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gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting Class Referencefinal
+ Inheritance diagram for gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting:
+ Collaboration diagram for gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting:

Description

Density fitting.

Class that implements the density fitting forces and potential

Note
the virial calculation is not yet implemented

Public Member Functions

 DensityFitting ()=default
 Construct the density fitting module.
 
void subscribeToPreProcessingNotifications (MdModulesNotifier *notifier) override
 Request to be notified during pre-processing. More...
 
void subscribeToSimulationSetupNotifications (MdModulesNotifier *notifier) override
 Request to be notified. The density fitting code subscribes to these notifications: More...
 
IMdpOptionProvidermdpOptionProvider () override
 From IMDModule.
 
void initForceProviders (ForceProviders *forceProviders) override
 Add this module to the force providers if active.
 
IMDOutputProvideroutputProvider () override
 This MDModule provides its own output.
 
void constructLocalAtomSet (LocalAtomSetManager *localAtomSetManager)
 Set up the local atom sets that are used by this module. More...
 
void setEnergyOutputRequest (MdModulesEnergyOutputToDensityFittingRequestChecker *energyOutputRequest)
 Request energy output to energy file during simulation.
 

Member Function Documentation

void gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting::constructLocalAtomSet ( LocalAtomSetManager localAtomSetManager)
inline

Set up the local atom sets that are used by this module.

Note
When density fitting is set up with MdModuleNotification in the constructor, this function is called back.
Parameters
[in]localAtomSetManagerthe manager to add local atom sets.
void gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting::subscribeToPreProcessingNotifications ( MdModulesNotifier notifier)
inlineoverridevirtual

Request to be notified during pre-processing.

Parameters
[in]notifierallows the module to subscribe to notifications from MdModules.

The density fitting code subscribes to these notifications:

  • setting atom group indices in the densityFittingOptions_ from an index group string by taking a parmeter const IndexGroupsAndNames &
  • 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

Implements gmx::IMDModule.

void gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting::subscribeToSimulationSetupNotifications ( MdModulesNotifier notifier)
inlineoverridevirtual

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

Implements gmx::IMDModule.


The documentation for this class was generated from the following file: