schrodinger.application.matsci.espresso.qeoutput module¶

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

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.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

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

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

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

Bases: object

Class to hold information about a k-point.

__init__(tag, vecs=None)¶

Initialize KPoint object from ElementTree element.

Parameters

tag (xml.etree.ElementTree.Element) – k_point tag
vecs (numpy array (3x3)) – Cell vectors

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.DOS(band, dos_fn)¶

Bases: object

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

__init__(band, dos_fn)¶

Initialize DOS object. ‘band’ can be None, in this case, dos_fn MUST point to the .dos file. If both ‘band’ and ‘dos_fn’ are present, former one has priority.

Parameters

band (BandStructure) – BandStructure object to extract eigenvalues and k-points from
dos_fn (str) – .dos filename. This file holds DOS plot data

canBroaden()¶

Can getDOS (broadening) be called on this object.

Return type: bool
Returns: True if it can, otherwise False

getDOS(degauss, delta_e=0.01)¶

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

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.

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

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.PhDOS(freqs, eigv=None, densities=None, min_pos_freq=0.001)¶

Bases: object

Phonon DOS class.

DOS_FREQ_GRID_SPACING = 1.0¶

DOS_FREQ_DEGAUSS = 10.0¶

MIN_POS_FREQ = 0.001¶

class Thermo(zpe, u, h, s, cv)¶

Bases: tuple

cv¶: Alias for field number 4

h¶: Alias for field number 2

s¶: Alias for field number 3

u¶: Alias for field number 1

zpe¶: Alias for field number 0

__init__(freqs, eigv=None, densities=None, min_pos_freq=0.001)¶

Initialize PhDOS object.

Parameters

freqs (list[float]) – Frequencies, in 1/cm
eigv (list[float]) – Optional eigenvectors
densities (list[float]) – Optional densities
min_pos_freq (float) – Minimum value of a frequency (cm-1), to be considered positive

property has_densities¶

Check whether self.densities are present.

Return type: bool
Returns: Whether self.densities are present

property has_eigv¶

Check whether eigenvectors are present.

Return type: bool
Returns: Whether eigenvectors are present

getEigv(struct)¶

Get eigenvectors from the modes.

Parameters: struct (structure.Structure) – Structure to use
Return type: numpy.array
Returns: Eigen vectors

classmethod fromPHDOS(file_fh)¶

Initialize PhDOS object from a .phdos file handler.

Parameters: file_fh (file) – File handler of phonon DOS from matdyn.x
Return type: PhDOS
Returns: New PhDOS object

classmethod fromSPM(spm_obj)¶

Initialize PhDOS object from a SPM file name / handler.

Parameters: spm_obj (str or file handler) – SPM file name or handler. If handler, it should have been opened in the rb mode
Return type: PhDOS
Returns: New PhDOS object

classmethod fromVIB(vib_fh)¶

Create new object from frequencies and modes from a VIB file handler.

Parameters: vib_fh (FILE) – VIB file handler
Return type: PhDOS
Returns: New PhDOS object

c_v(temperature)¶

Constant volume specific heat C_v at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/(K*mol).

Parameters: temperature (float) – Temperature at which to evaluate C_v, in K
Return type: float
Returns: Constant volume specific heat C_v in J/(K*mol)

entropy(temperature)¶

Vibrational entropy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/(K*mol).

Parameters: temperature (float) – Temperature at which to evaluate C_v, in K
Return type: float
Returns: Vibrational entropy in J/(K*mol)

internal_energy(temperature)¶

Phonon contribution to the internal energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol.

Parameters: temperature (float) – Temperature at which to evaluate energy, in K
Return type: float
Returns: Phonon contribution to the internal energy, in J/mol.

helmholtz_free_energy(temperature)¶

Phonon contribution to the Helmholtz free energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol.

Parameters: temperature (float) – Temperature at which to evaluate free energy, in K
Return type: float
Returns: Phonon contribution to the Helmholtz free energy, in J/mol

thermo(temp)¶

Compute thermo properties at temperature.

Parameters: temp (float) – Temperature in K
Return type: PhDOS.Thermo
Returns: Thermo properties

zero_point_energy()¶

Zero point energy energy of the system. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol.

