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from __future__ import division, unicode_literals, print_function

"""
This module provides classes to run and analyze boltztrap on pymatgen band
structure objects. Boltztrap is a software interpolating band structures and
computing materials properties from this band structure using Boltzmann
semi-classical transport theory.
Boltztrap has been developped by Georg Madsen.
http://www.icams.de/content/departments/ams/madsen/boltztrap.html
You need the version 1.2.3
References are::
Madsen, G. K. H., and Singh, D. J. (2006).
BoltzTraP. A code for calculating band-structure dependent quantities.
Computer Physics Communications, 175, 67-71
"""
__author__ = "Geoffroy Hautier"
__copyright__ = "Copyright 2013, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Geoffroy Hautier"
__email__ = "geoffroy@uclouvain.be"
__status__ = "Development"
__date__ = "August 23, 2013"
import os
import math
import numpy as np
import tempfile
from pymatgen.core.lattice import Lattice
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.electronic_structure.dos import Dos, Spin, CompleteDos
from pymatgen.electronic_structure.core import Orbital
from pymatgen.electronic_structure.plotter import DosPlotter
from monty.os.path import which
from monty.dev import requires
from monty.json import jsanitize
from pymatgen.core.units import Energy, Length
from pymatgen.core.physical_constants import e, ELECTRON_MASS
import subprocess
try:
import matplotlib.pyplot as plt
except ImportError:
pass
class BoltztrapRunner():
"""
This class is used to run Boltztrap on a band structure object.
Args:
bs:
A band structure object
nelec:
the number of electrons
dos_type:
two options here for the band structure integration: "HISTO"
(histogram) or "TETRA" using the tetrahedon method. TETRA
gives typically better results especially for DOSes but takes

more time
energy_grid:
the energy steps used for the integration. in eV
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
type:
type of boltztrap usage by default BOLTZ to compute transport co
efficients
but you can have also "FERMI" to compute fermi surface or more c
orrectly to
get certain bands interpolated
soc:
results from spin-orbit coupling (soc) computations give typical
ly non-polarized (no spin up or down)
results but 1 electron occupations. If the band structure comes
from a soc computation, you should set
soc to True (default False)
"""
@requires(which('x_trans'),
"BoltztrapRunner requires the executables 'x_trans' to be in "
"the path. Please download the Boltztrap at "
"http://www.icams.de/content/departments/ams/madsen/boltztrap"
".html and follow the instructions in the README to compile "
"Bolztrap accordingly. Then add x_trans to your path")
def __init__(self, bs, nelec, dos_type="HISTO", energy_grid=0.005,
lpfac=10, type="BOLTZ", band_nb=None, tauref=0, tauexp=0, tauen
=0, soc=False):
self.lpfac = lpfac
self._bs = bs
self._nelec = nelec
self.dos_type = dos_type
self.energy_grid = energy_grid
self.error = []
self.type = type
self.band_nb = band_nb
self.tauref=tauref
self.tauexp=tauexp
self.tauen=tauen
self.soc=soc
def _make_energy_file(self, file_name):
with open(file_name, 'w') as f:
f.write("test\n")
f.write(str(len(self._bs.kpoints))+"\n")
for i in range(len(self._bs.kpoints)):
tmp_eigs = []
for spin in self._bs._bands:
for j in range(int(math.floor(self._bs._nb_bands * 0.9))):
tmp_eigs.append(Energy(self._bs._bands[spin][j][i] self._bs.efermi, "eV").to("Ry"))
tmp_eigs.sort()
f.write("%12.8f %12.8f %12.8f %d\n"
% (self._bs.kpoints[i].frac_coords[0],
self._bs.kpoints[i].frac_coords[1],
self._bs.kpoints[i].frac_coords[2], len(tmp_eigs)))
for j in range(len(tmp_eigs)):

f.write("%18.8f\n" % float(tmp_eigs[j]))
def _make_struc_file(self, file_name):
sym = SpacegroupAnalyzer(self._bs._structure, symprec=0.01)
with open(file_name, 'w') as f:
f.write(self._bs._structure.composition.formula+" " +
str(sym.get_spacegroup_symbol())+"\n")
for i in range(3):
line = ''
for j in range(3):
line += "%12.5f" % (
Length(self._bs._structure.lattice.matrix[i][j],
"ang").to("bohr"))
f.write(line+'\n')
ops = sym.get_symmetry_dataset()['rotations']
f.write(str(len(ops))+"\n")
for c in ops:
f.write('\n'.join([' '.join([str(int(i)) for i in row])
for row in c]))
f.write('\n')
def _make_def_file(self, def_file_name):
with open(def_file_name,'w') as f:
so = ""
if self._bs.is_spin_polarized or self.soc:
so = "so"
f.write("5, 'boltztrap.intrans',
'old',
'formatted',0\n"+
"6,'boltztrap.outputtrans',
'unknown',
'formatted',0
\n"+
"20,'boltztrap.struct',
"10,'boltztrap.energy"+so+"',

