dftfe::dftfeWrapper Class Reference

wrapper class for dftfe More...

#include <dftfeWrapper.h>

Public Member Functions
	dftfeWrapper ()
	empty constructor
	dftfeWrapper (const std::string parameter_file, const MPI_Comm &mpi_comm_parent, const bool printParams=false, const bool setDeviceToMPITaskBindingInternally=false, const std::string solverMode="GS", const std::string restartFilesPath=".", const int _verbosity=1, const bool useDevice=false)
	constructor based on input parameter_file
	dftfeWrapper (const std::string parameter_file, const std::string restartCoordsFile, const std::string restartDomainVectorsFile, const MPI_Comm &mpi_comm_parent, const bool printParams=false, const bool setDeviceToMPITaskBindingInternally=false, const std::string solverMode="GS", const std::string restartFilesPath=".", const int _verbosity=1, const bool useDevice=false, const bool isScfRestart=true)
	constructor based on input parameter_file and restart coordinates and domain vectors file paths
	dftfeWrapper (const MPI_Comm &mpi_comm_parent, const bool useDevice, const std::vector< std::vector< double > > atomicPositionsCart, const std::vector< unsigned int > atomicNumbers, const std::vector< std::vector< double > > cell, const std::vector< bool > pbc, const std::vector< unsigned int > mpGrid=std::vector< unsigned int >{1, 1, 1}, const std::vector< bool > mpGridShift=std::vector< bool >{false, false, false}, const bool spinPolarizedDFT=false, const double startMagnetization=0.0, const double fermiDiracSmearingTemp=500.0, const unsigned int npkpt=0, const double meshSize=0.8, const double scfMixingParameter=0.2, const int verbosity=-1, const bool setDeviceToMPITaskBindingInternally=false)
	constructor based on input list of atomic coordinates, list of atomic numbers,cell, boundary conditions, Monkhorst-Pack k-point grid, and other optional parameters. This constructor currently only sets up GGA PBE pseudopotential DFT calculations using ONCV pseudopotentials in .upf format (read from DFTFE_PSP_PATH folder provided as an environment variable). The pseudpotential directory must contain files in the format: AtomicSymbol.upf
	~dftfeWrapper ()
void	reinit (const std::string parameter_file, const MPI_Comm &mpi_comm_parent, const bool printParams=false, const bool setDeviceToMPITaskBindingInternally=false, const std::string solverMode="GS", const std::string restartFilesPath=".", const int _verbosity=1, const bool useDevice=false)
	clear and reinitialize based on input parameter_file
void	reinit (const std::string parameter_file, const std::string restartCoordsFile, const std::string restartDomainVectorsFile, const MPI_Comm &mpi_comm_parent, const bool printParams=false, const bool setDeviceToMPITaskBindingInternally=false, const std::string solverMode="GS", const std::string restartFilesPath=".", const int _verbosity=1, const bool useDevice=false, const bool isScfRestart=true)
	clear and reinitialize based on input parameter_file and restart coordinates and domain vectors file paths
void	reinit (const MPI_Comm &mpi_comm_parent, const bool useDevice, const std::vector< std::vector< double > > atomicPositionsCart, const std::vector< unsigned int > atomicNumbers, const std::vector< std::vector< double > > cell, const std::vector< bool > pbc, const std::vector< unsigned int > mpGrid=std::vector< unsigned int >{1, 1, 1}, const std::vector< bool > mpGridShift=std::vector< bool >{false, false, false}, const bool spinPolarizedDFT=false, const double startMagnetization=0.0, const double fermiDiracSmearingTemp=500.0, const unsigned int npkpt=0, const double meshSize=0.8, const double scfMixingParameter=0.2, const int verbosity=-1, const bool setDeviceToMPITaskBindingInternally=false)
void	clear ()
void	run ()
	Legacy function (to be deprecated)
void	writeMesh ()
	Calls dftBasepointer public function writeMesh(). Here the inital density and mesh are stored in a file. Useful for visluiing meshes without running solve.
std::tuple< double, bool, double >	computeDFTFreeEnergy (const bool computeIonForces=true, const bool computeCellStress=false)
	solve ground-state and return DFT free energy which is sum of internal energy and negative of electronic entropic energy (in Hartree units)
void	computeStress ()
double	getDFTFreeEnergy () const
	Get DFT free energy (in Hartree units). This function can only be called after calling computeDFTFreeEnergy.
double	getElectronicEntropicEnergy () const
	Get electronic entropic energy (in Hartree units). This function can only be called after calling computeDFTFreeEnergy.
std::vector< std::vector< double > >	getForcesAtoms () const
	Get ionic forces: negative of gradient of DFT free energy with respect to ionic positions (in Hartree/Bohr units). This function can only be called after calling computeDFTFreeEnergy.
std::vector< std::vector< double > >	getCellStress () const
	Get cell stress: negative of gradient of DFT free energy with respect to affine strain components scaled by volume (Hartree/Bohr^3) units. This function can only be called after calling computeDFTFreeEnergy.
void	updateAtomPositions (const std::vector< std::vector< double > > atomsDisplacements)
	update atom positions and reinitialize all related data-structures
void	deformCell (const std::vector< std::vector< double > > deformationGradient)
	Deforms the cell by applying the given affine deformation gradient and reinitializes the underlying data-structures.
std::vector< std::vector< double > >	getAtomPositionsCart () const
	Gets the current atom Positions in cartesian form (in Bohr units) (origin at corner of cell against which the cell vectors are defined)
std::vector< std::vector< double > >	getAtomPositionsFrac () const
	Gets the current atom Positions in fractional form (only applicable for periodic and semi-periodic BCs). CAUTION: during relaxation and MD fractional coordinates may have negaive values.
std::vector< std::vector< double > >	getCell () const
	Gets the current cell vectors.
std::vector< bool >	getPBC () const
	Gets the boundary conditions for each cell vector direction.
std::vector< int >	getAtomicNumbers () const
	Gets the atomic numbers vector.
std::vector< int >	getValenceElectronNumbers () const
	Gets the number of valence electrons for each atom.
void	writeDomainAndAtomCoordinates (const std::string Path) const
	writes the current domain bounding vectors and atom coordinates to files for structural optimization and dynamics restarts. The coordinates are stored as: 1. fractional for semi-periodic/periodic 2. Cartesian for non-periodic.
dftBase *	getDftfeBasePtr ()
dftParameters *	getDftfeParamsPtr ()

