Categorizes atoms into bins for efficient solution of nuclear electrostatic self-potential. More...

#include <vselfBinsManager.h>

Public Member Functions
	vselfBinsManager (const MPI_Comm &mpi_comm_parent, const MPI_Comm &mpi_comm_domain, const MPI_Comm &mpi_intercomm_kpts, const dftParameters &dftParams)
	Constructor.

void	createAtomBins (std::vector< const dealii::AffineConstraints< double > * > &constraintsVector, const dealii::AffineConstraints< double > &onlyHangingNodeConstraints, const dealii::DoFHandler< 3 > &dofHandler, const dealii::AffineConstraints< double > &constraintMatrix, const std::vector< std::vector< double > > &atomLocations, const std::vector< std::vector< double > > &imagePositions, const std::vector< dftfe::Int > &imageIds, const std::vector< double > &imageCharges, const double radiusAtomBall)
	Categorize atoms into bins based on self-potential ball radius around each atom such that no two atoms in each bin has overlapping balls.

void	updateBinsBc (std::vector< const dealii::AffineConstraints< double > * > &constraintsVector, const dealii::AffineConstraints< double > &onlyHangingNodeConstraints, const dealii::DoFHandler< 3 > &dofHandler, const dealii::AffineConstraints< double > &constraintMatrix, const std::vector< std::vector< double > > &atomLocations, const std::vector< std::vector< double > > &imagePositions, const std::vector< dftfe::Int > &imageIds, const std::vector< double > &imageCharges, const bool vselfPerturbationUpdateForStress=false)
	Categorize atoms into bins based on self-potential ball radius around each atom such that no two atoms in each bin has overlapping balls.

void	solveVselfInBins (const std::shared_ptr< dftfe::basis::FEBasisOperations< double, double, dftfe::utils::MemorySpace::HOST > > &basisOperationsPtr, const dftfe::uInt offset, const dftfe::uInt matrixFreeQuadratureIdAX, const dealii::AffineConstraints< double > &hangingPeriodicConstraintMatrix, const std::vector< std::vector< double > > &imagePositions, const std::vector< dftfe::Int > &imageIds, const std::vector< double > &imageCharges, std::vector< std::vector< double > > &localVselfs, std::map< dealii::CellId, std::vector< double > > &bQuadValuesAllAtoms, std::map< dealii::CellId, std::vector< dftfe::Int > > &bQuadAtomIdsAllAtoms, std::map< dealii::CellId, std::vector< dftfe::Int > > &bQuadAtomIdsAllAtomsImages, std::map< dealii::CellId, std::vector< dftfe::uInt > > &bCellNonTrivialAtomIds, std::vector< std::map< dealii::CellId, std::vector< dftfe::uInt > > > &bCellNonTrivialAtomIdsBins, std::map< dealii::CellId, std::vector< dftfe::uInt > > &bCellNonTrivialAtomImageIds, std::vector< std::map< dealii::CellId, std::vector< dftfe::uInt > > > &bCellNonTrivialAtomImageIdsBins, const std::vector< double > &smearingWidths, std::vector< double > &smearedChargeScaling, const dftfe::uInt smearedChargeQuadratureId, const bool useSmearedCharges=false, const bool isVselfPerturbationSolve=false)
	Solve nuclear electrostatic self-potential of atoms in each bin one-by-one.

void	solveVselfInBinsPerturbedDomain (const std::shared_ptr< dftfe::basis::FEBasisOperations< double, double, dftfe::utils::MemorySpace::HOST > > &basisOperationsPtr, const dftfe::uInt mfBaseDofHandlerIndex, const dftfe::uInt matrixFreeQuadratureIdAX, const dftfe::uInt offset, const dealii::AffineConstraints< double > &hangingPeriodicConstraintMatrix, const std::vector< std::vector< double > > &imagePositions, const std::vector< dftfe::Int > &imageIds, const std::vector< double > &imageCharges, const std::vector< double > &smearingWidths, const dftfe::uInt smearedChargeQuadratureId, const bool useSmearedCharges=false)
	Solve nuclear electrostatic self-potential of atoms in each bin in a perturbed domain (used for cell stress calculation)

