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thermodynamics.py
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thermodynamics.py
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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Defect thermodynamics, such as defect phase diagrams, etc.
"""
import logging
from itertools import chain
import matplotlib.cm as cm
import matplotlib.pyplot as plt
import numpy as np
from monty.json import MSONable
from scipy.optimize import bisect
from scipy.spatial import HalfspaceIntersection
from pymatgen.analysis.defects.core import DefectEntry
from pymatgen.analysis.structure_matcher import PointDefectComparator
from pymatgen.electronic_structure.dos import FermiDos
__author__ = "Danny Broberg, Shyam Dwaraknath"
__copyright__ = "Copyright 2018, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Shyam Dwaraknath"
__email__ = "shyamd@lbl.gov"
__status__ = "Development"
__date__ = "Mar 15, 2018"
logger = logging.getLogger(__name__)
class DefectPhaseDiagram(MSONable):
"""
This is similar to a PhaseDiagram object in pymatgen,
but has ability to do quick analysis of defect formation energies
when fed DefectEntry objects.
uses many of the capabilities from PyCDT's DefectsAnalyzer class...
This class is able to get:
a) stability of charge states for a given defect,
b) list of all formation ens
c) transition levels in the gap
"""
def __init__(self, entries, vbm, band_gap, filter_compatible=True, metadata=None):
"""
Args:
dentries ([DefectEntry]): A list of DefectEntry objects
vbm (float): Valence Band energy to use for all defect entries.
NOTE if using band shifting-type correction then this VBM
should still be that of the GGA calculation
(the bandedgeshifting_correction accounts for shift's
contribution to formation energy).
band_gap (float): Band gap to use for all defect entries.
NOTE if using band shifting-type correction then this gap
should still be that of the Hybrid calculation you are shifting to.
filter_compatible (bool): Whether to consider entries which were ruled
incompatible by the DefectComaptibility class. Note this must be set to False
if you desire a suggestion for larger supercell sizes.
Default is True (to omit calculations which have "is_compatible"=False in
DefectEntry'sparameters)
metadata (dict): Dictionary of metadata to store with the PhaseDiagram. Has
no impact on calculations
"""
self.vbm = vbm
self.band_gap = band_gap
self.filter_compatible = filter_compatible
if filter_compatible:
self.entries = [e for e in entries if e.parameters.get("is_compatible", True)]
else:
self.entries = entries
for ent_ind, ent in enumerate(self.entries):
if "vbm" not in ent.parameters.keys() or ent.parameters["vbm"] != vbm:
logger.info(
"Entry {} did not have vbm equal to given DefectPhaseDiagram value."
" Manually overriding.".format(ent.name)
)
new_ent = ent.copy()
new_ent.parameters["vbm"] = vbm
self.entries[ent_ind] = new_ent
self.metadata = metadata or {}
self.find_stable_charges()
def as_dict(self):
"""
Returns:
Json-serializable dict representation of DefectPhaseDiagram
"""
d = {
"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
"entries": [entry.as_dict() for entry in self.entries],
"vbm": self.vbm,
"band_gap": self.band_gap,
"filter_compatible": self.filter_compatible,
"metadata": self.metadata,
}
return d
@classmethod
def from_dict(cls, d):
"""
Reconstitute a DefectPhaseDiagram object from a dict representation created using
as_dict().
Args:
d (dict): dict representation of DefectPhaseDiagram.
Returns:
DefectPhaseDiagram object
"""
entries = [DefectEntry.from_dict(entry_dict) for entry_dict in d.get("entries")]
vbm = d["vbm"]
band_gap = d["band_gap"]
filter_compatible = d.get("filter_compatible", True)
metadata = d.get("metadata", {})
if "entry_id" in d.keys() and "entry_id" not in metadata:
metadata["entry_id"] = d["entry_id"]
return cls(
entries,
vbm,
band_gap,
filter_compatible=filter_compatible,
metadata=metadata,
)
def find_stable_charges(self):
"""
Sets the stable charges and transition states for a series of
defect entries. This function uses scipy's HalfspaceInterection
to oncstruct the polygons corresponding to defect stability as
a function of the Fermi-level. The Halfspace Intersection
constructs N-dimensional hyperplanes, in this case N=2, based
on the equation of defect formation energy with considering chemical
potentials:
E_form = E_0^{Corrected} + Q_{defect}*(E_{VBM} + E_{Fermi})
Extra hyperplanes are constructed to bound this space so that
the algorithm can actually find enclosed region.
