Description

Input data storage for density fitting.

Public Member Functions
void	initMdpTransform (IKeyValueTreeTransformRules *rules) override
	From IMdpOptionProvider.

void	buildMdpOutput (KeyValueTreeObjectBuilder *builder) const override
	Build mdp parameters for density fitting to be output after pre-processing. More...

void	initMdpOptions (IOptionsContainerWithSections *options) override
	Connect option name and data.

bool	active () const
	Report if this set of options is active.

const DensityFittingParameters &	buildParameters ()
	Process input options to parameters, including input file reading.

void	setFitGroupIndices (const IndexGroupsAndNames &indexGroupsAndNames)
	Evaluate and store atom indices. More...

void	writeInternalParametersToKvt (KeyValueTreeObjectBuilder treeBuilder)
	Store the paramers that are not mdp options in the tpr file.

void	readInternalParametersFromKvt (const KeyValueTreeObject &tree)
	Set the internal parameters that are stored in the tpr file.

const std::string &	referenceDensityFileName () const
	Return the file name of the reference density.

void	checkEnergyCaluclationFrequency (EnergyCalculationFrequencyErrors *energyCalculationFrequencyErrors) const
	Check if input parameters are consistent with other simulation parameters.

Member Function Documentation

void gmx::DensityFittingOptions::buildMdpOutput ( KeyValueTreeObjectBuilder * builder ) const

overridevirtual

Build mdp parameters for density fitting to be output after pre-processing.

Parameters

[in,out] builder the builder for the mdp options output KV-tree.

Note: This should be symmetrical to option initialization without employing manual prefixing with the section name string once the legacy code blocking this design is removed.

void gmx::DensityFittingOptions::setFitGroupIndices ( const IndexGroupsAndNames & indexGroupsAndNames )

Evaluate and store atom indices.

During pre-processing, use the group string from the options to evaluate the indices of the atoms to be subject to forces from this module.

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