const std::map< dftfe::Int, std::set< dftfe::Int > > &	getAtomIdsBins () const
	get const reference map of binIds and atomIds

const std::map< dftfe::Int, std::set< dftfe::Int > > &	getAtomImageIdsBins () const
	get const reference map of binIds and atomIds

const std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > > &	getBoundaryFlagsBins () const

const std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > > &	getBoundaryFlagsBinsOnlyChargeId () const

const std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > > &	getClosestAtomIdsBins () const

const std::vector< std::map< dealii::types::global_dof_index, dealii::Point< 3 > > > &	getClosestAtomLocationsBins () const

const std::vector< distributedCPUVec< double > > &	getVselfFieldBins () const
	get const reference to solved vself fields

const std::vector< distributedCPUVec< double > > &	getVselfFieldDerRBins () const
	get const reference to del{vself}/del{R_i} fields

const std::vector< distributedCPUVec< double > > &	getPerturbedVselfFieldBins () const

const std::map< dftfe::uInt, dftfe::uInt > &	getAtomIdBinIdMapLocalAllImages () const
	get const reference to d_atomIdBinIdMapLocalAllImages

double	getStoredAdaptiveBallRadius () const
	get stored adaptive ball radius

Private Member Functions
void	locateAtomsInBins (const dealii::DoFHandler< 3 > &dofHandler)
	locate underlying fem nodes for atoms in bins.

void	createAtomBinsSanityCheck (const dealii::DoFHandler< 3 > &dofHandler, const dealii::AffineConstraints< double > &onlyHangingNodeConstraints)
	sanity check for Dirichlet boundary conditions on the vself balls in each bin

Private Attributes
std::vector< std::vector< double > >	d_atomLocations
	storage for input atomLocations argument in createAtomBins function

dftUtils::constraintMatrixInfo< dftfe::utils::MemorySpace::HOST >	d_constraintsOnlyHangingInfo
	storage for optimized constraints handling object

std::vector< dealii::AffineConstraints< double > >	d_vselfBinConstraintMatrices
	vector of constraint matrices for vself bins

std::map< dftfe::Int, std::set< dftfe::Int > >	d_bins
	map of binIds and atomIds

std::map< dftfe::Int, std::set< dftfe::Int > >	d_binsImages
	map of binIds and atomIds and imageIds

std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > >	d_boundaryFlag
	map of global dof index and vself solve boundary flag (chargeId or

std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > >	d_boundaryFlagOnlyChargeId

std::vector< std::map< dealii::types::global_dof_index, dealii::Point< 3 > > >	d_dofClosestChargeLocationMap
	map of global dof index to location of closest charge

std::vector< std::map< dealii::types::global_dof_index, double > >	d_vselfBinField
	map of global dof index and vself field initial value in each bin

std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > >	d_closestAtomBin
	map of global dof index and vself field initial value in each bin

std::map< dftfe::uInt, dftfe::uInt >	d_atomIdBinIdMapLocalAllImages

std::vector< distributedCPUVec< double > >	d_vselfFieldBins
	solved vself solution field for each bin

std::vector< distributedCPUVec< double > >	d_vselfFieldDerRBins
	solved del{vself}/del{R_i} solution field for each bin

std::vector< distributedCPUVec< double > >	d_vselfFieldPerturbedBins

std::vector< std::map< dealii::types::global_dof_index, double > >	d_atomsInBin

double	d_storedAdaptiveBallRadius

const dftParameters &	d_dftParams

const MPI_Comm	d_mpiCommParent

const MPI_Comm	mpi_communicator

const MPI_Comm	d_mpiInterCommKpts

const dftfe::uInt	n_mpi_processes

const dftfe::uInt	this_mpi_process

dealii::ConditionalOStream	pcout

Detailed Description

Categorizes atoms into bins for efficient solution of nuclear electrostatic self-potential.

