ES Interface

Each of the interfaces uses subclass of the DFTCoordinates class to parse the output.

Note

The interfaces are in beta stage. Please let us know if you encounter any errors.

Quantum Espresso

class PWCoordinates(filename, pwtype=None, to_angstrom=False)

Coordinates of the system from the PW data of Quantum Espresso. Subclass of the DFTCoordinates.

With initiallization reads either output or input of PW module of QE.

Parameters:

filename (str) – name of the PW input or output.
pwfile (str) – Name of PW input or output file. If the file doesn’t have proper extension, parameter pw_type should indicate the type.
pwtype (str) – Type of the coord_f. if not listed, will be inferred from extension of pwfile.
to_angstrom (bool) – True if automatically convert the units of cell and coordinates to Angstrom.

parse_output(filename, to_angstrom=False)

Method to read coordinates of atoms from PW output into the PWCoordinates instance.

Parameters:

filename (str) – the name of the output file.
to_angstrom (bool) – True if automatically convert the units of cell and coordinates to Angstrom.

Returns:

None

parse_input(filename, to_angstrom=False)

Method to read coordinates of atoms from PW input into the PWCoordinates instance.

Parameters:

filename (str) – the name of the output file.
to_angstrom (bool) – True if automatically convert the units of cell and coordinates to Angstrom.

cell_from_system(sdict)

Function to obtain cell from namelist SYSTEM read from PW input.

Parameters:

sdict (dict) – Dictinary generated from namelist SYSTEM of PW input.

Returns:

Cell is 3x3 matrix with entries:

[[a_x b_x c_x]
 [a_y b_y c_y]
 [a_z b_z c_z]],

where a, b, c are crystallographic vectors, and x, y, z are their coordinates in the cartesian reference frame.

Return type:

ndarray with shape (3,3)

celldms_from_abc(ibrav, abc_list)

Obtain celldms from ibrav value and a, b, c, cosab, cosac, cosbc parameters.

Using ibrav value and abc parameters from PW input generate celldm array, necessary to construct cell parameters. For details about abc and ibrav values see PW input documentation.

Parameters:

ibrav (int) – ibrav parameter of PW input.
abc_list (list) – List, of 6 parameters: a, b, c, cosab, cosac, cosbc

Returns:

list of 6 values, from which cell can be generated.

Return type:

celldm (list)

read_gipaw_tensors(lines, keyword=None, start=None, conversion=1)

Helper function to read GIPAW tensors from the list of lines.

Parameters:

lines (list of str) – List of strings contraining lines from the file. Output of open(file).readlines().
keyword (str) – Keyword in the line which indicates the beginning of the tensor data block.
start (int) – Index of the line which indicates the beginning of the tensor data block.
conversion (float) – Conversion factor from GIPAW units to the ones, used in this package.

Returns:

Array of tensors.

Return type:

ndarray with shape (n, 3, 3)

read_hyperfine(filename, spin=1)

Function to read hyperfine couplings from GIPAW output.

Parameters:

filename (str) – Name of the GIPAW hyperfine output.
spin (float) – Spin of the central spin. Default 1.

Returns:

Tuple containing:

ndarray with shape (n,): Array of Fermi contact terms.

ndarray with shape (n, 3,3): Array of spin dipolar hyperfine tensors.

Return type:

tuple

read_efg(filename)

Function to read electric field gradient tensors from GIPAW output.

Parameters:: filename (str) – Name of the GIPAW EFG-containing output.
Returns:: Array of EFG tensors.
Return type:: ndarray with shape (n, 3,3)

read_qe_namelists(input_string)

Read Fortran-like namelists from the large string.

Parameters:: input_string (str) – String representation of the QE input file.
Returns:: Dictionary, containing dicts for each namelist found in the input string.
Return type:: dict

get_ctype(lin)

Get coordinates type from the line of QE input/output.

Parameters:: str – Line from QE input/output containing string with coordinates type.
Returns:: type of the coordinates.
Return type:: str

ORCA

class ORCACoordinates(orca_output)

Coordinates of the system from the ORCA output. Subclass of the DFTCoordinates.

With initialization reads output of the ORCA.

Parameters:: orca_output (str or list of str) – either name of the output file or list of lines read from that file.

alat

The lattice parameter in angstrom.

Type:: float

cell

cell is 3x3 matrix with entries:

\[\begin{split}[&[a_x\ b_x\ c_x]\\ &[a_y\ b_y\ c_y]\\ &[a_z\ b_z\ c_z]]\end{split}\]

where a, b, c are crystallographic vectors, and x, y, z are their coordinates in the cartesian reference frame.