Static Public Member Functions
static void	globalHandlesInitialize (const MPI_Comm &mpi_comm_world)
	must be called only once at start of program from all processors after calling MPI_Init
static void	globalHandlesFinalize ()
	must be called only once at end of program from all processors but before calling MPI_Finalize

Private Member Functions
void	createScratchFolder ()
void	initialize (const bool setDeviceToMPITaskBindingInternally, const bool useDevice)

Private Attributes
MPI_Comm	d_mpi_comm_parent
dftBase *	d_dftfeBasePtr
dftParameters *	d_dftfeParamsPtr
std::string	d_scratchFolderName
bool	d_isDeviceToMPITaskBindingSetInternally

Detailed Description

wrapper class for dftfe

Author

Sambit Das

Constructor & Destructor Documentation

dftfeWrapper() [1/4]

dftfe::dftfeWrapper::dftfeWrapper

(

)

empty constructor

dftfeWrapper() [2/4]

dftfe::dftfeWrapper::dftfeWrapper	(	const std::string	parameter_file,
		const MPI_Comm &	mpi_comm_parent,
		const bool	printParams = false,
		const bool	setDeviceToMPITaskBindingInternally = false,
		const std::string	solverMode = "GS",
		const std::string	restartFilesPath = ".",
		const int	_verbosity = 1,
		const bool	useDevice = false )

constructor based on input parameter_file

dftfeWrapper() [3/4]

dftfe::dftfeWrapper::dftfeWrapper	(	const std::string	parameter_file,
		const std::string	restartCoordsFile,
		const std::string	restartDomainVectorsFile,
		const MPI_Comm &	mpi_comm_parent,
		const bool	printParams = false,
		const bool	setDeviceToMPITaskBindingInternally = false,
		const std::string	solverMode = "GS",
		const std::string	restartFilesPath = ".",
		const int	_verbosity = 1,
		const bool	useDevice = false,
		const bool	isScfRestart = true )