Author: Sambit Das, Phani Motamarri

Constructor & Destructor Documentation

◆ vselfBinsManager()

dftfe::vselfBinsManager::vselfBinsManager	(	const MPI_Comm &	mpi_comm_parent,
		const MPI_Comm &	mpi_comm_domain,
		const MPI_Comm &	mpi_intercomm_kpts,
		const dftParameters &	dftParams )

Constructor.

Parameters

mpi_comm_parent	parent mpi communicator
mpi_comm_domain	domain decomposition mpi communicator

Member Function Documentation

◆ createAtomBins()

void dftfe::vselfBinsManager::createAtomBins	(	std::vector< const dealii::AffineConstraints< double > * > &	constraintsVector,
		const dealii::AffineConstraints< double > &	onlyHangingNodeConstraints,
		const dealii::DoFHandler< 3 > &	dofHandler,
		const dealii::AffineConstraints< double > &	constraintMatrix,
		const std::vector< std::vector< double > > &	atomLocations,
		const std::vector< std::vector< double > > &	imagePositions,
		const std::vector< dftfe::Int > &	imageIds,
		const std::vector< double > &	imageCharges,
		const double	radiusAtomBall )

Categorize atoms into bins based on self-potential ball radius around each atom such that no two atoms in each bin has overlapping balls.

Parameters

[out]	constraintsVector	constraintsVector to which the vself bins solve constraint matrices will be pushed back
[in]	dofHandler	DofHandler object
[in]	constraintMatrix	dealii::AffineConstraints<double> which was used for the total electrostatics solve
[in]	atomLocations	global atom locations and charge values data
[in]	imagePositions	image atoms positions data
[in]	imageIds	image atoms Ids data
[in]	imageCharges	image atoms charge values data
[in]	radiusAtomBall	self-potential ball radius

◆ createAtomBinsSanityCheck()

void dftfe::vselfBinsManager::createAtomBinsSanityCheck	(	const dealii::DoFHandler< 3 > &	dofHandler,
		const dealii::AffineConstraints< double > &	onlyHangingNodeConstraints )

private

sanity check for Dirichlet boundary conditions on the vself balls in each bin

◆ getAtomIdBinIdMapLocalAllImages()

const std::map< dftfe::uInt, dftfe::uInt > & dftfe::vselfBinsManager::getAtomIdBinIdMapLocalAllImages ( ) const

get const reference to d_atomIdBinIdMapLocalAllImages

◆ getAtomIdsBins()

const std::map< dftfe::Int, std::set< dftfe::Int > > & dftfe::vselfBinsManager::getAtomIdsBins ( ) const

get const reference map of binIds and atomIds

◆ getAtomImageIdsBins()

const std::map< dftfe::Int, std::set< dftfe::Int > > & dftfe::vselfBinsManager::getAtomImageIdsBins ( ) const

get const reference map of binIds and atomIds

◆ getBoundaryFlagsBins()

const std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > > & dftfe::vselfBinsManager::getBoundaryFlagsBins ( ) const

get const reference to map of global dof index and vself solve boundary flag in each bin

◆ getBoundaryFlagsBinsOnlyChargeId()

const std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > > & dftfe::vselfBinsManager::getBoundaryFlagsBinsOnlyChargeId ( ) const

get const reference to map of global dof index and vself solve boundary flag in each bin

◆ getClosestAtomIdsBins()

const std::vector< std::map< dealii::types::global_dof_index, dftfe::Int > > & dftfe::vselfBinsManager::getClosestAtomIdsBins ( ) const

get const reference to map of global dof index and vself field initial value in each bin

◆ getClosestAtomLocationsBins()

const std::vector< std::map< dealii::types::global_dof_index, dealii::Point< 3 > > > & dftfe::vselfBinsManager::getClosestAtomLocationsBins ( ) const

get const reference to map of global dof index and vself field initial value in each bin