'old',

'formatted',0\n"+
'old',
'formatted',

0\n"+
"48,'boltztrap.engre',

'unknown',

'unformatted',0

\n"+
"49,'boltztrap.transdos',

'unknown',

'formatted',0

\n"+
"50,'boltztrap.sigxx',

'unknown',

'formatted',0\n"

+
"51,'boltztrap.sigxxx',

'unknown',

'formatted',0\n

"+
"21,'boltztrap.trace',

'unknown',

'formatted',0

\n"+
"22,'boltztrap.condtens',

'unknown',

'formatted

"24,'boltztrap.halltens',

'unknown',

'formatted

',0\n"+
',0\n"+
"30,'boltztrap_BZ.cube',

'unknown',

'formatted'

"35,'boltztrap.banddat',

'unknown',

'formatted'

,0\n"+
,0\n"+
"36,'boltztrap_band.gpl',

'unknown',

'formatted

',0\n")
def _make_proj_files(self, file_name, def_file_name):
for o in Orbital.all_orbitals:
for site_nb in range(0, len(self._bs._structure.sites)):
if o in self._bs._projections[Spin.up][0][0]:
with open(file_name+"_"+str(site_nb)+"_"+str(o), 'w') as f:
f.write(self._bs._structure.composition.formula+"\n")
f.write(str(len(self._bs.kpoints))+"\n")

for i in range(len(self._bs.kpoints)):
tmp_proj = []
for spin in self._bs._bands:
for j in range(int(math.floor(self._bs._nb_bands
* 0.9))):
tmp_proj.append(self._bs._projections[spin][
j][i][o][site_nb])
#TODO deal with the sorting going on at the energy l
evel!!!
f.write("%12.8f %12.8f %12.8f %d\n"
% (self._bs.kpoints[i].frac_coords[0],
self._bs.kpoints[i].frac_coords[1],
self._bs.kpoints[i].frac_coords[2], len(t
mp_proj)))
for j in range(len(tmp_proj)):
f.write("%18.8f\n" % float(tmp_proj[j]))
with open(def_file_name,'w') as f:
so = ""
if self._bs.is_spin_polarized:
so = "so"
f.write("5, 'boltztrap.intrans',
'old',
'formatted',0\n"+
"6,'boltztrap.outputtrans',
'unknown',
'formatted',0
\n"+
"20,'boltztrap.struct',
"10,'boltztrap.energy"+so+"',

'old',

'formatted',0\n"+
'old',
'formatted',

0\n"+
"48,'boltztrap.engre',

'unknown',

'unformatted',0

\n"+
"49,'boltztrap.transdos',

'unknown',

'formatted',0

\n"+
"50,'boltztrap.sigxx',

'unknown',

'formatted',0\n"

+
"51,'boltztrap.sigxxx',

'unknown',

'formatted',0\n

"+
"21,'boltztrap.trace',

'unknown',

'formatted',0

\n"+
"22,'boltztrap.condtens',

'unknown',

'formatted

"24,'boltztrap.halltens',

'unknown',

'formatted

',0\n"+
',0\n"+
"30,'boltztrap_BZ.cube',

'unknown',

'formatted'

"35,'boltztrap.banddat',

'unknown',

'formatted'

,0\n"+
,0\n"+
"36,'boltztrap_band.gpl',

'unknown',

'formatted

',0\n")
i = 1000
for o in Orbital.all_orbitals:
for site_nb in range(0, len(self._bs._structure.sites)):
if o in self._bs._projections[Spin.up][0][0]:
f.write(str(i)+",\'"+file_name+"_"+str(site_nb)+"_"+str(
o)
+ "\' \'old\', \'formatted\',0\n")
i += 1
def _make_intrans_file(self, file_name,
doping=[1e15, 1e16, 1e17, 1e18, 1e19, 1e20], type="BO
LTZ", band_nb=None,
tauref=0, tauexp=0, tauen=0):
if type == "BOLTZ":

with open(file_name, 'w') as fout:


