POSCAR (`cusp.poscar`)

Input data type for structure inputs passed to VASP calculations. Contrary to a plain structure data type the VaspPoscarData class offers multiple additional attributes like constraints or atomic velocities

Initializing the class

In general the constructor of the VaspPoscarData class is of the following form:

VaspPoscarData(structure=None, constraints=None, velocities=None, temperature=None)

Arguments:

structure (StructureData, Structure or Poscar) – The structure data used to generate the POSCAR data from.
constraints (list, optional) – Nx3 list (N the number of atoms) of bool introducing selective dynamics by adding constraints on the coordinates for every atom contained in the structure. (i.e. False: coordinate is not allowed to change, True coordinate is allowed to change)
velocities (list, optional) – Nx3 list (N the number of atoms) of float setting the velocities for every atom on the structure
temperature (float, optional) – Instead of passing an explicit list of velocities initialize the atomic velocities from a Maxwell-Boltzmann distribution at the given temperature

Example plain structure:

>>> from aiida.plugins import DataFactory
>>> from pymatgen.core import Lattice, Structure
>>> lattice = Lattice.cubic(3.359)
>>> structure = Structure(lattice, ["Po"], [.0, .0, .0])
>>> VaspPoscarData = DataFactory('cusp.poscar')
>>> cusp_poscar = VaspPoscarData(structure=structure)
>>> print(cusp_poscar.get_poscar())
Po1
1.0
3.359000 0.000000 0.000000
0.000000 3.359000 0.000000
0.000000 0.000000 3.359000
Po
1
direct
0.000000 0.000000 0.000000 Po

Example with constraints:

>>> from aiida.plugins import DataFactory
>>> from pymatgen.core import Lattice, Structure
>>> lattice = Lattice.cubic(3.359)
>>> structure = Structure(lattice, ["Po"], [.0, .0, .0])
>>> VaspPoscarData = DataFactory('cusp.poscar')
>>> cusp_poscar = VaspPoscarData(structure=structure, constraints=[[True, False, True]])
>>> print(cusp_poscar.get_poscar())
Po1
1.0
3.359000 0.000000 0.000000
0.000000 3.359000 0.000000
0.000000 0.000000 3.359000
Po
1
Selective dynamics
direct
0.000000 0.000000 0.000000 T F T Po

Recovering the stored structure data

In order to further analyze or re-use structures the VaspPoscarData class offers several methods to retrieve the stored structure. In particular, four different methods are available to recover the stored structure data in different formats:

VaspPoscarData.get_poscar()

Create and return a pymatgen.io.vasp.inputs.Poscar instance initialized from the node’s stored structure data contents.

Returns:: a pymatgen Poscar instance
Return type:: pymatgen.io.vasp.inputs.Poscar

VaspPoscarData.get_structure()

Create and return a pymatgen.core.structure.Structure instance from the node’s stored structure data contents.

Returns:: a pymatgen Structure instance
Return type:: pymatgen.core.structure.Structure

VaspPoscarData.get_atoms()

Create and return a ase.Atoms instance from the node’s stored structure data contents

Returns:: an ASE-Atoms instance
Return type:: ase.Atoms

VaspPoscarData.get_aiida_structure()

Create and return a aiida.orm.nodes.data.structure.StructureData instance from the node’s stored structure data contents

Returns:: an AiiDA StructureData instance
Return type:: aiida.orm.nodes.data.structure.StructureData

POSCAR (cusp.poscar)

Initializing the class

Recovering the stored structure data

POSCAR (`cusp.poscar`)