◆ getPerturbedVselfFieldBins()

const std::vector< distributedCPUVec< double > > & dftfe::vselfBinsManager::getPerturbedVselfFieldBins ( ) const

perturbation of vself solution field to be used to evaluate the Gateaux derivative of vself field with respect to affine strain components using central finite difference

◆ getStoredAdaptiveBallRadius()

double dftfe::vselfBinsManager::getStoredAdaptiveBallRadius ( ) const

get stored adaptive ball radius

◆ getVselfFieldBins()

const std::vector< distributedCPUVec< double > > & dftfe::vselfBinsManager::getVselfFieldBins ( ) const

get const reference to solved vself fields

◆ getVselfFieldDerRBins()

const std::vector< distributedCPUVec< double > > & dftfe::vselfBinsManager::getVselfFieldDerRBins ( ) const

get const reference to del{vself}/del{R_i} fields

◆ locateAtomsInBins()

void dftfe::vselfBinsManager::locateAtomsInBins ( const dealii::DoFHandler< 3 > & dofHandler )

private

locate underlying fem nodes for atoms in bins.

◆ solveVselfInBins()

void dftfe::vselfBinsManager::solveVselfInBins	(	const std::shared_ptr< dftfe::basis::FEBasisOperations< double, double, dftfe::utils::MemorySpace::HOST > > &	basisOperationsPtr,
		const dftfe::uInt	offset,
		const dftfe::uInt	matrixFreeQuadratureIdAX,
		const dealii::AffineConstraints< double > &	hangingPeriodicConstraintMatrix,
		const std::vector< std::vector< double > > &	imagePositions,
		const std::vector< dftfe::Int > &	imageIds,
		const std::vector< double > &	imageCharges,
		std::vector< std::vector< double > > &	localVselfs,
		std::map< dealii::CellId, std::vector< double > > &	bQuadValuesAllAtoms,
		std::map< dealii::CellId, std::vector< dftfe::Int > > &	bQuadAtomIdsAllAtoms,
		std::map< dealii::CellId, std::vector< dftfe::Int > > &	bQuadAtomIdsAllAtomsImages,
		std::map< dealii::CellId, std::vector< dftfe::uInt > > &	bCellNonTrivialAtomIds,
		std::vector< std::map< dealii::CellId, std::vector< dftfe::uInt > > > &	bCellNonTrivialAtomIdsBins,
		std::map< dealii::CellId, std::vector< dftfe::uInt > > &	bCellNonTrivialAtomImageIds,
		std::vector< std::map< dealii::CellId, std::vector< dftfe::uInt > > > &	bCellNonTrivialAtomImageIdsBins,
		const std::vector< double > &	smearingWidths,
		std::vector< double > &	smearedChargeScaling,
		const dftfe::uInt	smearedChargeQuadratureId,
		const bool	useSmearedCharges = false,
		const bool	isVselfPerturbationSolve = false )

Solve nuclear electrostatic self-potential of atoms in each bin one-by-one.

Parameters

[in]	matrix_free_data	MatrixFree object
[in]	offset	MatrixFree object starting offset for vself bins solve
[out]	phiExt	sum of the self-potential fields of all atoms and image atoms
[in]	phiExtConstraintMatrix	constraintMatrix corresponding to phiExt
[in]	imagePositions	image atoms positions data
[in]	imageIds	image atoms Ids data
[in]	imageCharges	image atoms charge values data *
[out]	localVselfs	peak self-potential values of atoms in the local processor

◆ solveVselfInBinsPerturbedDomain()

void dftfe::vselfBinsManager::solveVselfInBinsPerturbedDomain	(	const std::shared_ptr< dftfe::basis::FEBasisOperations< double, double, dftfe::utils::MemorySpace::HOST > > &	basisOperationsPtr,
		const dftfe::uInt	mfBaseDofHandlerIndex,
		const dftfe::uInt	matrixFreeQuadratureIdAX,
		const dftfe::uInt	offset,
		const dealii::AffineConstraints< double > &	hangingPeriodicConstraintMatrix,
		const std::vector< std::vector< double > > &	imagePositions,
		const std::vector< dftfe::Int > &	imageIds,
		const std::vector< double > &	imageCharges,
		const std::vector< double > &	smearingWidths,
		const dftfe::uInt	smearedChargeQuadratureId,
		const bool	useSmearedCharges = false )