fout.write("GENE
# use generic interface\n")
fout.write("1 0 0 0.0
# iskip (not presently used) idebu
g setgap shiftgap \n")
fout.write(
"0.0 %f 0.1 %6.1f
# Fermilevel (Ry),energygrid,energy sp
an around Fermilevel, "
"number of electrons\n"
% (Energy(self.energy_grid, "eV").to("Ry"), self._nelec))
fout.write("CALC
# CALC (calculate expansion
coeff), NOCALC read from file\n")
fout.write("%d
# lpfac, number of latt-po
ints per k-point\n" % self.lpfac)
fout.write("BOLTZ
# run mode (only BOLTZ is
supported)\n")
fout.write(".15
# (efcut) energy range of
chemical potential\n")
fout.write("1300. 100.
# Tmax, temperature grid
\n")
fout.write("-1. # energyrange of bands given DOS output sig_xxx
and dos_xxx (xxx is band number)\n")
fout.write(self.dos_type+"\n")
fout.write(str(tauref)+" "+str(tauexp)+" "+str(tauen)+" 0 0 0\n"
)
fout.write(str(2*len(doping))+"\n")
for d in doping:
fout.write(str(d)+"\n")
for d in doping:
fout.write(str(-d)+"\n")
elif type == "FERMI":
with open(file_name, 'w') as fout:
fout.write("GENE
# use generic interface\n")
fout.write("1 0 0 0.0
# iskip (not presently used) idebu
g setgap shiftgap \n")
fout.write(
"0.0 %f 0.1 %6.1f
# Fermilevel (Ry),energygrid,energy sp
an around Fermilevel, "
"number of electrons\n"
% (Energy(self.energy_grid, "eV").to("Ry"), self._nelec))
fout.write("CALC
# CALC (calculate expansion
coeff), NOCALC read from file\n")
fout.write("%d
# lpfac, number of latt-po
ints per k-point\n" % self.lpfac)
fout.write("FERMI
# run mode (only BOLTZ is
supported)\n")
fout.write(str(band_nb+1))
def _make_all_files(self, path):
if self._bs.is_spin_polarized or self.soc:
self._make_energy_file(os.path.join(path, "boltztrap.energyso"))
else:
self._make_energy_file(os.path.join(path, "boltztrap.energy"))
self._make_struc_file(os.path.join(path, "boltztrap.struct"))
self._make_intrans_file(os.path.join(path, "boltztrap.intrans"), type=se
lf.type, band_nb=self.band_nb)
self._make_def_file("BoltzTraP.def")
if len(self._bs._projections) != 0:
self._make_proj_files(os.path.join(path,"boltztrap.proj"), os.path.j
oin(path, "BoltzTraP.def"))

def run(self, prev_sigma=None, path_dir=None, convergence=True):


if self.type == "FERMI":
convergence=False
dir_bz_name = "boltztrap"
path_dir_orig = path_dir
if path_dir is None:
temp_dir = tempfile.mkdtemp()
path_dir_orig = temp_dir
path_dir = os.path.join(temp_dir, dir_bz_name)
else:
path_dir = os.path.join(path_dir_orig, dir_bz_name)
if not os.path.exists(path_dir):
os.mkdir(path_dir)
else:
for c in os.listdir(path_dir):
os.remove(path_dir+"/"+c)
os.chdir(path_dir)
self._make_all_files(path_dir)
if self._bs.is_spin_polarized or self.soc:
p = subprocess.Popen(["x_trans", "BoltzTraP", "-so"],
stdout=subprocess.PIPE,
stdin=subprocess.PIPE, stderr=subprocess.PIPE)
p.wait()
else:
p = subprocess.Popen(["x_trans", "BoltzTraP"],
stdout=subprocess.PIPE, stdin=subprocess.PIPE,
stderr=subprocess.PIPE)
p.wait()
for c in p.communicate():
if "STOP error in factorization" in c:
raise BoltztrapError("STOP error in factorization")
with open(os.path.join(path_dir, dir_bz_name+".outputtrans")) as f:
warning = False
for l in f:
if "WARNING" in l:
warning = True
break
if warning:
print("There was a warning! Increase lpfac to " + \
str(self.lpfac * 2))
self.lpfac *= 2
self._make_intrans_file(os.path.join(path_dir,
dir_bz_name + ".intrans"))
if self.lpfac > 100:
raise BoltztrapError("lpfac higher than 100 and still a warn
ing")
self.run(path_dir_orig)
#here we check if the doping levels were well computed
#sometimes boltztrap mess this up because of two small energy grids
analyzer = BoltztrapAnalyzer.from_files(path_dir)
doping_ok = True
for doping in ['n', 'p']:
for c in analyzer.mu_doping[doping]:
if len(analyzer.mu_doping[doping][c]) != len(analyzer.doping[dop
ing]):
doping_ok = False
break
if doping == 'p' and \

