gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup Class Reference

Description

Collect density fitting parameters only available during simulation setup.

Todo:

Implement builder pattern that will not use unqiue_ptr to check if parameters have been set or not.

To build the density fitting force provider during simulation setup, the DensityFitting class needs access to parameters that become available only during simulation setup.

This class collects these parameters via MDModulesNotifiers in the simulation setup phase and provides a check if all necessary parameters have been provided.

Public Member Functions
void	setLocalAtomSet (const LocalAtomSet &localAtomSet)
	Set the local atom set for the density fitting. More...
const LocalAtomSet &	localAtomSet () const
	Return local atom set for density fitting. More...
const TranslateAndScale &	transformationToDensityLattice () const
	Return transformation into density lattice. More...
basic_mdspan< const float, dynamicExtents3D >	referenceDensity () const
	Return reference density. More...
void	readReferenceDensityFromFile (const std::string &referenceDensityFileName)
	Reads the reference density from file. More...
void	normalizeReferenceDensity ()
	Normalize the reference density so that the sum over all voxels is unity.
void	setPeriodicBoundaryConditionType (const PbcType &pbcType)
	Set the periodic boundary condition via MDModuleNotifier. More...
PbcType	periodicBoundaryConditionType ()
	Get the periodic boundary conditions.
void	setSimulationTimeStep (double timeStep)
	Set the simulation time step.
double	simulationTimeStep () const
	Return the simulation time step.

Member Function Documentation

const LocalAtomSet& gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup::localAtomSet ( ) const

inline

Return local atom set for density fitting.

Exceptions

InternalError

if local atom set is not set

Returns

local atom set for density fitting

void gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup::readReferenceDensityFromFile ( const std::string &  referenceDensityFileName )

inline

Reads the reference density from file.

Reads and check file, then set and communicate the internal parameters related to the reference density with the file data.

Exceptions

FileIOError

if reading from file was not successful

basic_mdspan<const float, dynamicExtents3D> gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup::referenceDensity ( ) const

inline

Return reference density.

Exceptions

InternalError

if reference density is not set

Returns

the reference density

void gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup::setLocalAtomSet ( const LocalAtomSet &  localAtomSet )

inline

Set the local atom set for the density fitting.

Parameters

[in]

localAtomSet

of atoms to be fitted

void gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup::setPeriodicBoundaryConditionType ( const PbcType &  pbcType )

inline

Set the periodic boundary condition via MDModuleNotifier.

The pbc type is wrapped in PeriodicBoundaryConditionType to allow the MDModuleNotifier to statically distinguish the callback function type from other 'int' function callbacks.

Parameters

[in]

pbcType

enumerates the periodic boundary condition.

const TranslateAndScale& gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup::transformationToDensityLattice ( ) const

inline

Return transformation into density lattice.

Exceptions

InternalError

if transformation into density lattice is not set

Returns

transformation into density lattice

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

• src/gromacs/applied_forces/densityfitting/densityfitting.cpp