterRunFunctionPtr& registerRunFunction)
{
if (!isMasterRank_)
{
auto isFreeEnergyCalculationStep = freeEnergyCalculationStep_ == step;
if (isEnergyCalculationStep || writeEnergy)
{
- (*registerRunFunction)(
- std::make_unique<SimulatorRunFunction>(
- [this, time, isEnergyCalculationStep, isFreeEnergyCalculationStep]() {
- doStep(time, isEnergyCalculationStep, isFreeEnergyCalculationStep);
- }));
+ (*registerRunFunction)(std::make_unique<SimulatorRunFunction>(
+ [this, time, isEnergyCalculationStep, isFreeEnergyCalculationStep]() {
+ doStep(time, isEnergyCalculationStep, isFreeEnergyCalculationStep);
+ }));
}
else
{
- (*registerRunFunction)(
- std::make_unique<SimulatorRunFunction>(
- [this]() { energyOutput_->recordNonEnergyStep(); }));
+ (*registerRunFunction)(std::make_unique<SimulatorRunFunction>(
+ [this]() { energyOutput_->recordNonEnergyStep(); }));
}
}
}
}
-void EnergyElement::trajectoryWriterSetup(gmx_mdoutf *outf)
+void EnergyElement::trajectoryWriterSetup(gmx_mdoutf* outf)
{
- pull_t *pull_work = nullptr;
- energyOutput_ = std::make_unique<EnergyOutput>(
- mdoutf_get_fp_ene(outf), top_global_,
- inputrec_, pull_work, mdoutf_get_fp_dhdl(outf), false,
- mdModulesNotifier_);
+ pull_t* pull_work = nullptr;
+ energyOutput_ = std::make_unique<EnergyOutput>(mdoutf_get_fp_ene(outf), top_global_, inputrec_,
+ pull_work, mdoutf_get_fp_dhdl(outf), false,
+ mdModulesNotifier_);
if (!isMasterRank_)
{
return;
}
- initializeEnergyHistory(
- startingBehavior_, observablesHistory_, energyOutput_.get());
+ initializeEnergyHistory(startingBehavior_, observablesHistory_, energyOutput_.get());
// TODO: This probably doesn't really belong here...
// but we have all we need in this element,
// so we'll leave it here for now!
- double io = compute_io(inputrec_, top_global_->natoms, *groups_,
- energyOutput_->numEnergyTerms(), 1);
+ double io = compute_io(inputrec_, top_global_->natoms, *groups_, energyOutput_->numEnergyTerms(), 1);
if ((io > 2000) && isMasterRank_)
{
- 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);
}
if (!inputrec_->bContinuation)
{
if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
{
return std::make_unique<ITrajectoryWriterCallback>(
- [this](gmx_mdoutf *mdoutf, Step step, Time time, bool writeTrajectory, bool writeLog)
- {write(mdoutf, step, time, writeTrajectory, writeLog); });
+ [this](gmx_mdoutf* mdoutf, Step step, Time time, bool writeTrajectory,
+ bool writeLog) { write(mdoutf, step, time, writeTrajectory, writeLog); });
}
return nullptr;
}
if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
{
return std::make_unique<SignallerCallback>(
- [this](Step step, Time){energyWritingStep_ = step; });
+ [this](Step step, Time /*unused*/) { energyWritingStep_ = step; });
}
return nullptr;
}
if (event == EnergySignallerEvent::EnergyCalculationStep && isMasterRank_)
{
return std::make_unique<SignallerCallback>(
- [this](Step step, Time) {energyCalculationStep_ = step; });
+ [this](Step step, Time /*unused*/) { energyCalculationStep_ = step; });
}
if (event == EnergySignallerEvent::FreeEnergyCalculationStep && isMasterRank_)
{
return std::make_unique<SignallerCallback>(
- [this](Step step, Time){freeEnergyCalculationStep_ = step; });
+ [this](Step step, Time /*unused*/) { freeEnergyCalculationStep_ = step; });
}
return nullptr;
}
-void EnergyElement::doStep(
- Time time,
- bool isEnergyCalculationStep,
- bool isFreeEnergyCalculationStep)
+void EnergyElement::doStep(Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep)
{
enerd_->term[F_ETOT] = enerd_->term[F_EPOT] + enerd_->term[F_EKIN];