Parameters: temperature (float) – Temperature at which to evaluate ZPE, in K
Return type: float
Returns: Phonon contribution to ZPE, in J/mol

getDOS(degauss=10.0, delta_e=1.0)¶

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

Parameters

degauss (float) – Broadening (cm-1)
delta_e (float) – Energy grid spacing (cm-1)

Return type

numpy.array[float], numpy.array[float]

Returns

Frequencies and corresponding DOS

class schrodinger.application.matsci.espresso.qeoutput.PhDOSTensors(eps_e, born_raw)¶

Bases: object

Phonon DOS tensors class.

__init__(eps_e, born_raw)¶

Initialize the object.

Parameters

eps_e (list[float]) – Dielectric electron tensor (3x3)
born_row (list[float]) – Born charges (1D list). See tensors method.

classmethod fromFile(file_fh)¶

Read electronic dielectric constant and Born charges from file.

Parameters: file_fh (FILE) – born.charges file handler
Return type: PhDOSTensors
Returns: Newly created tensors object

tensors(nat)¶

Get electronic dielectric constant tensor and Born effective charges.

Parameters: nat (int) – Number of atoms to use to wrap Born effective charges
Return type: numpy.array[float], numpy.array[float]
Returns: Electronic dielectric constant tensor, Born effective charges

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.

NUM_IDX = 5¶

LDOS_IDX = 0¶

ADOS_IDX = 1¶

EDOS_IDX = 2¶

AIDOS_IDX = 3¶

ALDOS_IDX = 4¶

__init__(proj, wfc_types, efermi, band)¶

Initialize PDOS object. Constructor only assigns values, call getPDOS for broadening.

Parameters

proj (dict of 3d numpy.array) – Dict with SPIN_UP, SPIN_DW (optional) keys, each containing a 3D array containing: index of projected atom wavefunction, index of k-point, index of band and WFC projection as value.
wfc_types (list of WfcType) – List containing wavefunction types description
efermi (float) – Fermi energy in eV

getPDOS(degauss, delta_e=0.01)¶

Calculate PDOS and set in self.pdos. Saves degauss in self.degauss.

Parameters

degauss (float) – Broadening (eV) for computing PDOS
delta_e (float) – Energy grid spacing eV

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).

__init__(kpoints, eigenvals, efermi, struct=None)¶

Initialize BandStructure object.

Param

List of k-points for this band structure

Parameters

eigenvals (dict) –

Energies of the band structure in the shape:

{SPIN_UP: numpy.array([iband, jkpoint]),              SPIN_DW: numpy.array([iband, jkpoint])}

SPIN_DW key can be present or not depending on the calculation type

Parameters

efermi (float) – Fermi energy in Hartree
struct (structure.Structure) – Related structure

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

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 where: - 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

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”)

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

class schrodinger.application.matsci.espresso.qeoutput.Output(qegz_fn, tree=None, dos_fn=None, **kwargs)¶

Bases: object

Class to deal with QE XML output parsing.

PROPERTIES = ('struct', 'band', 'dos', 'pdos', 'esm', 'neb', 'phdos', 'phband', 'dynamics', 'epsilon', 'hpu', 'nmr')¶

EPS_METAL_ERR = 'Metallic system encountered in epsilon calculation.'¶

__init__(qegz_fn, tree=None, dos_fn=None, **kwargs)¶

Initialize Output object. Supported properties are requested in kwargs and defined in self.PROPERTIES.

Parameters

qegz_fn (str) – Archive name of the compressed .save folder
tree (ElementTree or None) – Use tree if not None otherwise read tree from the file
dos_fn (str or None) – File to read dos property from, will be used if dos=True

classmethod getProperties(**kwargs)¶

Get properties (namedtuple) from kwargs. Supported properties are defined in self.PROPERTIES.

Return type: namedtuple
Returns: Properties requested

setDOSFromFile(dos_fn)¶

Parse .dos file and set DOS into self.dos.

Parameters: dos_fn (str) – File to read dos property from

processEpsilonFile(tgz, tgz_file)¶

Process file from archive, if it is epsilon, return parsed data

Parameters

tgz (TarFile) – Tar archive
tgz_file (str) – Filename

Return type

dict or None

Returns

Dict with one key (real or imag) and corresponding data in value or None if extensions didn’t match

Raises

ValueError – When numpy can’t parse the data

processFile(tgz, tgz_file, options)¶

Process file from archive and set object properties.