Type:: ndarray with shape (3, 3)

coordinates

array with the coordinates of atoms in the cell.

Type:: ndarray with shape (n, 3)

names

array with the names of atoms in the cell.

Type:: ndarray with shape (n,)

cell_units

Units of cell coordinates: ‘bohr’, ‘angstrom’, ‘alat’.

Type:: str

coordinates_units

Units of atom coordinates: ‘crystal’, ‘bohr’, ‘angstrom’, ‘alat’.

Type:: str

read_output(orca_output)

Method to read coordinates of atoms from ORCA output into the ORCACoordinates instance.

Parameters:: orca_output (str or list of str) – either name of the output file or list of lines read from that file.

Base class

class DFTCoordinates

Abstract class of a container of the DFT output coordinates.

alat

The lattice parameter in angstrom.

Type:: float

cell

cell is 3x3 matrix with entries:

\[\begin{split}[&[a_x\ b_x\ c_x]\\ &[a_y\ b_y\ c_y]\\ &[a_z\ b_z\ c_z]]\end{split}\]

where a, b, c are crystallographic vectors and x, y, z are their coordinates in the cartesian reference frame.

Type:: ndarray with shape (3, 3)

coordinates

Array with the coordinates of atoms in the cell.

Type:: ndarray with shape (n, 3)

names

Array with the names of atoms in the cell.

Type:: ndarray with shape (n,)

cell_units

Units of cell coordinates: ‘bohr’, ‘angstrom’, ‘alat’.

Type:: str

coordinates_units

Units of atom coordinates: ‘crystal’, ‘bohr’, ‘angstrom’, ‘alat’.

Type:: str

to_angstrom(inplace=False)

Method to transform cell and coordinates units to angstroms.

Parameters:: inplace (bool) – if True changes attributes inplace. Otherwise returns copy.
Returns:: Instance of the subclass with units of coordinates and cell of Angstroms.
Return type:: DFTCoordinates or subclass

get_angstrom(coordinate, units)

Change given coordinates to angstrom.

Parameters:

coordinates (ndarray with shape (n, 3) or (3,)) – Coordinates to change.
units (str) – Initial units of the coordinates.

Returns:

Coordinates in angstrom.

Return type:

ndarray (n, 3)

change_to_angstrom(coordinates, units, alat=None, cell=None)

Change coordinates to angstrom.

Parameters:

coordinates (ndarray with shape (n, 3) or (3,)) – Coordinates to change.
units (str) – Initial units of the coordinates.
alat (float) – The lattice parameter in angstrom.
cell (ndarray with shape (3,3)) –
cell is 3x3 matrix with entries:

\[\begin{split}[&[a_x\ b_x\ c_x]\\ &[a_y\ b_y\ c_y]\\ &[a_z\ b_z\ c_z]]\end{split}\]

where a, b, c are crystallographic vectors, and x, y, z are their coordinates in the cartesian reference frame.

Returns:

Coordinates in angstrom.

Return type:

ndarray with shape (n, 3)

fortran_value(value)

Get value from Fortran-type variable.

Parameters:: value (str) – Value read from Fortran-type input.
Returns:: value in Python format.
Return type:: value (bool, str, float)

yield_index(word, lines, start=0, case_sensitive=False)

Generator which yields indexes of the lines containing specific word.

Parameters:

word (str) – Word to find in the line.
lines (list of str) – List of strings contraining lines from the file. Output of open(file).readlines().
start (int) – First index from which to start search.
case_sensitive (bool) – If True looks for the exact match. Otherwise the search is case insensitive.

Yields:

i (int) – Index of the line containing word.

find_first_index(word, lines, start=0, case_sensitive=False)

Function to find first appearance of the index in the list of lines.

Parameters:

word (str) – Word to find in the line.
lines (list of str) – List of strings contraining lines from the file. Output of open(file).readlines().
start (int) – First index from which to start search.
case_sensitive (bool) – If True looks for the exact match. Otherwise the search is case insensitive.

Returns:

Index of the first line from the start containing word.

Return type:

i (int)

set_isotopes(array, isotopes=None, inplace=True, spin_types=None)

Function to set the most common isotopes for the array containing DFT output. If some other isotope is specified, the A tensors are scaled accordingly.

Parameters:

array (BathArray) – Array with DFT spins.
isotopes (dict) – Dictionary with chosen isotopes.
inplace (bool) – True if change the array inplace.
spin_types (SpinDict) – If provided, allows for custom defined SpinType instances.

Returns:

Array with DFT spins with correct isotopes.

Return type:

array (BathArray)