sorted(analyzer.mu_doping[doping][c], reverse=True) != a
nalyzer.mu_doping[doping][c]:
doping_ok = False
break
if doping == 'n' and sorted(analyzer.mu_doping[doping][c]) != an
alyzer.mu_doping[doping][c]:
doping_ok = False
break
if not doping_ok:
self.energy_grid /= 10
print("lowers energy grid to " + str(self.energy_grid))
if self.energy_grid < 0.00005:
raise BoltztrapError("energy grid lower than 0.00005 and still n
o good doping")
self._make_intrans_file(path_dir + "/" + dir_bz_name + ".intrans")
self.run(prev_sigma=None, path_dir=path_dir_orig)
analyzer = BoltztrapAnalyzer.from_files(path_dir)
#here, we test if a property (eff_mass tensor) converges
if convergence is False:
return path_dir
if prev_sigma is None or \
abs(sum(analyzer.get_eig_average_eff_mass_tensor()['n']) / 3
- prev_sigma)\
/ prev_sigma > 0.05:
if prev_sigma is not None:
print((abs(sum(analyzer.get_eig_average_eff_mass_tensor()['n'])
/ 3 - prev_sigma) / prev_sigma, \
self.lpfac, \
analyzer.get_average_eff_mass_tensor(300, 1e18)))
self.lpfac *= 2
if self.lpfac > 100:
raise BoltztrapError("lpfac higher than 100 and still not conver
ged")
self._make_intrans_file(path_dir + "/" + dir_bz_name + ".intrans")
self.run(
prev_sigma=sum(analyzer.get_eig_average_eff_mass_tensor()
['n']) / 3, path_dir=path_dir_orig)
return path_dir
class BoltztrapError(Exception):
"""
Exception class for boltztrap.
Raised when the boltztrap gives an error
"""
def __init__(self, msg):
self.msg = msg
def __str__(self):
return "BoltztrapError : " + self.msg
class BoltztrapAnalyzer():
"""
Class used to store all the data from a boltztrap run
"""
def __init__(self, gap, mu_steps, cond, seebeck, kappa, hall, doping,
mu_doping, seebeck_doping, cond_doping, kappa_doping,

hall_doping, dos, dos_partial, carrier_conc, vol, warning):


"""
Constructor taking directly all the data generated by Boltztrap. You
won't probably use it directly but instead use the from_files and
from_dict methods.
Args:
gap: The gap after interpolation in eV
mu_steps: The steps of electron chemical potential (or Fermi
level) in eV.
cond: The electronic conductivity tensor divided by a constant
relaxation time (sigma/tau) at different temperature and
fermi levels.
The format is {temperature: [array of 3x3 tensors at each
fermi level in mu_steps]}. The units are 1/(Ohm*m*s).
seebeck: The Seebeck tensor at different temperatures and fermi
levels. The format is {temperature: [array of 3x3 tensors at
each fermi level in mu_steps]}. The units are V/K
kappa: The electronic thermal conductivity tensor divided by a
constant relaxation time (kappa/tau) at different temperature
and fermi levels. The format is {temperature: [array of 3x3
tensors at each fermi level in mu_steps]}
The units are W/(m*K*s)
hall: The hall tensor at different temperature and fermi levels
The format is {temperature: [array of 27 coefficients list at
each fermi level in mu_steps]}
The units are m^3/C
doping: The different doping levels that have been given to
Boltztrap. The format is {'p':[],'n':[]} with an array of
doping levels. The units are cm^-3
mu_doping: Gives the electron chemical potential (or Fermi level)
for a given set of doping.
Format is {'p':{temperature: [fermi levels],'n':{temperature:
[fermi levels]}}
the fermi level array is ordered according to the doping
levels in doping units for doping are in cm^-3 and for Fermi
level in eV
seebeck_doping: The Seebeck tensor at different temperatures and
doping levels. The format is {'p': {temperature: [Seebeck
tensors]}, 'n':{temperature: [Seebeck tensors]}}
The [Seebeck tensors] array is ordered according to the
doping levels in doping units for doping are in cm^-3 and for
Seebeck in V/K
cond_doping: The electronic conductivity tensor divided by a
constant relaxation time (sigma/tau) at different
temperatures and doping levels
The format is {'p':{temperature: [conductivity tensors]},
'n':{temperature: [conductivity tensors]}}
The [conductivity tensors] array is ordered according to the
doping levels in doping units for doping are in cm^-3 and for
conductivity in 1/(Ohm*m*s)
kappa_doping: The thermal conductivity tensor divided by a constant
relaxation time (kappa/tau) at different temperatures and
doping levels.
The format is {'p':{temperature: [thermal conductivity
tensors]},'n':{temperature: [thermal conductivity tensors]}}
The [thermal conductivity tensors] array is ordered according
to the doping levels in doping units for doping are in cm^-3
and for thermal conductivity in W/(m*K*s)
hall_doping: The Hall tensor at different temperatures and doping
levels.

The format is {'p':{temperature: [Hall tensors]},


'n':{temperature: [Hall tensors]}}
The [Hall tensors] array is ordered according to the doping
levels in doping and each Hall tensor is represented by a 27
coefficients list.
The units are m^3/C
carrier_conc: The concentration of carriers in electron (or hole)
per unit cell
dos: The dos computed by Boltztrap given as a pymatgen Dos object
dos_partial: Data for the partial DOS projected on sites and
orbitals
vol: Volume of the unit cell in angstrom cube (A^3)
warning: True if Boltztrap spitted out a warning
"""
self.gap = gap
self.mu_steps = mu_steps
self.cond = cond
self.seebeck = seebeck
self.kappa = kappa
self.hall = hall
self.warning = warning
self.doping = doping
self.mu_doping = mu_doping
self.seebeck_doping = seebeck_doping
self.cond_doping = cond_doping
self.kappa_doping = kappa_doping
self.hall_doping = hall_doping
self.carrier_conc = carrier_conc
self.dos = dos
self.vol = vol
self._dos_partial = dos_partial
@staticmethod
def _make_boltztrap_analyzer_from_data(
data_full, data_hall, data_dos, temperature_steps, mu_steps,
efermi, gap, doping, data_doping_full, data_doping_hall, vol,
warning=False):
"""
Make a BoltztrapAnalyzer object from raw data typically parse from
files.
"""
cond = {t: [] for t in temperature_steps}
seebeck = {t: [] for t in temperature_steps}
kappa = {t: [] for t in temperature_steps}
hall = {t: [] for t in temperature_steps}
carrier_conc = {t: [] for t in temperature_steps}
dos_full = {'energy': [], 'density': []}
warning = warning
new_doping = {'p': [], 'n': []}
for d in doping:
if d > 0:
new_doping['p'].append(d)
else:
new_doping['n'].append(-d)
mu_doping = {'p': {t: [] for t in temperature_steps},
'n': {t: [] for t in temperature_steps}}
seebeck_doping = {'p': {t: [] for t in temperature_steps},
'n': {t: [] for t in temperature_steps}}
cond_doping = {'p': {t: [] for t in temperature_steps},

'n': {t: [] for t in temperature_steps}}


kappa_doping = {'p': {t: [] for t in temperature_steps},
'n': {t: [] for t in temperature_steps}}
hall_doping = {'p': {t: [] for t in temperature_steps},
'n': {t: [] for t in temperature_steps}}
for d in data_full:
carrier_conc[d[1]].append(d[2])
tens_cond = [[d[3], d[4], d[5]],
[d[6], d[7], d[8]],
[d[9], d[10], d[11]]]
cond[d[1]].append(tens_cond)
tens_seebeck = [[d[12], d[13], d[14]],
[d[15], d[16], d[17]],
[d[18], d[19], d[20]]]
seebeck[d[1]].append(tens_seebeck)
tens_kappa = [[d[21], d[22], d[23]],
[d[24], d[25], d[26]],
[d[27], d[28], d[29]]]
kappa[d[1]].append(tens_kappa)
for d in data_hall:
hall_tens = d[3:]
hall[d[1]].append(hall_tens)
for d in data_doping_full:
tens_cond = [[d[2], d[3], d[4]],
[d[5], d[6], d[7]],
[d[8], d[9], d[10]]]
tens_seebeck = [[d[11], d[12], d[13]],
[d[14], d[15], d[16]],
[d[17], d[18], d[19]]]
tens_kappa = [[d[20], d[21], d[22]],
[d[23], d[24], d[25]],
[d[26], d[27], d[28]]]
if d[1] < 0:
mu_doping['n'][d[0]].append(Energy(d[-1], "Ry").to("eV"))
cond_doping['n'][d[0]].append(tens_cond)
seebeck_doping['n'][d[0]].append(tens_seebeck)
kappa_doping['n'][d[0]].append(tens_kappa)
else:
mu_doping['p'][d[0]].append(Energy(d[-1], "Ry").to("eV"))
cond_doping['p'][d[0]].append(tens_cond)
seebeck_doping['p'][d[0]].append(tens_seebeck)
kappa_doping['p'][d[0]].append(tens_kappa)
for i in range(len(data_doping_hall)):
hall_tens = [data_hall[i][j] for j in range(3, len(data_hall[i]))]
if data_doping_hall[i][1] < 0:
hall_doping['n'][data_doping_hall[i][0]].append(hall_tens)
else:
hall_doping['p'][data_doping_hall[i][0]].append(hall_tens)
for t in data_dos['total']:
dos_full['energy'].append(t[0])
dos_full['density'].append(t[1])
dos = Dos(efermi, dos_full['energy'], {Spin.up: dos_full['density']})
dos_partial = data_dos['partial']

return BoltztrapAnalyzer(
gap, mu_steps, cond, seebeck, kappa, hall, new_doping, mu_doping,
seebeck_doping, cond_doping, kappa_doping, hall_doping, dos, dos_par
tial, carrier_conc,
vol, warning)
def get_complete_dos(self, structure):
"""
Gives a CompleteDos object with the DOS from the interpolated projected
band structure
Args:
the structure (necessary to identify sites for projection)
Returns:
a CompleteDos object
"""
pdoss = {}
for s in self._dos_partial:
if structure.sites[int(s)] not in pdoss:
pdoss[structure.sites[int(s)]] = {}
for o in self._dos_partial[s]:
if Orbital.from_string(o) not in pdoss[structure.sites[int(s)]]:
pdoss[structure.sites[int(s)]][Orbital.from_string(o)] = {}
pdoss[structure.sites[int(s)]][Orbital.from_string(o)][Spin.up]
= self._dos_partial[s][o]
return CompleteDos(structure, total_dos=self.dos, pdoss=pdoss)
def get_mu_bounds(self, temp=300):
return min(self.mu_doping['p'][temp]), max(self.mu_doping['n'][temp])
def get_average_eff_mass_tensor(self, temperature=300, doping=1e18):
"""
Gives the average effective mass tensor at a given temperature and
doping level.
The average effective mass tensor is defined as the integrated
average of the second derivative
This effective mass tensor takes into account:
-non-parabolicity
-multiple extrema
-multiple bands
Args:
temperature: The temperature in K
doping: The doping in cm^-3
Returns:
a dictionary {'p':[[]],'n':[[]]}
The arrays are 3x3 and represent the effective mass tensor
The 'p' links to hole effective mass tensor and 'n' to electron
effective mass tensor.
"""
index = None
import math
results = {'p': [], 'n': []}
for t in ['n', 'p']:
for d in range(len(self.doping[t])):
if math.fabs(self.doping[t][d]-doping) < 0.001:
index = d
results[t] = np.linalg.inv(
self.cond_doping[t][temperature][index]) * doping \
* 10 ** 6 * e ** 2 / ELECTRON_MASS
return results

def get_eig_average_eff_mass_tensor(self, temperature=300, doping=1e18):


"""
Gives the eigenvalues of the average effective mass tensor at a given
temperature and doping level. The average effective mass tensor is
defined as the integrated average of the second derivative
This effective mass tensor takes into account:
-non-parabolicity
-multiple extrema
-multiple bands
Args:
temperature: The temperature in K
doping: The doping in cm^-3
Returns:
a dictionnary {'p':[],'n':[]}
The list contains the sorted three eigenvalues of the symmetric
tensor. The 'p' links to hole effective mass tensor and 'n' to
electron effective mass tensor.
"""
return {'p':
sorted(np.linalg.eigh(self.get_average_eff_mass_tensor(
temperature=temperature, doping=doping)['p'])[0]),
'n':
sorted(np.linalg.eigh(self.get_average_eff_mass_tensor(
temperature=temperature, doping=doping)['n'])[0])}
def get_seebeck_eig(self):
"""
Gives the three eigenvalues of the seebeck tensor at different doping le
vels
Returns:
a dictionnary {'p':[],'n':[]}
The list contains the sorted three eigenvalues of the symmetric
Seebeck tensor. The 'p' links to Seebeck at p-type doping and 'n' to
the Seebeck at n-type doping.
"""
full_tensor = self.seebeck_doping
result = {doping: {t: [] for t in self.seebeck_doping[doping]} for dopin
g in self.seebeck_doping}
for doping in full_tensor:
for temp in full_tensor[doping]:
for i in range(len(self.doping[doping])):
result[doping][temp].append(sorted(np.linalg.eigh(full_tenso
r[doping][temp][i])[0]))
return result
@staticmethod
def from_files(path_dir):
"""
get a BoltztrapAnalyzer object from a set of files
Args:
path_dir: directory where the boltztrap files are
Returns:
a BoltztrapAnalyzer object
"""
t_steps = set()
m_steps = set()
gap = None
doping = []

data_doping_full = []
data_doping_hall = []
with open(os.path.join(path_dir, "boltztrap.condtens"), 'r') as f:
data_full = []
for line in f:
if not line.startswith("#"):
t_steps.add(int(float(line.split()[1])))
m_steps.add(float(line.split()[0]))
data_full.append([float(c) for c in line.split()])
with open(os.path.join(path_dir, "boltztrap.halltens"), 'r') as f:
data_hall = []
for line in f:
if not line.startswith("#"):
data_hall.append([float(c) for c in line.split()])
data_dos = {'total': [], 'partial':{}}
with open(os.path.join(path_dir, "boltztrap.transdos"), 'r') as f:
count_series = 0
for line in f:
if not line.startswith(" #"):
data_dos['total'].append([Energy(float(line.split()[0]), "Ry
").to("eV"),
float(line.split()[1])])
else:
count_series += 1
if count_series>1:
break
#data_dos['total'].append([float(line.split()[0]),
#
float(line.split()[1])])
for file_name in os.listdir(path_dir):
if file_name.endswith("transdos") and file_name != 'boltztrap.transd
os':
tokens = file_name.split(".")[1].split("_")
with open(os.path.join(path_dir, file_name), 'r') as f:
for line in f:
if not line.startswith(" #"):
if tokens[1] not in data_dos['partial']:
data_dos['partial'][tokens[1]] = {}
if tokens[2] not in data_dos['partial'][tokens[1]]:
data_dos['partial'][tokens[1]][tokens[2]] = []
data_dos['partial'][tokens[1]][tokens[2]].append(flo
at(line.split()[1]))
with open(os.path.join(path_dir, "boltztrap.outputtrans"), 'r') as f:
warning = False
step = 0
for line in f:
if "WARNING" in line:
warning = True
if line.startswith("VBM"):
efermi = Energy(line.split()[1], "Ry").to("eV")
if step == 2:
l_tmp = line.split("-")[1:]
doping.extend([-float(d) for d in l_tmp])
step = 0
if step == 1:

doping.extend([float(d) for d in line.split()])


step = 2
if line.startswith("Doping levels to be output for") or \
line.startswith(" Doping levels to be output for"):
step = 1
if line.startswith("Egap:"):
gap = float(line.split()[1])
if len(doping) != 0:
with open(os.path.join(path_dir, "boltztrap.condtens_fixdoping"), 'r
') as f:
for line in f:
if not line.startswith("#") and len(line) > 2:
data_doping_full.append([float(c)
for c in line.split()])
with open(os.path.join(path_dir, "boltztrap.halltens_fixdoping"), 'r
') as f:
for line in f:
if not line.startswith("#") and len(line) > 2:
data_doping_hall.append([float(c) for c in line.split()]
)
with open(os.path.join(path_dir, "boltztrap.struct"), 'r') as f:
tokens = f.readlines()
vol = Lattice([[Length(float(tokens[i].split()[j]), "bohr").to("ang"
)
for j in range(3)] for i in range(1, 4)]).volume
return BoltztrapAnalyzer._make_boltztrap_analyzer_from_data(
data_full, data_hall, data_dos, sorted([t for t in t_steps]),
sorted([Energy(m, "Ry").to("eV") for m in m_steps]), efermi, Energy(
gap, "Ry").to("eV"),
doping, data_doping_full, data_doping_hall, vol, warning)
def as_dict(self):
results = {'gap': self.gap,
'mu_steps': self.mu_steps,
'cond': self.cond,
'seebeck': self.seebeck,
'kappa': self.kappa,
'hall': self.hall,
'warning': self.warning, 'doping': self.doping,
'mu_doping': self.mu_doping,
'seebeck_doping': self.seebeck_doping,
'cond_doping': self.cond_doping,
'kappa_doping': self.kappa_doping,
'hall_doping': self.hall_doping,
'dos': self.dos.as_dict(),
'dos_partial': self._dos_partial,
'carrier_conc': self.carrier_conc,
'vol': self.vol}
return jsanitize(results)
@staticmethod
def from_dict(data):
def _make_float_array(a):

res = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]]
for i in range(3):
for j in range(3):
res[i][j] = float(a[i][j])
return res
def _make_float_hall(a):
return [i for i in a[:27]]
return BoltztrapAnalyzer(
float(data['gap']), [float(d) for d in data['mu_steps']],
{int(d): [_make_float_array(v) for v in data['cond'][d]]
for d in data['cond']},
{int(d): [_make_float_array(v) for v in data['seebeck'][d]]
for d in data['seebeck']},
{int(d): [_make_float_array(v) for v in data['kappa'][d]]
for d in data['kappa']},
{int(d): [_make_float_hall(v) for v in data['hall'][d]]
for d in data['hall']},
{'p': [float(d) for d in data['doping']['p']],
'n': [float(d) for d in data['doping']['n']]},
{'p': {int(d): [float(v) for v in data['mu_doping']['p'][d]]
for d in data['mu_doping']['p']},
'n': {int(d): [float(v) for v in data['mu_doping']['n'][d]]
for d in data['mu_doping']['n']}},
{'p': {int(d): [_make_float_array(v)
for v in data['seebeck_doping']['p'][d]]
for d in data['seebeck_doping']['p']},
'n': {int(d): [_make_float_array(v)
for v in data['seebeck_doping']['n'][d]]
for d in data['seebeck_doping']['n']}},
{'p': {int(d): [_make_float_array(v)
for v in data['cond_doping']['p'][d]]
for d in data['cond_doping']['p']},
'n': {int(d): [_make_float_array(v)
for v in data['cond_doping']['n'][d]]
for d in data['cond_doping']['n']}},
{'p': {int(d): [_make_float_array(v)
for v in data['kappa_doping']['p'][d]]
for d in data['kappa_doping']['p']},
'n': {int(d): [_make_float_array(v)
for v in data['kappa_doping']['n'][d]]
for d in data['kappa_doping']['n']}},
{'p': {int(d): [_make_float_hall(v)
for v in data['hall_doping']['p'][d]]
for d in data['hall_doping']['p']},
'n': {int(d): [_make_float_hall(v)
for v in data['hall_doping']['n'][d]]
for d in data['hall_doping']['n']}},
Dos.from_dict(data['dos']), data['dos_partial'], data['carrier_conc'
],
data['vol'], str(data['warning']))
class BoltztrapPlotter():
"""
class containing methods to plot the data from Boltztrap.
Args:
bz: a BoltztrapAnalyzer object
"""

def __init__(self, bz):


self._bz = bz
def _plot_doping(self, temp):
limit = 2.21e15
plt.axvline(self._bz.mu_doping['n'][temp][1], linewidth=3.0,
linestyle="--")
plt.text(self._bz.mu_doping['n'][temp][1] + 0.01,
limit,
"$n$=10$^{" + str(math.log10(self._bz.doping['n'][1])) + "}$",
color='b')
plt.axvline(self._bz.mu_doping['n'][temp][-1], linewidth=3.0,
linestyle="--")
plt.text(self._bz.mu_doping['n'][temp][-1] + 0.01,
limit,
"$n$=10$^{" + str(math.log10(self._bz.doping['n'][-1]))
+ "}$", color='b')
plt.axvline(self._bz.mu_doping['p'][temp][1], linewidth=3.0,
linestyle="--")
plt.text(self._bz.mu_doping['p'][temp][1] + 0.01,
limit,
"$p$=10$^{" + str(math.log10(self._bz.doping['p'][1])) + "}$",
color='b')
plt.axvline(self._bz.mu_doping['p'][temp][-1], linewidth=3.0,
linestyle="--")
plt.text(self._bz.mu_doping['p'][temp][-1] + 0.01,
limit, "$p$=10$^{" +
str(math.log10(self._bz.doping['p'][-1])) + "}$",
color='b')
def _plot_BG_limits(self):
plt.axvline(0.0, color='k', linewidth=3.0)
plt.axvline(self._bz.gap, color='k', linewidth=3.0)
def plot_seebeck(self, temp=300, xlim=None):
"""
Plot the seebeck coefficient in function of Fermi level
Args:
temp:
the temperature
xlim:
a list of min and max fermi energy by default (0, and band gap)
Returns:
a matplotlib object
"""
plt.plot(self._bz.mu_steps, [np.linalg.eigh(c)[0] * 1e6
for c in self._bz.seebeck[temp]],
linewidth=3.0)
self._plot_BG_limits()
self._plot_doping(temp)
plt.legend(['S$_1$', 'S$_2$', 'S$_3$'])
if xlim is None:
plt.xlim(-0.5, self._bz.gap + 0.5)
else:
plt.xlim(xlim[0], xlim[1])
plt.ylabel("Seebeck \n coefficient ($\mu$V/K)", fontsize=30.0)
plt.xlabel("E-E$_f$ (eV)", fontsize=30)
plt.xticks(fontsize=25)
plt.yticks(fontsize=25)

return plt
def plot_conductivity(self, temp=300, tau=None, xlim=None):
"""
Plot the conductivity in function of Fermi level. Semi-log plot
Args:
temp: the temperature
xlim: a list of min and max fermi energy by default (0, and band
gap)
tau: A relaxation time in s. By default none and the plot is by
units of relaxation time
Returns:
a matplotlib object
"""
if tau is None:
plt.semilogy(self._bz.mu_steps, [sorted(np.linalg.eigh(c)[0] * 0.01)
for c in self._bz.cond[temp]],
linewidth=3.0)
else:
plt.semilogy(self._bz.mu_steps, [sorted(np.linalg.eigh(c)[0] * 0.01
* tau)
for c in self._bz.cond[temp]],
linewidth=3.0)
self._plot_BG_limits()
self._plot_doping(temp)
plt.legend(['$\sigma_1$', '$\sigma_2$', '$\sigma_3$'])
if xlim is None:
plt.xlim(-0.5, self._bz.gap + 0.5)
else:
plt.xlim(xlim)
if tau is None:
plt.ylim([1e13, 1e20])
else:
plt.ylim([1e13*tau,1e20*tau])
if tau is None:
plt.ylabel("conductivity, $\sigma$/${\\tau}$ (1/($\Omega$ m s))",
fontsize=30.0)
else:
plt.ylabel("conductivity,\n $\sigma$ (1/($\Omega$ m))",
fontsize=30.0)
plt.xlabel("E-E$_f$ (eV)", fontsize=30.0)
plt.xticks(fontsize=25)
plt.yticks(fontsize=25)
return plt
def plot_dos(self, sigma=0.05):
"""
plot dos
Args:
sigma: a smearing
Returns:
a matplotlib object
"""
plotter = DosPlotter(sigma=sigma)
plotter.add_dos("t", self._bz.dos)
return plotter.get_plot()
def plot_carriers(self, temp=300):
"""
Plot the carrier concentration in function of Fermi level

Args:
temp: the temperature
Returns:
a matplotlib object
"""
plt.semilogy(self._bz.mu_steps,
abs(self._bz.carrier_conc[temp]/(self._bz.vol*1e-24)),
linewidth=3.0, color='r')
self._plot_BG_limits()
self._plot_doping(temp)
plt.xlim(-0.5, self._bz.gap+0.5)
plt.ylim(1e14,1e22)
plt.ylabel("carrier concentration (cm-3)", fontsize=30.0)
plt.xlabel("E-E$_f$ (eV)", fontsize=30)
plt.xticks(fontsize=25)
plt.yticks(fontsize=25)
return plt