Parameters

tgz (TarFile) – Tar archive
tgz_file (str) – Filename
options (namedtuple) – Properties to get

getTree(qegz_fn, options)¶

Get data in from of tree from archived file

Parameters

qegz_fn (str) – Archive name
options (namedtuple) – Properties to get

Returns

Data from data-file-schema.xml

Return type

xml.etree.ElementTree

getMDStepStruct(root, step, timestep)¶

Extract MD step structure from step XML.

Parameters

root (xml.etree.ElementTree.Element) – Root XML element
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

static getFreePositions(root, natom)¶

Get atom free_positions from the XML data

Parameters

root (xml.etree.ElementTree.Element) – Root XML element
natom (int) – Number of atoms in the structure

Return type

numpy.array

Returns

Atom free positions

getMaeStructure()¶

Get structure with lower triangular form of lattice vectors matrix

Return type: structure.Structure
Returns: Updated structure

static parseHP(hp_fh)¶

Parse and return data from the Hubbard_parameters.dat.

Parameters: hp_fh (File handler object) – Handler of the Hubbard_parameters.dat
Return type: dict
Returns: Dictionary with atom indexes as keys and Hubbard U as values

class schrodinger.application.matsci.espresso.qeoutput.MagresAtom(data)¶

Bases: object

Class that holds atom NMR properties.

__init__(data)¶

Initialize object.

Parameters: data (Any) – Data that will be converted to a 3x3 float tensor
Raises: typeError – On Error

property iso¶

Get isotropic sigma value.

Return type: float
Returns: Isotropic sigma value, ppm

shift(ref=0.0)¶

Get referenced chemical shift.

Parameters: ref (float) – Reference value.
Return type: float
Returns: Referenced chemical shift

toAtom(atom)¶

Set sigma to a structure atom (as a property).

Parameters: atom (structure.StructureAtom) – Atom to update

classmethod fromAtom(atom)¶

Read sigma from structure atom.

Parameters: atom (structure.StructureAtom) – Atom to read from
Return type: bool, MagresAtom or str
Return type: Whether sigma read successfully. If true, return MagresAtom object. If false, return error message

classmethod fromList(data)¶

Given a list of values, try to initialize MagresAtom object.

Parameters: data (list[Any]) – List of values that are convertible to 3x3 tensor
Return type: bool, MagresAtom or str
Return type: Whether sigma read successfully. If true, return MagresAtom object. If false, return error message

class schrodinger.application.matsci.espresso.qeoutput.Magres(struct, ms_atoms)¶

Bases: object

Class to hold magres data of a structure.

TAG_RE = re.compile('[\\[<](?P<tag>.*?)[>\\]](.*?)[<\\[]/(?P=tag)[\\]>]', re.MULTILINE|re.DOTALL)¶

TAGS = ('atoms', 'magres', 'calculation')¶

class ATTR(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

Bases: schrodinger.application.matsci.msutils.KeywordEnum

units = 'units'¶

lattice = 'lattice'¶

atom = 'atom'¶

ms = 'ms'¶

sus = 'sus'¶

calc_name = 'calc_name'¶

calc_code = 'calc_code'¶

calc_code_version = 'calc_code_version'¶

UNITS = {ATTR.atom: 'Angstrom', ATTR.lattice: 'Angstrom', ATTR.ms: 'ppm', ATTR.sus: '10^-6.cm^3.mol^-1'}¶

__init__(struct, ms_atoms)¶

Initialize object.

Parameters

struct (structure.Structure) – Input structure
dict[int – MagresAtom]: Dict of magres atoms

static getLineData(text)¶

Generator that returns split lines.

Parameters: text (str) – (Multi-line) text
Yield list[str]: List from a split line

classmethod fromFile(text)¶

Create Magres object from text.

Parameters: text (str) – Multiline magres text
Return type: bool, Magres or str
Return type: Whether structure updated successfully. If true, return Magres objectIf false, return an error message

toStructure(struct)¶

Set magres atom properties to a structure.

Parameters: struct (structure.Structure) – Structure to update
Return type: bool, None or str
Return type: Whether structure updated successfully. If false, return an error message

classmethod fromStructure(struct)¶

Read magres atoms from structure.

Parameters: struct (structure.Structure) – Structure to read
Return type: bool, Magres or str
Return type: Whether structure updated successfully. If true, return Magres object. If false, return an error message