Solve nuclear electrostatic self-potential of atoms in each bin in a perturbed domain (used for cell stress calculation)

◆ updateBinsBc()

void dftfe::vselfBinsManager::updateBinsBc	(	std::vector< const dealii::AffineConstraints< double > * > &	constraintsVector,
		const dealii::AffineConstraints< double > &	onlyHangingNodeConstraints,
		const dealii::DoFHandler< 3 > &	dofHandler,
		const dealii::AffineConstraints< double > &	constraintMatrix,
		const std::vector< std::vector< double > > &	atomLocations,
		const std::vector< std::vector< double > > &	imagePositions,
		const std::vector< dftfe::Int > &	imageIds,
		const std::vector< double > &	imageCharges,
		const bool	vselfPerturbationUpdateForStress = false )

Categorize atoms into bins based on self-potential ball radius around each atom such that no two atoms in each bin has overlapping balls.

Parameters

[out]	constraintsVector	constraintsVector to which the vself bins solve constraint matrices will be pushed back
[in]	dofHandler	DofHandler object
[in]	constraintMatrix	dealii::AffineConstraints<double> which was used for the total electrostatics solve
[in]	atomLocations	global atom locations and charge values data
[in]	imagePositions	image atoms positions data
[in]	imageIds	image atoms Ids data
[in]	imageCharges	image atoms charge values data

Member Data Documentation

◆ d_atomIdBinIdMapLocalAllImages

std::map<dftfe::uInt, dftfe::uInt> dftfe::vselfBinsManager::d_atomIdBinIdMapLocalAllImages

private

Internal data: stores the map of atom Id (only in the local processor) to the vself bin Id. Populated in solve vself in Bins

◆ d_atomLocations

std::vector<std::vector<double> > dftfe::vselfBinsManager::d_atomLocations

private

storage for input atomLocations argument in createAtomBins function

◆ d_atomsInBin

std::vector<std::map<dealii::types::global_dof_index, double> > dftfe::vselfBinsManager::d_atomsInBin

private

Map of locally relevant global dof index and the atomic charge in each bin

◆ d_bins

std::map<dftfe::Int, std::set<dftfe::Int> > dftfe::vselfBinsManager::d_bins

private

map of binIds and atomIds

◆ d_binsImages

std::map<dftfe::Int, std::set<dftfe::Int> > dftfe::vselfBinsManager::d_binsImages

private

map of binIds and atomIds and imageIds

◆ d_boundaryFlag

std::vector<std::map<dealii::types::global_dof_index, dftfe::Int> > dftfe::vselfBinsManager::d_boundaryFlag

private

map of global dof index and vself solve boundary flag (chargeId or

◆ d_boundaryFlagOnlyChargeId

std::vector<std::map<dealii::types::global_dof_index, dftfe::Int> > dftfe::vselfBinsManager::d_boundaryFlagOnlyChargeId

private

map of global dof index and vself solve boundary flag (only chargeId)in each bin

◆ d_closestAtomBin

std::vector<std::map<dealii::types::global_dof_index, dftfe::Int> > dftfe::vselfBinsManager::d_closestAtomBin

private

map of global dof index and vself field initial value in each bin

◆ d_constraintsOnlyHangingInfo

dftUtils::constraintMatrixInfo<dftfe::utils::MemorySpace::HOST> dftfe::vselfBinsManager::d_constraintsOnlyHangingInfo

