pymatgen.electronic_structure.boltztrap2 module

BoltzTraP2 is a python software interpolating band structures and computing materials properties from dft band structure using Boltzmann semi-classical transport theory. This module provides a pymatgen interface to BoltzTraP2. Some of the code is written following the examples provided in BoltzTraP2

BoltzTraP2 has been developed by Georg Madsen, Jesús Carrete, Matthieu J. Verstraete.

https://gitlab.com/sousaw/BoltzTraP2 https://www.sciencedirect.com/science/article/pii/S0010465518301632

References are:

Georg K.H.Madsen, Jesús Carrete, Matthieu J.Verstraete BoltzTraP2, a program for interpolating band structures and calculating semi-classical transport coefficients Computer Physics Communications 231, 140-145, 2018

Madsen, G. K. H., and Singh, D. J. (2006). BoltzTraP. A code for calculating band-structure dependent quantities. Computer Physics Communications, 175, 67-71

Todo: - DONE: spin polarized bands - read first derivative of the eigenvalues from vasprun.xml (mommat) - handle magnetic moments (magmom)

class BandstructureLoader(bs_obj, structure=None, nelect=None, mommat=None, magmom=None)

Bases: object

Loader for Bandstructure object

Parameters:

• bs_obj – BandStructure object.

• structure – Structure object. It is needed if it is not contained in the BandStructure obj.

• nelect – Number of electrons in the calculation.

• momat – Matrix of derivatives of energy eigenvalues. Not implemented yet.

• magmom – Matrix of magnetic moments in non collinear calculations. Not implemented yet.

Example

vrun = Vasprun(‘vasprun.xml’) bs = vrun.get_band_structure() st = vrun.final_structure ne = vrun.parameters[‘NELECT’] data = BandstructureLoader(bs,st,ne)

bandana(emin=-inf, emax=inf)

Cut out bands outside the range (emin,emax)

get_lattvec()

Returns:

The lattice vectors.

get_volume()

Returns:

Volume

set_upper_lower_bands(e_lower, e_upper)

Set fake upper/lower bands, useful to set the same energy range in the spin up/down bands when calculating the DOS

class BztInterpolator(data, lpfac=10, energy_range=1.5, curvature=True, save_bztInterp=False, load_bztInterp=False, save_bands=False, fname='bztInterp.json.gz')

Bases: object

Interpolate the dft band structures

Parameters:

• data – A loader

• lpfac – the number of interpolation points in the real space. By default 10 gives 10 time more points in the real space than the number of kpoints given in reciprocal space.

• energy_range – usually the interpolation is not needed on the entire energy range but on a specific range around the fermi level. This energy in eV fix the range around the fermi level (E_fermi-energy_range,E_fermi+energy_range) of bands that will be interpolated and taken into account to calculate the transport properties.

• curvature – boolean value to enable/disable the calculation of second derivative related transport properties (Hall coefficient).

• save_bztInterp – Default False. If True coefficients and equivalences are saved in fname file.

• load_bztInterp – Default False. If True the coefficients and equivalences are loaded from fname file, not calculated. It can be faster than re-calculate them in some cases.

• save_bands – Default False. If True interpolated bands are also stored. It can be slower than interpolate them. Not recommended.

• fname – File path where to store/load from the coefficients and equivalences.

Example

data = VasprunLoader().from_file(‘vasprun.xml’) bztInterp = BztInterpolator(data)

get_band_structure(kpaths=None, kpoints_lbls_dict=None, density=20)

Return a BandStructureSymmLine object interpolating bands along a High symmetry path calculated from the structure using HighSymmKpath function. If kpaths and kpoints_lbls_dict are provided, a custom path is interpolated. kpaths: List of lists of following kpoints labels defining

the segments of the path. E.g. [[‘L’,’M’],[‘L’,’X’]]

kpoints_lbls_dict: Dict where keys are the kpoint labels used in kpaths

and values are their fractional coordinates. E.g. {‘L’:np.array(0.5,0.5,0.5)},

‘M’:np.array(0.5,0.,0.5), ‘X’:np.array(0.5,0.5,0.)}

density: Number of points in each segment.

get_dos(partial_dos=False, npts_mu=10000, T=None, progress=False)

Return a Dos object interpolating bands

Parameters:

• partial_dos – if True, projections will be interpolated as well and partial doses will be return. Projections must be available in the loader.

• npts_mu – number of energy points of the Dos

• T – parameter used to smooth the Dos

• progress – Default False, If True a progress bar is shown when partial dos are computed.

get_partial_doses(tdos, eband_ud, spins, enr, npts_mu, T, progress)

Return a CompleteDos object interpolating the projections

tdos: total dos previously calculated npts_mu: number of energy points of the Dos T: parameter used to smooth the Dos progress: Default False, If True a progress bar is shown.

load(fname='bztInterp.json.gz')

Load the coefficient, equivalences, bands from fname

save(fname='bztInterp.json.gz', bands=False)

Save the coefficient, equivalences to fname. If bands is True, also interpolated bands are stored.

class BztPlotter(bzt_transP=None, bzt_interp=None)

Bases: object

Plotter to plot transport properties, interpolated bands along some high symmetry k-path, and DOS.

Example

bztPlotter = BztPlotter(bztTransp,bztInterp) fig = self.bztPlotter.plot_props(‘S’, ‘mu’, ‘temp’, temps=[300, 500]) fig.show()

Parameters:

• bzt_transP –

• bzt_interp –

plot_bands()

Plot a band structure on symmetry line using BSPlotter()

plot_dos(T=None, npoints=10000)

Plot the total Dos using DosPlotter()

plot_props(prop_y, prop_x, prop_z='temp', output='avg_eigs', dop_type='n', doping=None, temps=None, xlim=(-2, 2), ax=None)

Function to plot the transport properties.

Parameters:

• prop_y – property to plot among (“Conductivity”,”Seebeck”,”Kappa”,”Carrier_conc”, “Hall_carrier_conc_trace”). Abbreviations are possible, like “S” for “Seebeck”

• prop_x – independent variable in the x-axis among (‘mu’,’doping’,’temp’)

• prop_z – third variable to plot multiple curves (‘doping’,’temp’)

• output – ‘avg_eigs’ to plot the average of the eigenvalues of the properties tensors; ‘eigs’ to plot the three eigenvalues of the properties tensors.

• dop_type – ‘n’ or ‘p’ to specify the doping type in plots that use doping levels as prop_x or prop_z

• doping – list of doping level to plot, useful to reduce the number of curves when prop_z=’doping’

• temps – list of temperatures to plot, useful to reduce the number of curves when prop_z=’temp’

• xlim – chemical potential range in eV, useful when prop_x=’mu’

• ax – figure.axes where to plot. If None, a new figure is produced.

Example: bztPlotter.plot_props(‘S’,’mu’,’temp’,temps=[600,900,1200]).show() more example are provided in the notebook “How to use Boltztra2 interface.ipynb”.

class BztTransportProperties(BztInterpolator, temp_r=None, doping=None, npts_mu=4000, CRTA=1e-14, margin=None, save_bztTranspProps=False, load_bztTranspProps=False, fname='bztTranspProps.json.gz')

Bases: object

Compute Seebeck, Conductivity, Electrical part of thermal conductivity and Hall coefficient, conductivity effective mass, Power Factor tensors w.r.t. the chemical potential and temperatures, from dft band structure via interpolation.

Parameters:

• BztInterpolator – a BztInterpolator previously generated

• temp_r – numpy array of temperatures at which to calculate transport properties

• doping – doping levels at which to calculate transport properties. If provided, transport properties w.r.t. these doping levels are also computed. See compute_properties_doping() method for details.

• npts_mu – number of energy points at which to calculate transport properties

• CRTA – constant value of the relaxation time

• save_bztTranspProps – Default False. If True all computed transport properties will be stored in fname file.

• load_bztTranspProps – Default False. If True all computed transport properties will be loaded from fname file.

• fname – File path where to save/load transport properties.

Upon creation, it contains properties tensors w.r.t. the chemical potential of size (len(temp_r),npts_mu,3,3):

Conductivity_mu (S/m), Seebeck_mu (microV/K), Kappa_mu (W/(m*K)), Power_Factor_mu (milliW/K m); cond_Effective_mass_mu (m_e) calculated as Ref.

Also:

Carrier_conc_mu: carrier concentration of size (len(temp_r),npts_mu) Hall_carrier_conc_trace_mu: trace of Hall carrier concentration of size

(len(temp_r),npts_mu)

mu_r_eV: array of energies in eV and with E_fermi at 0.0

where all the properties are calculated.

Example

bztTransp = BztTransportProperties(bztInterp,temp_r = np.arange(100,1400,100))

compute_properties_doping(doping, temp_r=None)

Calculate all the properties w.r.t. the doping levels in input.

Parameters:

doping – numpy array specifying the doping levels

When executed, it add the following variable at the BztTransportProperties object:

Conductivity_doping, Seebeck_doping, Kappa_doping, Power_Factor_doping, cond_Effective_mass_doping are dictionaries with ‘n’ and ‘p’ keys and arrays of dim (len(temp_r),len(doping),3,3) as values. Carriers_conc_doping: carriers concentration for each doping level and T. mu_doping_eV: the chemical potential corrispondent to each doping level.

load(fname='bztTranspProps.json.gz')

Load the transport properties from fname file.

save(fname='bztTranspProps.json.gz')

Save the transport properties to fname file.

class VasprunBSLoader(obj, structure=None, nelect=None)

Bases: object

Loader for Bandstructure and Vasprun pmg objects

Parameters:

• obj – Either a pmg Vasprun or a BandStructure object.

• structure – Structure object in case is not included in the BandStructure object.

• nelect – number of electrons in case a BandStructure obj is provided.

Example

vrun = Vasprun(‘vasprun.xml’) data = VasprunBSLoader(vrun)

bandana(emin=-inf, emax=inf)

Cut out bands outside the range (emin,emax)

classmethod from_file(vasprun_file)

Get a vasprun.xml file and return a VasprunBSLoader

get_lattvec()

Returns:

The lattice vectors.

get_volume()

Returns:

Volume

class VasprunLoader(vrun_obj=None)

Bases: object

Loader for Vasprun object

vrun_obj: Vasprun object.

bandana(emin=-inf, emax=inf)

Cut out bands outside the range (emin,emax)

classmethod from_file(vasprun_file)

Get a vasprun.xml file and return a VasprunLoader

get_lattvec()

Returns:

Lattice vectors

get_volume()

Returns:

Volume of cell

merge_up_down_doses(dos_up, dos_dn)

Merge the up and down DOSs. Args: dos_up: Up DOS. dos_dn: Down DOS Return: CompleteDos object