Package schrodinger :: Package application :: Package matsci :: Package espresso :: Module qeinput :: Class StructureType

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Class StructureType

object --+
         |
        StructureType

Class to generate QE input XML section related to structure.

Instance Methods

[hide private]

__init__(self, struct, frac_coords=None)
Initialize StructureType object.

str

getAtomicStructure(self)
Generate XML input related to atomic_structure.

str

getAtomicSpecies(self, ppfiles, ecutwfc, ecutrho)
Generate XML input related to atomic species.

float

_getPPNelect(self, zvals)
Get number of the valence electrons based on the Z valence values of the pseudopotentials.

dict, float, float, float

fetchPPDB(self, functional)
Get pseudopotentials file paths and other related data from the database having the same functional and family.

_getAtomicSpecies(self)
Extract number of electrons (in self.nelect) and species (in self.species) from self.struct.

str

_getCell(self)
Generate XML input related to cell.

_validatePBCs(self)
Check that PBCs are present for the self.structure.

structure.Structure

moveAtomsIntoCell(self, frac_coords=None, overlap_distance=0.5)
Get structure with all the atoms moved into the first cell.

alignStructWithPlane(self, vector_index)
Slide structure (self.struct) along the axis such that all atoms are on top of the plane perpendicular to the axis defined by vector_index.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

X = 0
hash(x)

Y = 1

Z = 2

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, struct, frac_coords=None)
(Constructor)

Initialize StructureType object.

Parameters:

struct (structure.Structure) - Structure to generate XML from.
frac_coords (numpy arrays of arrays of 3 floats or None) - Fractional coordinates

Overrides: object.__init__

getAtomicStructure(self)

Generate XML input related to atomic_structure.

Returns: str: cell xml data

getAtomicSpecies(self, ppfiles, ecutwfc, ecutrho)

Generate XML input related to atomic species.

Parameters:

ecutwfc (float) - Energy cutoff
ecutrho (float) - Density cutoff
ppfiles (dict[str:str])

Returns: str

species xml data

_getPPNelect(self, zvals)

Get number of the valence electrons based on the Z valence values of the pseudopotentials.

Parameters:

zvals (dict) - Dict with valence electrons: {'element': 'zval'}

Returns: float

Total number of valence electrons for self.struct

fetchPPDB(self, functional)

Get pseudopotentials file paths and other related data from the database having the same functional and family.

Parameters:

functional (str) - DFT Functional (one of the DFT_FUNCTIONALS)

Returns: dict, float, float, float

Dict with paths to PPs ({'element': 'path'}), number of valence electrons, max ecutwfc, max ecutrho for elements

_getCell(self)

Generate XML input related to cell.

Returns: str: cell xml data

_validatePBCs(self)

Check that PBCs are present for the self.structure. Also set the space group in self.space_group.

moveAtomsIntoCell(self, frac_coords=None, overlap_distance=0.5)

Get structure with all the atoms moved into the first cell.

Parameters:

frac_coords (numpy arrays of arrays of 3 floats or None) - Fractional coordinates
overlap_distance (float) - Distance between two atoms, such that they are considered overlapping

Returns: structure.Structure

Structure with all the atoms moved inside first unit cell

alignStructWithPlane(self, vector_index)

Slide structure (self.struct) along the axis such that all atoms are on top of the plane perpendicular to the axis defined by vector_index.

Parameters:

vector_index (int) - Vector index (X or Y or Z) to align structure to the perpendicular plane

Class StructureType

__init__(self, struct, frac_coords=None) (Constructor)

getAtomicStructure(self)

getAtomicSpecies(self, ppfiles, ecutwfc, ecutrho)

_getPPNelect(self, zvals)

fetchPPDB(self, functional)

_getCell(self)

_validatePBCs(self)

moveAtomsIntoCell(self, frac_coords=None, overlap_distance=0.5)

alignStructWithPlane(self, vector_index)

init(self, struct, frac_coords=None)
(Constructor)