private

storage for optimized constraints handling object

◆ d_dftParams

const dftParameters& dftfe::vselfBinsManager::d_dftParams

private

◆ d_dofClosestChargeLocationMap

std::vector<std::map<dealii::types::global_dof_index, dealii::Point<3> > > dftfe::vselfBinsManager::d_dofClosestChargeLocationMap

private

map of global dof index to location of closest charge

◆ d_mpiCommParent

const MPI_Comm dftfe::vselfBinsManager::d_mpiCommParent

private

◆ d_mpiInterCommKpts

const MPI_Comm dftfe::vselfBinsManager::d_mpiInterCommKpts

private

◆ d_storedAdaptiveBallRadius

double dftfe::vselfBinsManager::d_storedAdaptiveBallRadius

private

Vself ball radius. This is stored after the first call to createAtomBins and reused for subsequent calls

◆ d_vselfBinConstraintMatrices

std::vector<dealii::AffineConstraints<double> > dftfe::vselfBinsManager::d_vselfBinConstraintMatrices

private

vector of constraint matrices for vself bins

◆ d_vselfBinField

std::vector<std::map<dealii::types::global_dof_index, double> > dftfe::vselfBinsManager::d_vselfBinField

private

map of global dof index and vself field initial value in each bin

◆ d_vselfFieldBins

std::vector<distributedCPUVec<double> > dftfe::vselfBinsManager::d_vselfFieldBins

private

solved vself solution field for each bin

◆ d_vselfFieldDerRBins

std::vector<distributedCPUVec<double> > dftfe::vselfBinsManager::d_vselfFieldDerRBins

private

solved del{vself}/del{R_i} solution field for each bin

◆ d_vselfFieldPerturbedBins

std::vector<distributedCPUVec<double> > dftfe::vselfBinsManager::d_vselfFieldPerturbedBins

private

perturbation of vself solution field to be used to evaluate the Gateaux derivative of vself field with respect to affine strain components using central finite difference

◆ mpi_communicator

const MPI_Comm dftfe::vselfBinsManager::mpi_communicator

private

◆ n_mpi_processes

const dftfe::uInt dftfe::vselfBinsManager::n_mpi_processes

private

◆ pcout

dealii::ConditionalOStream dftfe::vselfBinsManager::pcout

private

◆ this_mpi_process

const dftfe::uInt dftfe::vselfBinsManager::this_mpi_process

private

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

workspace/include/vselfBinsManager.h

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ vselfBinsManager()

Member Function Documentation

◆ createAtomBins()

◆ createAtomBinsSanityCheck()

◆ getAtomIdBinIdMapLocalAllImages()

◆ getAtomIdsBins()

◆ getAtomImageIdsBins()

◆ getBoundaryFlagsBins()

◆ getBoundaryFlagsBinsOnlyChargeId()

◆ getClosestAtomIdsBins()

◆ getClosestAtomLocationsBins()

◆ getPerturbedVselfFieldBins()

◆ getStoredAdaptiveBallRadius()

◆ getVselfFieldBins()

◆ getVselfFieldDerRBins()

◆ locateAtomsInBins()

◆ solveVselfInBins()

◆ solveVselfInBinsPerturbedDomain()

◆ updateBinsBc()

Member Data Documentation

◆ d_atomIdBinIdMapLocalAllImages

◆ d_atomLocations

◆ d_atomsInBin

◆ d_bins

◆ d_binsImages

◆ d_boundaryFlag

◆ d_boundaryFlagOnlyChargeId

◆ d_closestAtomBin

◆ d_constraintsOnlyHangingInfo

◆ d_dftParams

◆ d_dofClosestChargeLocationMap

◆ d_mpiCommParent

◆ d_mpiInterCommKpts

◆ d_storedAdaptiveBallRadius

◆ d_vselfBinConstraintMatrices

◆ d_vselfBinField

◆ d_vselfFieldBins

◆ d_vselfFieldDerRBins

◆ d_vselfFieldPerturbedBins

◆ mpi_communicator

◆ n_mpi_processes

◆ pcout

◆ this_mpi_process