*/
class DensityFitting final : public IMDModule
{
+
public:
- /*! \brief Construct the density fitting module.
+ //! Construct the density fitting module.
+ explicit DensityFitting() = default;
+
+ /*! \brief Request to be notified during pre-processing.
*
* \param[in] notifier allows the module to subscribe to notifications from MdModules.
*
* - storing its internal parameters in a tpr file by writing to a
* key-value-tree during pre-processing by a function taking a
* KeyValueTreeObjectBuilder as parameter
- * - reading its internal parameters from a key-value-tree during
- * simulation setup by taking a const KeyValueTreeObject & parameter
- * - constructing local atom sets in the simulation parameter setup
- * by taking a LocalAtomSetManager * as parameter
- * - the type of periodic boundary conditions that are used
- * by taking a PeriodicBoundaryConditionType as parameter
- * - the writing of checkpoint data
- * by taking a MdModulesWriteCheckpointData as parameter
- * - the reading of checkpoint data
- * by taking a MdModulesCheckpointReadingDataOnMaster as parameter
- * - the broadcasting of checkpoint data
- * by taking MdModulesCheckpointReadingBroadcast as parameter
*/
- explicit DensityFitting(MdModulesNotifier* notifier)
+ void subscribeToPreProcessingNotifications(MdModulesNotifier* notifier) override
{
// Callbacks for several kinds of MdModuleNotification are created
// and subscribed, and will be dispatched correctly at run time
// based on the type of the parameter required by the lambda.
+ if (!densityFittingOptions_.active())
+ {
+ return;
+ }
+
// Setting the atom group indices from index group string
const auto setFitGroupIndicesFunction = [this](const IndexGroupsAndNames& indexGroupsAndNames) {
densityFittingOptions_.setFitGroupIndices(indexGroupsAndNames);
};
notifier->preProcessingNotifications_.subscribe(writeInternalParametersFunction);
- // Reading internal parameters during simulation setup
- const auto readInternalParametersFunction = [this](const KeyValueTreeObject& tree) {
- densityFittingOptions_.readInternalParametersFromKvt(tree);
- };
- notifier->simulationSetupNotifications_.subscribe(readInternalParametersFunction);
-
// Checking for consistency with all .mdp options
const auto checkEnergyCaluclationFrequencyFunction =
[this](EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) {
densityFittingOptions_.checkEnergyCaluclationFrequency(energyCalculationFrequencyErrors);
};
notifier->preProcessingNotifications_.subscribe(checkEnergyCaluclationFrequencyFunction);
+ }
+
+ /*! \brief Request to be notified.
+ * The density fitting code subscribes to these notifications:
+ * - reading its internal parameters from a key-value-tree during
+ * simulation setup by taking a const KeyValueTreeObject & parameter
+ * - constructing local atom sets in the simulation parameter setup
+ * by taking a LocalAtomSetManager * as parameter
+ * - the type of periodic boundary conditions that are used
+ * by taking a PeriodicBoundaryConditionType as parameter
+ * - the writing of checkpoint data
+ * by taking a MdModulesWriteCheckpointData as parameter
+ * - the reading of checkpoint data
+ * by taking a MdModulesCheckpointReadingDataOnMaster as parameter
+ * - the broadcasting of checkpoint data
+ * by taking MdModulesCheckpointReadingBroadcast as parameter
+ */
+ void subscribeToSimulationSetupNotifications(MdModulesNotifier* notifier) override
+ {
+ if (!densityFittingOptions_.active())
+ {
+ return;
+ }
+
+ // Reading internal parameters during simulation setup
+ const auto readInternalParametersFunction = [this](const KeyValueTreeObject& tree) {
+ densityFittingOptions_.readInternalParametersFromKvt(tree);
+ };
+ notifier->simulationSetupNotifications_.subscribe(readInternalParametersFunction);
// constructing local atom sets during simulation setup
const auto setLocalAtomSetFunction = [this](LocalAtomSetManager* localAtomSetManager) {
*/
void constructLocalAtomSet(LocalAtomSetManager* localAtomSetManager)
{
- if (densityFittingOptions_.active())
- {
- LocalAtomSet atomSet =
- localAtomSetManager->add(densityFittingOptions_.buildParameters().indices_);
- densityFittingSimulationParameters_.setLocalAtomSet(atomSet);
- }
+ LocalAtomSet atomSet = localAtomSetManager->add(densityFittingOptions_.buildParameters().indices_);
+ densityFittingSimulationParameters_.setLocalAtomSet(atomSet);
}
/*! \brief Request energy output to energy file during simulation.
