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.