pyepfd_io module

This module contains classes the deals with I/O operations based on a finite-difference phonon calculations performed using PyEPFD’s coord_util.ionic_mover and elph_classes.phonon_calculator classes.

class pyepfd_io.write_pyepfd_info(inp_dynmat=None, dynmat=None, ref_dynmat=None, mass=None, etotals=None, opt_coord=None, atoms=None, cell=None, mode='enmfd', deltax=0.001, deltae=0.001, ngrid=1, file_name='test.xml', asr='crystal')

Bases: object

This class writes a checkpoint xml file containing crucial informations after a phonon calculation.

Arguments:

inp_dynmat = Input dynamical matrix for NMFD/ENMFD phonon. It is a numpy array of 3 N x 3 N; where N is the number of atoms.

dynmat = Obtained dynamical matrix after FD/NMFD/ENMFD phonon calculation. It is also numpy array of 3 N x 3 N; where N is the number of atoms.

ref_dynmat = Refined dynamical matrix after FD/NMFD/ENMFD phonon calculation. Refinement is done applying asr to dynmat. It is also a numpy array of 3 N x 3 N; where N is the number of atoms.

mass = (3 N ) numpy array of mass matrix

cell = A numpy array of length 6. First 3 numbers are cell length (atomic unit) and last three numbers are angles (degrees) between cell vectors.

etotals = (6 N + 1) numpy array of Born-Openheimer energies (<etotals> for qbox)

opt_coord = (3 N) numpy array of Cartesian coordinates of optimized geometry.

atoms = List of strings of length N containing atom-symbols.

mode = Finite displacement mode.

deltax = A displacement (float) in atomic unit (Bohr)

deltae = Energy scaled displacement (float) in atomic_unit (Hartree)

ngrid = Number of displacement grid points for central difference

asr Acoustic sum rule.

file_name = Output/ checkpoint file name

Returns

An output with file name file_name.

class pyepfd_io.read_pyepfd_info(file_path='RESTART')

Bases: object

This class reads a checkpoint/restart file created by pyepfd after a phonon calculation. This information is stored in several objects within this class.

Arguments:

file_path = Path to the restart/ checkpoint file

Returns:

Creates following objects within the class.

asr = A string storing asr information.

deltax = Normal mode displacement ( deltax in other classes) information.

deltae = Energy scaled displacement (deltae in other classes) in atomic_unit (Hartree)

ngrid = Number of displacement grid points for central difference

inp_dynmatrix = Input dynamical matrix for NMFD/ENMFD phonon. It is a numpy array of 3 N x 3 N; where N is the number of atoms.

dynmatrix = Obtained dynamical matrix after FD/NMFD/ENMFD phonon calculation. It is also numpy array of 3 N x 3 N; where N is the number of atoms.

ref_dynmatrix = Refined dynamical matrix after FD/NMFD/ENMFD phonon calculation. Refinement is done applying asr to dynmat. It is also a numpy array of 3 N x 3 N; where N is the number of atoms.

mass = Mass matrix

coord = Coordinates of optimized geometry. A float array of length N.

atoms = A list of atoms with length N .

cell = A numpy array of length 6. First 3 numbers are cell length (atomic unit) and last three numbers are angles (degrees) between cell vectors.