constructor based on input parameter_file and restart coordinates and domain vectors file paths

dftfeWrapper() [4/4]

dftfe::dftfeWrapper::dftfeWrapper	(	const MPI_Comm &	mpi_comm_parent,
		const bool	useDevice,
		const std::vector< std::vector< double > >	atomicPositionsCart,
		const std::vector< unsigned int >	atomicNumbers,
		const std::vector< std::vector< double > >	cell,
		const std::vector< bool >	pbc,
		const std::vector< unsigned int >	mpGrid = std::vector< unsigned int >{1, 1, 1},
		const std::vector< bool >	mpGridShift = std::vector< bool >{false, false, false},
		const bool	spinPolarizedDFT = false,
		const double	startMagnetization = 0.0,
		const double	fermiDiracSmearingTemp = 500.0,
		const unsigned int	npkpt = 0,
		const double	meshSize = 0.8,
		const double	scfMixingParameter = 0.2,
		const int	verbosity = -1,
		const bool	setDeviceToMPITaskBindingInternally = false )

constructor based on input list of atomic coordinates, list of atomic numbers,cell, boundary conditions, Monkhorst-Pack k-point grid, and other optional parameters. This constructor currently only sets up GGA PBE pseudopotential DFT calculations using ONCV pseudopotentials in .upf format (read from DFTFE_PSP_PATH folder provided as an environment variable). The pseudpotential directory must contain files in the format: AtomicSymbol.upf

Parameters

[in]	mpi_comm_parent	mpi communicator to be used by the dftfeWrapper.
[in]	useDevice	toggle use of Device accelerated DFT-FE
[in]	atomicPositionsCart	vector of atomic positions for each atom (in Bohr units), Origin is at cell corner
[in]	atomicNumbers	vector of atomic numbers
[in]	cell	3 \times 3 matrix in Bohr units, cell[i] denotes the ith cell vector. DFT-FE requires the cell vectors to form a right-handed coordinate system i.e. dotProduct(crossProduct(cell[0],cell[1]),cell[2])>0
[in]	pbc	vector of bools denoting periodic boundary conditions along the three cell vectors, false denotes non-periodic and true is periodic
[in]	mpgrid	vector of Monkhorst-Pack grid points along the reciprocal lattice vector directions for sampling the Brillouin zone along periodic directions. Default value is a Gamma point.
[in]	mpgridShift	vector of bools where false denotes no shift and true denotes shift by half the Monkhost-Pack grid spacing. Default value is no shift.
[in]	spinPolarizedDFT	toggles spin-polarized DFT calculations. Default value is false
[in]	startMagnetization	Starting magnetization to be used for spin-polarized DFT calculations (must be between -0.5 and +0.5). Corresponding magnetization per simulation domain will be (2 x START MAGNETIZATION x Number of electrons) in Bohr magneton units.
[in]	fermiDiracSmearingTemp	Fermi-Dirac smearing temperature in Kelvin. Default value is 500 K.
[in]	npkpt	Number of groups of MPI tasks across which the work load of the irreducible k-points is parallelised. npkpt must be a divisor of total number of MPI tasks. Default value of 0 internally sets npkt to an heuristically determined value.
[in]	meshSize	Finite-element mesh size around the atoms in Bohr units. The default value of 0.8 is sufficient to achieve chemical accuracy in energy (0.1 mHa/atom discretization error) and forces (0.1 mHa/Bohr discretization error) for the ONCV pseudo-dojo pseudopotentials. Note that this function assumes a sixth order finite-element interpolating polynomial
[in]	scfMixingParameter	mixing paramter for SCF fixed point iteration. Currently the Anderson mixing strategy is used.
[in]	verbosity	printing verbosity. Default value is -1: no printing
[in]	setDeviceToMPITaskBindingInternally	This option is only valid for Device runs. If set to true Device to MPI task binding is set inside the DFT-FE code. Default behaviour is false which assumes the binding has been externally set.

