schrodinger.application.matsci.espresso.qeoutput module

Classes and functions to deal reading XML generated by Quantum Espresso.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.espresso.qeoutput.BandStructure(kpoints, eigenvals, efermi, struct=None)

Bases: object

This class is based on the class from pymatgen (MIT license).

generatePlotData()

Generate distances between k-points (in self.distances) for plotting band structure.

getBandGap()

Get band gap data.

Return type:dict
Returns:dict with keys ENERGY_KEY, DIRECT_KEY, TRANSITION_KEY: ENERGY_KEY: band gap energy DIRECT_KEY: A boolean telling if the gap is direct or not TRANSITION_KEY: kpoint labels of the transition (e.g., “Gamma-X”)
getVbmCbm(vbm=True)

Return data about the valence band maximum (VBM) or conduction band minimum (CBM).

Parameters:vbm (bool) – If True calculates VBM, if False CBM
Return type:dict
Returns:
dict with keys BAND_INDEX_KEY, KPOINT_INDEX_KEY, KPOINT_KEY,
ENERGY_KEY
  • BAND_INDEX_KEY: A dict with spin keys pointing to a list of the

indices of the band containing the VBM (please note that you can have several bands sharing the VBM) {SPIN_UP:[], SPIN_DW:[]} - KPOINT_INDEX_KEY: The list of indices in self.kpoints for the kpoint vbm. Please note that there can be several kpoint_indices relating to the same kpoint (e.g., Gamma can occur at different spots in the band structure line plot) - KPOINT_KEY: The kpoint (as a kpoint object) - ENERGY_KEY: The energy of the VBM
isMetal()

Check if the band structure indicates a metal by looking if the Fermi level crosses a band.

Return type:bool
Returns:True, if the system is metallic
class schrodinger.application.matsci.espresso.qeoutput.DOS(band, dos_fn)

Bases: object

Basic DOS class, based on the class from pymatgen (MIT license).

getCbmVbm(tol=0.001, abs_tol=False, spin=None)

Get Conduction Band Minimum (cbm) and Valence Band Maximum (vbm).

Param:

tolerance in occupations for determining the cbm/vbm
Parameters:
  • abs_tol (bool) – An absolute tolerance (True) or a relative one (False)
  • spin (str or None) – Possible values are None - finds the cbm/vbm in the summed densities, SPIN_UP - finds the cbm/vbm in the up spin channel, SPIN_DW - finds the cbm/vbm in the down spin channel.
Return type:

float, float
Returns:

cbm and vbm in Ry corresponding to the gap
getDOS(degauss, delta_e=0.01)

Broaden energies and set DOS in self.dos. This requires self.band to be set in the constructor.

Parameters:
  • degauss (float) – Used only if dos is True, broadening (eV) for computing DOS
  • delta_e (float) – Used only if dos is True, energy grid spacing (in eV)
Raises:

ValueError – If self.band is None
getDensities(spin=None)

Get density of states for a particular spin.

Parameters:spin (str or None) – Can be SPIN_UP or SPIN_DW or None.
Return type:numpy.array
Returns:Density of states for a particular spin. If Spin is None, the sum of all spins is returned.
getGap(tol=0.001, abs_tol=False, spin=None)

Get the gap.

Param:

tolerance in occupations for determining the gap
Parameters:
  • abs_tol (bool) – An absolute tolerance (True) or a relative one (False)
  • spin (str or None) – Possible values are None - finds the gap in the summed densities, SPIN_UP - finds the gap in the up spin channel, SPIN_DW - finds the gap in the down spin channel.
Return type:

float
Returns:

gap in Ry or 0.0, if it is a metal
class schrodinger.application.matsci.espresso.qeoutput.EsmType(data, bc_type, efield)

Bases: tuple

bc_type

Alias for field number 1

data

Alias for field number 0

efield

Alias for field number 2

class schrodinger.application.matsci.espresso.qeoutput.KPoint(tag, vecs=None)

Bases: object

Class to hold information about a k-point.

getCoords(coords_str)

Return list of coordinates.

Parameters:coords_str (str) – String representing K-point coordinates
Return type:list of three floats
Returns:K-point coordinates
getCoordsStr(frac=False)

Get string representation of the coordinates.

Parameters:frac (bool) – If True, self.frac_coords are returned, otherwise self.cart_coords
Return type:str
Returns:String representation of the coordinates
static getKptFromCfg(kpt)
class schrodinger.application.matsci.espresso.qeoutput.KptLegend(label, coords)

Bases: tuple

coords

Alias for field number 1

label

Alias for field number 0

class schrodinger.application.matsci.espresso.qeoutput.OrderedDefaultDict(default_factory=None, *args, **kwargs)

Bases: collections.OrderedDict, collections.defaultdict

This class implements ordered default dict functionality.

class schrodinger.application.matsci.espresso.qeoutput.OutStruct(struct, std_struct)

Bases: tuple

std_struct

Alias for field number 1

struct

Alias for field number 0

class schrodinger.application.matsci.espresso.qeoutput.Output(qegz_fn, struct=False, band=False, dos=False, pdos=False, esm=False, neb=False, phdos=False, phband=False, dynamics=False, tree=None)

Bases: object

Class to deal with QE XML output parsing.

getMDStepStruct(step, timestep)

Extract MD step structure from step XML.

Parameters:
  • step (xml.etree.ElementTree.Element) – step element
  • timestep (float) – MD time step
Return type:

structure.Structure, structure.Structure or None
Returns:

Structure of the MD step, standardized structure if requested and found
class schrodinger.application.matsci.espresso.qeoutput.PDOS(proj, wfc_types, efermi, band)

Bases: object

Class that holds partial DOS (PDOS) data. Call getPDOS to get broadened data.

ADOS_IDX = 1
AIDOS_IDX = 3
ALDOS_IDX = 4
EDOS_IDX = 2
LDOS_IDX = 0
NUM_IDX = 5
getPDOS(degauss, delta_e=0.01)

Calculate PDOS and set in self.pdos.

Parameters:
  • degauss (float) – Broadening (eV) for computing PDOS
  • delta_e (float) – Energy grid spacing eV
class schrodinger.application.matsci.espresso.qeoutput.PhDOS(table)

Bases: object

Phonon DOS class.

XAXIS_PROP = 'r_j_Frequency_(cm-1)'
getPhDOS(degauss, delta_e=0.01)

Broaden frequencies and set PhDOS in self.phdos.

Parameters:
  • degauss (float) – Broadening for computing DOS in cm-1
  • delta_e (float) – Energy grid spacing in cm-1
class schrodinger.application.matsci.espresso.qeoutput.WfcType(atom_idx, atom_type, n_qn, l_qn, m_qn)

Bases: tuple

atom_idx

Alias for field number 0

atom_type

Alias for field number 1

l_qn

Alias for field number 3

m_qn

Alias for field number 4

n_qn

Alias for field number 2

schrodinger.application.matsci.espresso.qeoutput.gaussian_delta(eigenval, energies, degauss)

Get Gaussian-function values

Parameters:
  • eigenval (float) – Energy at which to calculate Gaussian delta
  • energies (numpy.array) – Energy grid
  • degauss (float) – Broadening
Return type:

numpy.array
Returns:

delta values on the grid