if (vRescaleThermostat_)
}
if (integratorHasConservedEnergyQuantity(inputrec_))
{
- enerd_->term[F_ECONSERVED] = enerd_->term[F_ETOT] +
- NPT_energy(inputrec_, &dummyLegacyState_, nullptr);
+ enerd_->term[F_ECONSERVED] =
+ enerd_->term[F_ETOT] + NPT_energy(inputrec_, &dummyLegacyState_, nullptr);
}
- energyOutput_->addDataAtEnergyStep(
- isFreeEnergyCalculationStep, isEnergyCalculationStep,
- time, mdAtoms_->mdatoms()->tmass, enerd_, &dummyLegacyState_,
- inputrec_->fepvals, inputrec_->expandedvals,
- statePropagatorData_->constPreviousBox(),
- shakeVirial_, forceVirial_, totalVirial_, pressure_,
- ekind_, muTot_, constr_);
+ energyOutput_->addDataAtEnergyStep(isFreeEnergyCalculationStep, isEnergyCalculationStep, time,
+ mdAtoms_->mdatoms()->tmass, enerd_, &dummyLegacyState_,
+ inputrec_->fepvals, inputrec_->expandedvals,
+ statePropagatorData_->constPreviousBox(), shakeVirial_,
+ forceVirial_, totalVirial_, pressure_, ekind_, muTot_, constr_);
}
-void EnergyElement::write(gmx_mdoutf *outf, Step step, Time time, bool writeTrajectory, bool writeLog)
+void EnergyElement::write(gmx_mdoutf* outf, Step step, Time time, bool writeTrajectory, bool writeLog)
{
if (writeLog)
{
energyOutput_->printHeader(fplog_, step, time);
}
- bool do_dr = do_per_step(step, inputrec_->nstdisreout);
- bool do_or = do_per_step(step, inputrec_->nstorireout);
+ bool do_dr = do_per_step(step, inputrec_->nstdisreout);
+ bool do_or = do_per_step(step, inputrec_->nstorireout);
// energyOutput_->printAnnealingTemperatures(writeLog ? fplog_ : nullptr, groups_, &(inputrec_->opts));
- Awh *awh = nullptr;
- energyOutput_->printStepToEnergyFile(
- mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or,
- writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
+ Awh* awh = nullptr;
+ energyOutput_->printStepToEnergyFile(mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or,
+ writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
}
void EnergyElement::addToForceVirial(const tensor virial, Step step)
return &needToSumEkinhOld_;
}
-void EnergyElement::writeCheckpoint(t_state gmx_unused *localState, t_state *globalState)
+void EnergyElement::writeCheckpoint(t_state gmx_unused* localState, t_state* globalState)
{
if (isMasterRank_)
{
}
}
-void EnergyElement::initializeEnergyHistory(
- StartingBehavior startingBehavior,
- ObservablesHistory *observablesHistory,
- EnergyOutput *energyOutput)
+void EnergyElement::initializeEnergyHistory(StartingBehavior startingBehavior,
+ ObservablesHistory* observablesHistory,
+ EnergyOutput* energyOutput)
{
if (startingBehavior != StartingBehavior::NewSimulation)
{
energyOutput->fillEnergyHistory(observablesHistory->energyHistory.get());
}
-void EnergyElement::setVRescaleThermostat(const gmx::VRescaleThermostat *vRescaleThermostat)
+void EnergyElement::setVRescaleThermostat(const gmx::VRescaleThermostat* vRescaleThermostat)
{
vRescaleThermostat_ = vRescaleThermostat;
if (vRescaleThermostat_)
{
- dummyLegacyState_.flags |= (1u << estTHERM_INT);
+ dummyLegacyState_.flags |= (1U << estTHERM_INT);
}
}
-void EnergyElement::setParrinelloRahamnBarostat(const gmx::ParrinelloRahmanBarostat *parrinelloRahmanBarostat)
+void EnergyElement::setParrinelloRahamnBarostat(const gmx::ParrinelloRahmanBarostat* parrinelloRahmanBarostat)
{
parrinelloRahmanBarostat_ = parrinelloRahmanBarostat;
if (parrinelloRahmanBarostat_)
{
- dummyLegacyState_.flags |= (1u << estBOX) | (1u << estBOXV);
+ dummyLegacyState_.flags |= (1U << estBOX) | (1U << estBOXV);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff