This class generates and stores adaptive finite element meshes for the real-space dft problem. More...

#include <triangulationManager.h>

Public Member Functions
	triangulationManager (const MPI_Comm &mpi_comm_parent, const MPI_Comm &mpi_comm_domain, const MPI_Comm &interpoolcomm, const MPI_Comm &interBandGroupComm, const unsigned int FEOrder, const dftParameters &dftParams)
	Constructor.

	~triangulationManager ()

void	generateSerialUnmovedAndParallelMovedUnmovedMesh (const std::vector< std::vector< double > > &atomLocations, const std::vector< std::vector< double > > &imageAtomLocations, const std::vector< int > &imageIds, const std::vector< double > &nearestAtomDistances, const std::vector< std::vector< double > > &domainBoundingVectors, const bool generateSerialTria)
	generates parallel moved and unmoved meshes, and serial unmoved mesh.

void	generateCoarseMeshesForRestart (const std::vector< std::vector< double > > &atomLocations, const std::vector< std::vector< double > > &imageAtomLocations, const std::vector< int > &imageIds, const std::vector< double > &nearestAtomDistances, const std::vector< std::vector< double > > &domainBoundingVectors, const bool generateSerialTria)
	generates the coarse meshes for restart.

void	generateAutomaticMeshApriori (const dealii::DoFHandler< 3 > &dofHandler, dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation, const std::vector< distributedCPUVec< double > > &eigenVectorsArrayIn, const unsigned int FEOrder)
	returns generates A-posteriori refined mesh

dealii::parallel::distributed::Triangulation< 3 > &	getSerialMeshUnmoved ()
	returns constant reference to serial unmoved triangulation

dealii::parallel::distributed::Triangulation< 3 > &	getParallelMeshMoved ()
	returns reference to parallel moved triangulation

dealii::parallel::distributed::Triangulation< 3 > &	getParallelMeshUnmoved ()
	returns constant reference to parallel unmoved triangulation

void	resetMesh (dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulationA, dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulationB)
	resets the vertices of meshB moved to vertices of meshA.

void	generateResetMeshes (const std::vector< std::vector< double > > &domainBoundingVectors, const bool generateSerialTria)
	generates reset meshes to the last mesh generated by auto mesh approach. This is used in Gaussian update of meshes during electrostatics

void	saveTriangulationsSolutionVectors (std::string path, const unsigned int feOrder, const unsigned int nComponents, const std::vector< const distributedCPUVec< double > * > &solutionVectors, const MPI_Comm &interpoolComm, const MPI_Comm &interBandGroupComm)
	serialize the triangulations and the associated solution vectors

void	loadTriangulationsSolutionVectors (std::string path, const unsigned int feOrder, const unsigned int nComponents, std::vector< distributedCPUVec< double > * > &solutionVectors)
	de-serialize the triangulations and the associated solution vectors

void	generateMesh (dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation, dealii::parallel::distributed::Triangulation< 3 > &serialTriangulation, std::vector< std::vector< bool > > &parallelTriaCurrentRefinement, std::vector< std::vector< bool > > &serialTriaCurrentRefinement, const bool generateSerialTria=false, const bool enableManualRepartitioning=false)
	internal function which generates a parallel and serial mesh using a adaptive refinement strategy.

Private Member Functions
void	generateCoarseMesh (dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation)
	internal function which generates a coarse mesh which is required for the load function call in restarts.

bool	refinementAlgorithmA (dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation, std::vector< unsigned int > &locallyOwnedCellsRefineFlags, std::map< dealii::CellId, unsigned int > &cellIdToCellRefineFlagMapLocal, const bool smoothenCellsOnPeriodicBoundary=false, const double smootheningFactor=2.0)
	internal function which sets refinement flags based on a custom created algorithm

bool	consistentPeriodicBoundaryRefinement (dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation, std::vector< unsigned int > &locallyOwnedCellsRefineFlags, std::map< dealii::CellId, unsigned int > &cellIdToCellRefineFlagMapLocal)
	internal function which sets refinement flags to have consistent refinement across periodic boundary

bool	checkPeriodicSurfaceRefinementConsistency (dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation)
	check that triangulation has consistent refinement across periodic boundary including for ghost cells

bool	checkConstraintsConsistency (dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation)
	check that FEOrder=1 dofHandler using the triangulation has parallel consistent combined hanging node and periodic constraints

void	refineSerialMesh (const std::map< dealii::CellId, unsigned int > &cellIdToCellRefineFlagMapLocal, const MPI_Comm &mpi_comm, dealii::parallel::distributed::Triangulation< 3 > &serialTriangulation, const dealii::parallel::distributed::Triangulation< 3 > &parallelTriangulation, std::vector< bool > &serialTriaCurrentRefinement)
	internal function which refines the serial mesh based on refinement flags from parallel mesh. This ensures that we get the same mesh in serial and parallel.

void	saveSupportTriangulations (std::string path)
	internal function to serialize support triangulations. No solution data is attached to them

void	loadSupportTriangulations (std::string path)
	internal function to de-serialize support triangulations. No solution data is read from them

Private Attributes
dealii::parallel::distributed::Triangulation< 3 >	d_parallelTriangulationUnmoved

dealii::parallel::distributed::Triangulation< 3 >	d_parallelTriangulationMoved

dealii::parallel::distributed::Triangulation< 3 >	d_serialTriangulationUnmoved

std::vector< std::vector< bool > >	d_parallelTriaCurrentRefinement

std::vector< std::vector< bool > >	d_serialTriaCurrentRefinement

std::vector< std::vector< double > >	d_atomPositions

std::vector< std::vector< double > >	d_imageAtomPositions

std::vector< std::vector< double > >	d_meshSizes

std::vector< int >	d_imageIds

std::vector< double >	d_nearestAtomDistances

std::vector< std::vector< double > >	d_domainBoundingVectors

const unsigned int	d_max_refinement_steps = 40

const unsigned int	d_FEOrder

const dftParameters &	d_dftParams

const MPI_Comm	d_mpiCommParent

const MPI_Comm	mpi_communicator

const MPI_Comm	interpoolcomm

const MPI_Comm	interBandGroupComm

const unsigned int	this_mpi_process

const unsigned int	n_mpi_processes

dealii::ConditionalOStream	pcout

dealii::TimerOutput	computing_timer

Detailed Description

This class generates and stores adaptive finite element meshes for the real-space dft problem.

The class uses an adpative mesh generation strategy to generate finite element mesh for given domain based on five input parameters: BASE MESH SIZE, ATOM BALL RADIUS, MESH SIZE ATOM BALL, MESH SIZE NEAR ATOM and MAX REFINEMENT STEPS (Refer to utils/dftParameters.cc for their corresponding internal variable names). Additionaly, this class also applies periodicity to mesh. The class stores two types of meshes: moved and unmoved. They are essentially the same meshes, except that we move the nodes of the moved mesh (in the meshMovement class) such that the atoms lie on the nodes. However, once the mesh is moved, dealii has issues using that mesh for further refinement, which is why we also carry an unmoved triangulation.

Author: Phani Motamarri, Sambit Das, Krishnendu Ghosh

Constructor & Destructor Documentation

◆ triangulationManager()

dftfe::triangulationManager::triangulationManager	(	const MPI_Comm &	mpi_comm_parent,
		const MPI_Comm &	mpi_comm_domain,
		const MPI_Comm &	interpoolcomm,
		const MPI_Comm &	interBandGroupComm,
		const unsigned int	FEOrder,
		const dftParameters &	dftParams )

Constructor.

Parameters

mpi_comm_parent	parent mpi communicator
mpi_comm_domain	domain decomposition mpi communicator
interpool_comm	mpi interpool communicator over k points
interBandGroupComm	mpi interpool communicator over band groups

◆ ~triangulationManager()

dftfe::triangulationManager::~triangulationManager ( )

triangulationManager destructor

Member Function Documentation

◆ checkConstraintsConsistency()

bool dftfe::triangulationManager::checkConstraintsConsistency ( dealii::parallel::distributed::Triangulation< 3 > & parallelTriangulation )

private

check that FEOrder=1 dofHandler using the triangulation has parallel consistent combined hanging node and periodic constraints

◆ checkPeriodicSurfaceRefinementConsistency()

bool dftfe::triangulationManager::checkPeriodicSurfaceRefinementConsistency ( dealii::parallel::distributed::Triangulation< 3 > & parallelTriangulation )

private

check that triangulation has consistent refinement across periodic boundary including for ghost cells

◆ consistentPeriodicBoundaryRefinement()

bool dftfe::triangulationManager::consistentPeriodicBoundaryRefinement	(	dealii::parallel::distributed::Triangulation< 3 > &	parallelTriangulation,
		std::vector< unsigned int > &	locallyOwnedCellsRefineFlags,
		std::map< dealii::CellId, unsigned int > &	cellIdToCellRefineFlagMapLocal )

private

internal function which sets refinement flags to have consistent refinement across periodic boundary

Returns: bool boolean flag is any local cell has refinement flag set

◆ generateAutomaticMeshApriori()

void dftfe::triangulationManager::generateAutomaticMeshApriori	(	const dealii::DoFHandler< 3 > &	dofHandler,
		dealii::parallel::distributed::Triangulation< 3 > &	parallelTriangulation,
		const std::vector< distributedCPUVec< double > > &	eigenVectorsArrayIn,
		const unsigned int	FEOrder )

returns generates A-posteriori refined mesh

Parameters

dofHandler	corresponds to starting mesh which has to refined
parallelTriangulation	corresponds to starting triangulation
eigenVectorsArrayIn	solution vectors used to compute errors in each cell required for refinement
FEOrder	finite-element interpolating polynomial

◆ generateCoarseMesh()

void dftfe::triangulationManager::generateCoarseMesh ( dealii::parallel::distributed::Triangulation< 3 > & parallelTriangulation )

private

internal function which generates a coarse mesh which is required for the load function call in restarts.

◆ generateCoarseMeshesForRestart()

void dftfe::triangulationManager::generateCoarseMeshesForRestart	(	const std::vector< std::vector< double > > &	atomLocations,
		const std::vector< std::vector< double > > &	imageAtomLocations,
		const std::vector< int > &	imageIds,
		const std::vector< double > &	nearestAtomDistances,
		const std::vector< std::vector< double > > &	domainBoundingVectors,
		const bool	generateSerialTria )

generates the coarse meshes for restart.

Parameters

atomLocations	vector containing cartesian coordinates at atoms with respect to origin (center of domain).
imageAtomLocations	vector containing cartesian coordinates of image atoms with respect to origin.
domainBoundingVectors	vector of domain bounding vectors (refer to description of input parameters.
generateSerialMesh	bool to toggle to generation of serial tria

◆ generateMesh()

void dftfe::triangulationManager::generateMesh	(	dealii::parallel::distributed::Triangulation< 3 > &	parallelTriangulation,
		dealii::parallel::distributed::Triangulation< 3 > &	serialTriangulation,
		std::vector< std::vector< bool > > &	parallelTriaCurrentRefinement,
		std::vector< std::vector< bool > > &	serialTriaCurrentRefinement,
		const bool	generateSerialTria = false,
		const bool	enableManualRepartitioning = false )

internal function which generates a parallel and serial mesh using a adaptive refinement strategy.

◆ generateResetMeshes()

void dftfe::triangulationManager::generateResetMeshes	(	const std::vector< std::vector< double > > &	domainBoundingVectors,
		const bool	generateSerialTria )

generates reset meshes to the last mesh generated by auto mesh approach. This is used in Gaussian update of meshes during electrostatics

◆ generateSerialUnmovedAndParallelMovedUnmovedMesh()

void dftfe::triangulationManager::generateSerialUnmovedAndParallelMovedUnmovedMesh	(	const std::vector< std::vector< double > > &	atomLocations,
		const std::vector< std::vector< double > > &	imageAtomLocations,
		const std::vector< int > &	imageIds,
		const std::vector< double > &	nearestAtomDistances,
		const std::vector< std::vector< double > > &	domainBoundingVectors,
		const bool	generateSerialTria )

generates parallel moved and unmoved meshes, and serial unmoved mesh.

Parameters

atomLocations	vector containing cartesian coordinates at atoms with respect to origin (center of domain).
imageAtomLocations	vector containing cartesian coordinates of image atoms with respect to origin.
domainBoundingVectors	vector of domain bounding vectors (refer to description of input parameters.
generateSerialMesh	bool to toggle to generation of serial tria

◆ getParallelMeshMoved()

dealii::parallel::distributed::Triangulation< 3 > & dftfe::triangulationManager::getParallelMeshMoved ( )

returns reference to parallel moved triangulation

◆ getParallelMeshUnmoved()

dealii::parallel::distributed::Triangulation< 3 > & dftfe::triangulationManager::getParallelMeshUnmoved ( )

returns constant reference to parallel unmoved triangulation

◆ getSerialMeshUnmoved()

dealii::parallel::distributed::Triangulation< 3 > & dftfe::triangulationManager::getSerialMeshUnmoved ( )

returns constant reference to serial unmoved triangulation

◆ loadSupportTriangulations()

void dftfe::triangulationManager::loadSupportTriangulations ( std::string path )

private

internal function to de-serialize support triangulations. No solution data is read from them

◆ loadTriangulationsSolutionVectors()

void dftfe::triangulationManager::loadTriangulationsSolutionVectors	(	std::string	path,
		const unsigned int	feOrder,
		const unsigned int	nComponents,
		std::vector< distributedCPUVec< double > * > &	solutionVectors )

de-serialize the triangulations and the associated solution vectors

Parameters

[input]feOrder	finite element polynomial order of the dofHandler on which solution vectors to be de-serialized are based upon
[input]nComponents	number of components of the dofHandler on which solution vectors to be de-serialized are based upon
[output]solutionVectors	vector of parallel distributed de-serialized solution vectors. The vector length must match the input vector length used in the call to saveTriangulationSolutionVectors

◆ refinementAlgorithmA()

bool dftfe::triangulationManager::refinementAlgorithmA	(	dealii::parallel::distributed::Triangulation< 3 > &	parallelTriangulation,
		std::vector< unsigned int > &	locallyOwnedCellsRefineFlags,
		std::map< dealii::CellId, unsigned int > &	cellIdToCellRefineFlagMapLocal,
		const bool	smoothenCellsOnPeriodicBoundary = false,
		const double	smootheningFactor = 2.0 )

private

internal function which sets refinement flags based on a custom created algorithm

Returns: bool boolean flag is any local cell has refinement flag set

◆ refineSerialMesh()

void dftfe::triangulationManager::refineSerialMesh	(	const std::map< dealii::CellId, unsigned int > &	cellIdToCellRefineFlagMapLocal,
		const MPI_Comm &	mpi_comm,
		dealii::parallel::distributed::Triangulation< 3 > &	serialTriangulation,
		const dealii::parallel::distributed::Triangulation< 3 > &	parallelTriangulation,
		std::vector< bool > &	serialTriaCurrentRefinement )

private

internal function which refines the serial mesh based on refinement flags from parallel mesh. This ensures that we get the same mesh in serial and parallel.

◆ resetMesh()

void dftfe::triangulationManager::resetMesh	(	dealii::parallel::distributed::Triangulation< 3 > &	parallelTriangulationA,
		dealii::parallel::distributed::Triangulation< 3 > &	parallelTriangulationB )

resets the vertices of meshB moved to vertices of meshA.

◆ saveSupportTriangulations()

void dftfe::triangulationManager::saveSupportTriangulations ( std::string path )

private

internal function to serialize support triangulations. No solution data is attached to them

◆ saveTriangulationsSolutionVectors()

void dftfe::triangulationManager::saveTriangulationsSolutionVectors	(	std::string	path,
		const unsigned int	feOrder,
		const unsigned int	nComponents,
		const std::vector< const distributedCPUVec< double > * > &	solutionVectors,
		const MPI_Comm &	interpoolComm,
		const MPI_Comm &	interBandGroupComm )

serialize the triangulations and the associated solution vectors

Parameters

[input]feOrder	finite element polynomial order of the dofHandler on which solution vectors are based upon
[input]nComponents	number of components of the dofHandler on which solution vectors are based upon
[input]solutionVectors	vector of parallel distributed solution vectors to be serialized
[input]interpoolComm	This communicator is used to ensure serialization happens only in k point pool
[input]interBandGroupComm	This communicator to ensure serialization happens only in band group

Member Data Documentation

◆ computing_timer

dealii::TimerOutput dftfe::triangulationManager::computing_timer

private

◆ d_atomPositions

std::vector<std::vector<double> > dftfe::triangulationManager::d_atomPositions

private

◆ d_dftParams

const dftParameters& dftfe::triangulationManager::d_dftParams

private

◆ d_domainBoundingVectors

std::vector<std::vector<double> > dftfe::triangulationManager::d_domainBoundingVectors

private

◆ d_FEOrder

const unsigned int dftfe::triangulationManager::d_FEOrder

private

FEOrder to be used for checking parallel consistency of periodic+hanging node constraints

◆ d_imageAtomPositions

std::vector<std::vector<double> > dftfe::triangulationManager::d_imageAtomPositions

private

◆ d_imageIds

std::vector<int> dftfe::triangulationManager::d_imageIds

private

◆ d_max_refinement_steps

const unsigned int dftfe::triangulationManager::d_max_refinement_steps = 40

private

◆ d_meshSizes

std::vector<std::vector<double> > dftfe::triangulationManager::d_meshSizes

private

◆ d_mpiCommParent

const MPI_Comm dftfe::triangulationManager::d_mpiCommParent

private

◆ d_nearestAtomDistances

std::vector<double> dftfe::triangulationManager::d_nearestAtomDistances

private

◆ d_parallelTriaCurrentRefinement

std::vector<std::vector<bool> > dftfe::triangulationManager::d_parallelTriaCurrentRefinement

private

◆ d_parallelTriangulationMoved

dealii::parallel::distributed::Triangulation<3> dftfe::triangulationManager::d_parallelTriangulationMoved

private

◆ d_parallelTriangulationUnmoved

dealii::parallel::distributed::Triangulation<3> dftfe::triangulationManager::d_parallelTriangulationUnmoved

private

◆ d_serialTriaCurrentRefinement

std::vector<std::vector<bool> > dftfe::triangulationManager::d_serialTriaCurrentRefinement

private

◆ d_serialTriangulationUnmoved

dealii::parallel::distributed::Triangulation<3> dftfe::triangulationManager::d_serialTriangulationUnmoved

private

◆ interBandGroupComm

const MPI_Comm dftfe::triangulationManager::interBandGroupComm

private

◆ interpoolcomm

const MPI_Comm dftfe::triangulationManager::interpoolcomm

private

◆ mpi_communicator

const MPI_Comm dftfe::triangulationManager::mpi_communicator

private

◆ n_mpi_processes

const unsigned int dftfe::triangulationManager::n_mpi_processes

private

◆ pcout

dealii::ConditionalOStream dftfe::triangulationManager::pcout

private

◆ this_mpi_process

const unsigned int dftfe::triangulationManager::this_mpi_process

private

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

workspace/include/triangulationManager.h

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ triangulationManager()

◆ ~triangulationManager()

Member Function Documentation

◆ checkConstraintsConsistency()

◆ checkPeriodicSurfaceRefinementConsistency()

◆ consistentPeriodicBoundaryRefinement()

◆ generateAutomaticMeshApriori()

◆ generateCoarseMesh()

◆ generateCoarseMeshesForRestart()

◆ generateMesh()

◆ generateResetMeshes()

◆ generateSerialUnmovedAndParallelMovedUnmovedMesh()

◆ getParallelMeshMoved()

◆ getParallelMeshUnmoved()

◆ getSerialMeshUnmoved()

◆ loadSupportTriangulations()

◆ loadTriangulationsSolutionVectors()

◆ refinementAlgorithmA()

◆ refineSerialMesh()

◆ resetMesh()

◆ saveSupportTriangulations()

◆ saveTriangulationsSolutionVectors()

Member Data Documentation

◆ computing_timer

◆ d_atomPositions

◆ d_dftParams

◆ d_domainBoundingVectors

◆ d_FEOrder

◆ d_imageAtomPositions

◆ d_imageIds

◆ d_max_refinement_steps

◆ d_meshSizes

◆ d_mpiCommParent

◆ d_nearestAtomDistances

◆ d_parallelTriaCurrentRefinement

◆ d_parallelTriangulationMoved

◆ d_parallelTriangulationUnmoved

◆ d_serialTriaCurrentRefinement

◆ d_serialTriangulationUnmoved

◆ interBandGroupComm

◆ interpoolcomm

◆ mpi_communicator

◆ n_mpi_processes

◆ pcout

◆ this_mpi_process