*/
void writeCheckpointData(MdModulesWriteCheckpointData checkpointWriting)
{
- if (densityFittingOptions_.active())
- {
- const DensityFittingForceProviderState& state = forceProvider_->stateToCheckpoint();
- checkpointWriting.builder_.addValue<std::int64_t>(
- DensityFittingModuleInfo::name_ + "-stepsSinceLastCalculation",
- state.stepsSinceLastCalculation_);
- checkpointWriting.builder_.addValue<real>(
- DensityFittingModuleInfo::name_ + "-adaptiveForceConstantScale",
- state.adaptiveForceConstantScale_);
- KeyValueTreeObjectBuilder exponentialMovingAverageKvtEntry =
- checkpointWriting.builder_.addObject(DensityFittingModuleInfo::name_
- + "-exponentialMovingAverageState");
- exponentialMovingAverageStateAsKeyValueTree(exponentialMovingAverageKvtEntry,
- state.exponentialMovingAverageState_);
- }
+ const DensityFittingForceProviderState& state = forceProvider_->stateToCheckpoint();
+ checkpointWriting.builder_.addValue<std::int64_t>(
+ DensityFittingModuleInfo::name_ + "-stepsSinceLastCalculation",
+ state.stepsSinceLastCalculation_);
+ checkpointWriting.builder_.addValue<real>(
+ DensityFittingModuleInfo::name_ + "-adaptiveForceConstantScale",
+ state.adaptiveForceConstantScale_);
+ KeyValueTreeObjectBuilder exponentialMovingAverageKvtEntry = checkpointWriting.builder_.addObject(
+ DensityFittingModuleInfo::name_ + "-exponentialMovingAverageState");
+ exponentialMovingAverageStateAsKeyValueTree(exponentialMovingAverageKvtEntry,
+ state.exponentialMovingAverageState_);
}
/*! \brief Read the internal parameters from the checkpoint file on master
*/
void readCheckpointDataOnMaster(MdModulesCheckpointReadingDataOnMaster checkpointReading)
{
- if (densityFittingOptions_.active())
+ if (checkpointReading.checkpointedData_.keyExists(DensityFittingModuleInfo::name_
+ + "-stepsSinceLastCalculation"))
{
- if (checkpointReading.checkpointedData_.keyExists(DensityFittingModuleInfo::name_
- + "-stepsSinceLastCalculation"))
- {
- densityFittingState_.stepsSinceLastCalculation_ =
- checkpointReading
- .checkpointedData_[DensityFittingModuleInfo::name_
- + "-stepsSinceLastCalculation"]
- .cast<std::int64_t>();
- }
- if (checkpointReading.checkpointedData_.keyExists(DensityFittingModuleInfo::name_
- + "-adaptiveForceConstantScale"))
- {
- densityFittingState_.adaptiveForceConstantScale_ =
- checkpointReading
- .checkpointedData_[DensityFittingModuleInfo::name_
- + "-adaptiveForceConstantScale"]
- .cast<real>();
- }
- if (checkpointReading.checkpointedData_.keyExists(DensityFittingModuleInfo::name_
- + "-exponentialMovingAverageState"))
- {
- densityFittingState_.exponentialMovingAverageState_ = exponentialMovingAverageStateFromKeyValueTree(
- checkpointReading
- .checkpointedData_[DensityFittingModuleInfo::name_ + "-exponentialMovingAverageState"]
- .asObject());
- }
+ densityFittingState_.stepsSinceLastCalculation_ =
+ checkpointReading
+ .checkpointedData_[DensityFittingModuleInfo::name_
+ + "-stepsSinceLastCalculation"]
+ .cast<std::int64_t>();
+ }
+ if (checkpointReading.checkpointedData_.keyExists(DensityFittingModuleInfo::name_
+ + "-adaptiveForceConstantScale"))
+ {
+ densityFittingState_.adaptiveForceConstantScale_ =
+ checkpointReading
+ .checkpointedData_[DensityFittingModuleInfo::name_
+ + "-adaptiveForceConstantScale"]
+ .cast<real>();
+ }
+ if (checkpointReading.checkpointedData_.keyExists(DensityFittingModuleInfo::name_
+ + "-exponentialMovingAverageState"))
+ {
+ densityFittingState_.exponentialMovingAverageState_ = exponentialMovingAverageStateFromKeyValueTree(
+ checkpointReading
+ .checkpointedData_[DensityFittingModuleInfo::name_ + "-exponentialMovingAverageState"]
+ .asObject());
}
}
*/
void broadcastCheckpointData(MdModulesCheckpointReadingBroadcast checkpointBroadcast)
{
- if (densityFittingOptions_.active())
+ if (PAR(&(checkpointBroadcast.cr_)))
{
- if (PAR(&(checkpointBroadcast.cr_)))
- {
- block_bc(&(checkpointBroadcast.cr_), densityFittingState_.stepsSinceLastCalculation_);
- block_bc(&(checkpointBroadcast.cr_), densityFittingState_.adaptiveForceConstantScale_);
- block_bc(&(checkpointBroadcast.cr_), densityFittingState_.exponentialMovingAverageState_);
- }
+ block_bc(&(checkpointBroadcast.cr_), densityFittingState_.stepsSinceLastCalculation_);
+ block_bc(&(checkpointBroadcast.cr_), densityFittingState_.adaptiveForceConstantScale_);
+ block_bc(&(checkpointBroadcast.cr_), densityFittingState_.exponentialMovingAverageState_);
}
}
} // namespace
-std::unique_ptr<IMDModule> DensityFittingModuleInfo::create(MdModulesNotifier* notifier)
+std::unique_ptr<IMDModule> DensityFittingModuleInfo::create()
{
- return std::make_unique<DensityFitting>(notifier);
+ return std::make_unique<DensityFitting>();
}
const std::string DensityFittingModuleInfo::name_ = "density-guided-simulation";
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff