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

Density fitting.

Class that implements the density fitting forces and potential

Note
the virial calculation is not yet implemented

Public Member Functions

 DensityFitting (MdModulesNotifier *notifier)
 Construct the density fitting module. 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.
 
void writeCheckpointData (MdModulesWriteCheckpointData checkpointWriting)
 Write internal density fitting data to checkpoint file. More...
 
void readCheckpointDataOnMaster (MdModulesCheckpointReadingDataOnMaster checkpointReading)
 Read the internal parameters from the checkpoint file on master. More...
 
void broadcastCheckpointData (MdModulesCheckpointReadingBroadcast checkpointBroadcast)
 Broadcast the internal parameters. More...
 

Constructor & Destructor Documentation

gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting::DensityFitting ( MdModulesNotifier *  notifier)
inlineexplicit

Construct the density fitting module.

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_ 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
  • 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

Member Function Documentation

void gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting::broadcastCheckpointData ( MdModulesCheckpointReadingBroadcast  checkpointBroadcast)
inline

Broadcast the internal parameters.

Parameters
[in]checkpointBroadcastcontaining the communication record to broadcast the checkpoint information
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::readCheckpointDataOnMaster ( MdModulesCheckpointReadingDataOnMaster  checkpointReading)
inline

Read the internal parameters from the checkpoint file on master.

Parameters
[in]checkpointReadingholding the checkpoint information
void gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting::writeCheckpointData ( MdModulesWriteCheckpointData  checkpointWriting)
inline

Write internal density fitting data to checkpoint file.

Parameters
[in]checkpointWritingenables writing to the Key-Value-Tree that is used for storing the checkpoint information
Note
The provided state to checkpoint has to change if checkpointing is moved before the force provider call in the MD-loop.

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