~dftfeWrapper()

dftfe::dftfeWrapper::~dftfeWrapper

(

)

Member Function Documentation

clear()

void dftfe::dftfeWrapper::clear

(

)

computeDFTFreeEnergy()

std::tuple< double, bool, double > dftfe::dftfeWrapper::computeDFTFreeEnergy	(	const bool	computeIonForces = true,
		const bool	computeCellStress = false )

solve ground-state and return DFT free energy which is sum of internal energy and negative of electronic entropic energy (in Hartree units)

Returns

tuple of ground-state energy, boolean flag on whether scf converged, and L2 norm of residual electron-density of the last SCF iteration

computeStress()

void dftfe::dftfeWrapper::computeStress

(

)

createScratchFolder()

void dftfe::dftfeWrapper::createScratchFolder ( )

private

deformCell()

void dftfe::dftfeWrapper::deformCell

(

const std::vector< std::vector< double > >

deformationGradient

)

Deforms the cell by applying the given affine deformation gradient and reinitializes the underlying data-structures.

Parameters

[in]

deformationGradient

deformation gradient matrix given by F[i][j]=\frac{\partial x_i}{\partial X_j}

getAtomicNumbers()

std::vector< int > dftfe::dftfeWrapper::getAtomicNumbers

(

)

const

Gets the atomic numbers vector.

Returns

vector of atomic numbers

getAtomPositionsCart()

std::vector< std::vector< double > > dftfe::dftfeWrapper::getAtomPositionsCart

(

)

const

Gets the current atom Positions in cartesian form (in Bohr units) (origin at corner of cell against which the cell vectors are defined)

Returns

array of coords for each atom

getAtomPositionsFrac()

std::vector< std::vector< double > > dftfe::dftfeWrapper::getAtomPositionsFrac

(

)

const

Gets the current atom Positions in fractional form (only applicable for periodic and semi-periodic BCs). CAUTION: during relaxation and MD fractional coordinates may have negaive values.

Returns

array of coords for each atom

getCell()

std::vector< std::vector< double > > dftfe::dftfeWrapper::getCell

(

)

const

Gets the current cell vectors.

Returns

3 \times 3 matrix, cell[i][j] corresponds to jth component of ith cell vector (in Bohr units)

getCellStress()

std::vector< std::vector< double > > dftfe::dftfeWrapper::getCellStress

(

)

const

Get cell stress: negative of gradient of DFT free energy with respect to affine strain components scaled by volume (Hartree/Bohr^3) units. This function can only be called after calling computeDFTFreeEnergy.

Returns

cell stress 3 \times 3 matrix given by sigma[i][j]=\frac{1}{\Omega}\frac{\partial E}{\partial \epsilon_{ij}}

getDftfeBasePtr()

dftBase * dftfe::dftfeWrapper::getDftfeBasePtr

(

)

getDftfeParamsPtr()

dftParameters * dftfe::dftfeWrapper::getDftfeParamsPtr

(

)

getDFTFreeEnergy()

double dftfe::dftfeWrapper::getDFTFreeEnergy

(

)

const

Get DFT free energy (in Hartree units). This function can only be called after calling computeDFTFreeEnergy.

getElectronicEntropicEnergy()

double dftfe::dftfeWrapper::getElectronicEntropicEnergy

(

)

const

Get electronic entropic energy (in Hartree units). This function can only be called after calling computeDFTFreeEnergy.

getForcesAtoms()

std::vector< std::vector< double > > dftfe::dftfeWrapper::getForcesAtoms

(

)

const

Get ionic forces: negative of gradient of DFT free energy with respect to ionic positions (in Hartree/Bohr units). This function can only be called after calling computeDFTFreeEnergy.

Returns

vector of forces on each atom

getPBC()

std::vector< bool > dftfe::dftfeWrapper::getPBC

(

)

const

Gets the boundary conditions for each cell vector direction.

Returns

vector of bools, false denotes non-periodic BC and true denotes periodic BC

getValenceElectronNumbers()

std::vector< int > dftfe::dftfeWrapper::getValenceElectronNumbers

(

)

const

Gets the number of valence electrons for each atom.

Returns

array of number of valence for each atom

globalHandlesFinalize()

static void dftfe::dftfeWrapper::globalHandlesFinalize ( )

static

must be called only once at end of program from all processors but before calling MPI_Finalize

globalHandlesInitialize()

static void dftfe::dftfeWrapper::globalHandlesInitialize ( const MPI_Comm & mpi_comm_world )

static

must be called only once at start of program from all processors after calling MPI_Init

initialize()

void dftfe::dftfeWrapper::initialize ( const bool setDeviceToMPITaskBindingInternally, const bool useDevice )

private

reinit() [1/3]

void dftfe::dftfeWrapper::reinit	(	const MPI_Comm &	mpi_comm_parent,
		const bool	useDevice,
		const std::vector< std::vector< double > >	atomicPositionsCart,
		const std::vector< unsigned int >	atomicNumbers,
		const std::vector< std::vector< double > >	cell,
		const std::vector< bool >	pbc,
		const std::vector< unsigned int >	mpGrid = std::vector< unsigned int >{1, 1, 1},
		const std::vector< bool >	mpGridShift = std::vector< bool >{false, false, false},
		const bool	spinPolarizedDFT = false,
		const double	startMagnetization = 0.0,
		const double	fermiDiracSmearingTemp = 500.0,
		const unsigned int	npkpt = 0,
		const double	meshSize = 0.8,
		const double	scfMixingParameter = 0.2,
		const int	verbosity = -1,
		const bool	setDeviceToMPITaskBindingInternally = false )

reinit() [2/3]

void dftfe::dftfeWrapper::reinit	(	const std::string	parameter_file,
		const MPI_Comm &	mpi_comm_parent,
		const bool	printParams = false,
		const bool	setDeviceToMPITaskBindingInternally = false,
		const std::string	solverMode = "GS",
		const std::string	restartFilesPath = ".",
		const int	_verbosity = 1,
		const bool	useDevice = false )

clear and reinitialize based on input parameter_file

reinit() [3/3]

void dftfe::dftfeWrapper::reinit	(	const std::string	parameter_file,
		const std::string	restartCoordsFile,
		const std::string	restartDomainVectorsFile,
		const MPI_Comm &	mpi_comm_parent,
		const bool	printParams = false,
		const bool	setDeviceToMPITaskBindingInternally = false,
		const std::string	solverMode = "GS",
		const std::string	restartFilesPath = ".",
		const int	_verbosity = 1,
		const bool	useDevice = false,
		const bool	isScfRestart = true )

clear and reinitialize based on input parameter_file and restart coordinates and domain vectors file paths

run()

void dftfe::dftfeWrapper::run

(

)

Legacy function (to be deprecated)

updateAtomPositions()

void dftfe::dftfeWrapper::updateAtomPositions

(

const std::vector< std::vector< double > >

atomsDisplacements

)

update atom positions and reinitialize all related data-structures

Parameters

[in]

atomsDisplacements

vector of displacements for each atom (in Bohr units)

writeDomainAndAtomCoordinates()

void dftfe::dftfeWrapper::writeDomainAndAtomCoordinates

(

const std::string

Path

)

const

writes the current domain bounding vectors and atom coordinates to files for structural optimization and dynamics restarts. The coordinates are stored as: 1. fractional for semi-periodic/periodic 2. Cartesian for non-periodic.

Parameters

[in]

Path

The folder path to store the atom coordinates required during restart.

writeMesh()

void dftfe::dftfeWrapper::writeMesh

(

)

Calls dftBasepointer public function writeMesh(). Here the inital density and mesh are stored in a file. Useful for visluiing meshes without running solve.

Member Data Documentation

d_dftfeBasePtr

dftBase* dftfe::dftfeWrapper::d_dftfeBasePtr

private

d_dftfeParamsPtr

dftParameters* dftfe::dftfeWrapper::d_dftfeParamsPtr

private

d_isDeviceToMPITaskBindingSetInternally

bool dftfe::dftfeWrapper::d_isDeviceToMPITaskBindingSetInternally

private

d_mpi_comm_parent

MPI_Comm dftfe::dftfeWrapper::d_mpi_comm_parent

private

d_scratchFolderName

std::string dftfe::dftfeWrapper::d_scratchFolderName

private

---

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

• workspace/include/dftfeWrapper.h