This code was modeled after the Halfspace Intersection code for
the Pourbaix Diagram
"""
def similar_defects(entryset):
"""
Used for grouping similar defects of different charges
Can distinguish identical defects even if they are not in same position
"""
pdc = PointDefectComparator(check_charge=False, check_primitive_cell=True, check_lattice_scale=False)
grp_def_sets = []
grp_def_indices = []
for ent_ind, ent in enumerate(entryset):
# TODO: more pythonic way of grouping entry sets with PointDefectComparator.
# this is currently most time intensive part of DefectPhaseDiagram
matched_ind = None
for grp_ind, defgrp in enumerate(grp_def_sets):
if pdc.are_equal(ent.defect, defgrp[0].defect):
matched_ind = grp_ind
break
if matched_ind is not None:
grp_def_sets[matched_ind].append(ent.copy())
grp_def_indices[matched_ind].append(ent_ind)
else:
grp_def_sets.append([ent.copy()])
grp_def_indices.append([ent_ind])
return zip(grp_def_sets, grp_def_indices)
# Limits for search
# E_fermi = { -1 eV to band gap+1}
# E_formation = { (min(Eform) - 30) to (max(Eform) + 30)}
all_eform = [one_def.formation_energy(fermi_level=self.band_gap / 2.0) for one_def in self.entries]
min_y_lim = min(all_eform) - 30
max_y_lim = max(all_eform) + 30
limits = [[-1, self.band_gap + 1], [min_y_lim, max_y_lim]]
stable_entries = {}
finished_charges = {}
transition_level_map = {}
# Grouping by defect types
for defects, index_list in similar_defects(self.entries):
defects = list(defects)
# prepping coefficient matrix for half-space intersection
# [-Q, 1, -1*(E_form+Q*VBM)] -> -Q*E_fermi+E+-1*(E_form+Q*VBM) <= 0 where E_fermi and E are the variables
# in the hyperplanes
hyperplanes = np.array(
[
[
-1.0 * entry.charge,
1,
-1.0 * (entry.energy + entry.charge * self.vbm),
]
for entry in defects
]
)
border_hyperplanes = [
[-1, 0, limits[0][0]],
[1, 0, -1 * limits[0][1]],
[0, -1, limits[1][0]],
[0, 1, -1 * limits[1][1]],
]
hs_hyperplanes = np.vstack([hyperplanes, border_hyperplanes])
interior_point = [self.band_gap / 2, min(all_eform) - 1.0]
hs_ints = HalfspaceIntersection(hs_hyperplanes, np.array(interior_point))
# Group the intersections and coresponding facets
ints_and_facets = zip(hs_ints.intersections, hs_ints.dual_facets)
# Only inlcude the facets corresponding to entries, not the boundaries
total_entries = len(defects)
ints_and_facets = filter(
lambda int_and_facet: all(np.array(int_and_facet[1]) < total_entries),
ints_and_facets,
)
# sort based on transition level
ints_and_facets = list(sorted(ints_and_facets, key=lambda int_and_facet: int_and_facet[0][0]))
# log a defect name for tracking (using full index list to avoid naming
# in-equivalent defects with same name)
str_index_list = [str(ind) for ind in sorted(index_list)]
track_name = defects[0].name + "@" + str("-".join(str_index_list))
if len(ints_and_facets):
# Unpack into lists
_, facets = zip(*ints_and_facets)
# Map of transition level: charge states
transition_level_map[track_name] = {
intersection[0]: [defects[i].charge for i in facet] for intersection, facet in ints_and_facets
}
stable_entries[track_name] = list({defects[i] for dual in facets for i in dual})
finished_charges[track_name] = [defect.charge for defect in defects]
else:
# if ints_and_facets is empty, then there is likely only one defect...
if len(defects) != 1:
# confirm formation energies dominant for one defect over other identical defects
name_set = [one_def.name + "_chg" + str(one_def.charge) for one_def in defects]
vb_list = [one_def.formation_energy(fermi_level=limits[0][0]) for one_def in defects]
cb_list = [one_def.formation_energy(fermi_level=limits[0][1]) for one_def in defects]
vbm_def_index = vb_list.index(min(vb_list))
name_stable_below_vbm = name_set[vbm_def_index]
cbm_def_index = cb_list.index(min(cb_list))
name_stable_above_cbm = name_set[cbm_def_index]
if name_stable_below_vbm != name_stable_above_cbm:
raise ValueError(
"HalfSpace identified only one stable charge out of list: {}\n"
"But {} is stable below vbm and {} is "
"stable above cbm.\nList of VBM formation energies: {}\n"
"List of CBM formation energies: {}"
"".format(
name_set,
name_stable_below_vbm,
name_stable_above_cbm,
vb_list,
cb_list,
)
)
logger.info("{} is only stable defect out of {}".format(name_stable_below_vbm, name_set))
transition_level_map[track_name] = {}
stable_entries[track_name] = list([defects[vbm_def_index]])
finished_charges[track_name] = [one_def.charge for one_def in defects]
else:
transition_level_map[track_name] = {}
stable_entries[track_name] = list([defects[0]])
finished_charges[track_name] = [defects[0].charge]
self.transition_level_map = transition_level_map
self.transition_levels = {
defect_name: list(defect_tls.keys()) for defect_name, defect_tls in transition_level_map.items()
}
self.stable_entries = stable_entries
self.finished_charges = finished_charges
self.stable_charges = {
defect_name: [entry.charge for entry in entries] for defect_name, entries in stable_entries.items()
}
@property
def defect_types(self):
"""
List types of defects existing in the DefectPhaseDiagram
"""
return list(self.finished_charges.keys())
@property
def all_stable_entries(self):
"""
List all stable entries (defect+charge) in the DefectPhaseDiagram
"""
return set(chain.from_iterable(self.stable_entries.values()))
@property
def all_unstable_entries(self):
"""
List all unstable entries (defect+charge) in the DefectPhaseDiagram
"""
all_stable_entries = self.all_stable_entries
return [e for e in self.entries if e not in all_stable_entries]
def defect_concentrations(self, chemical_potentials, temperature=300, fermi_level=0.0):
"""
Give list of all concentrations at specified efermi in the DefectPhaseDiagram
args:
chemical_potentials = {Element: number} is dict of chemical potentials to provide formation energies for
temperature = temperature to produce concentrations from
fermi_level: (float) is fermi level relative to valence band maximum
Default efermi = 0 = VBM energy
returns:
list of dictionaries of defect concentrations
"""
concentrations = []
for dfct in self.all_stable_entries:
concentrations.append(
{
"conc": dfct.defect_concentration(
chemical_potentials=chemical_potentials,
temperature=temperature,
fermi_level=fermi_level,
),
"name": dfct.name,
"charge": dfct.charge,
}
)
return concentrations
def suggest_charges(self, tolerance=0.1):
"""
Suggest possible charges for defects to compute based on proximity
of known transitions from entires to VBM and CBM
Args:
tolerance (float): tolerance with respect to the VBM and CBM to
` continue to compute new charges
"""
recommendations = {}
for def_type in self.defect_types:
test_charges = np.arange(
np.min(self.stable_charges[def_type]) - 1,
np.max(self.stable_charges[def_type]) + 2,
)
test_charges = [charge for charge in test_charges if charge not in self.finished_charges[def_type]]
if len(self.transition_level_map[def_type].keys()):
# More positive charges will shift the minimum transition level down
# Max charge is limited by this if its transition level is close to VBM
min_tl = min(self.transition_level_map[def_type].keys())
if min_tl < tolerance:
max_charge = max(self.transition_level_map[def_type][min_tl])
test_charges = [charge for charge in test_charges if charge < max_charge]
# More negative charges will shift the maximum transition level up
# Minimum charge is limited by this if transition level is near CBM
max_tl = max(self.transition_level_map[def_type].keys())
if max_tl > (self.band_gap - tolerance):
min_charge = min(self.transition_level_map[def_type][max_tl])
test_charges = [charge for charge in test_charges if charge > min_charge]
else:
test_charges = [charge for charge in test_charges if charge not in self.stable_charges[def_type]]
recommendations[def_type] = test_charges
return recommendations
def suggest_larger_supercells(self, tolerance=0.1):
"""
Suggest larger supercells for different defect+chg combinations based on use of
compatibility analysis. Does this for any charged defects which have is_compatible = False,
and the defect+chg formation energy is stable at fermi levels within the band gap.
NOTE: Requires self.filter_compatible = False
Args:
tolerance (float): tolerance with respect to the VBM and CBM for considering
larger supercells for a given charge
"""
if self.filter_compatible:
raise ValueError("Cannot suggest larger supercells if filter_compatible is True.")
recommendations = {}
for def_type in self.defect_types:
template_entry = self.stable_entries[def_type][0].copy()
defect_indices = [int(def_ind) for def_ind in def_type.split("@")[-1].split("-")]
for charge in self.finished_charges[def_type]:
chg_defect = template_entry.defect.copy()
chg_defect.set_charge(charge)
for entry_index in defect_indices:
entry = self.entries[entry_index]
if entry.charge == charge:
break
if entry.parameters.get("is_compatible", True):
continue
# consider if transition level is within
# tolerance of band edges
suggest_bigger_supercell = True
for tl, chgset in self.transition_level_map[def_type].items():
sorted_chgset = list(chgset)
sorted_chgset.sort(reverse=True)
if charge == sorted_chgset[0] and tl < tolerance:
suggest_bigger_supercell = False
elif charge == sorted_chgset[1] and tl > (self.band_gap - tolerance):
suggest_bigger_supercell = False
if suggest_bigger_supercell:
if def_type not in recommendations:
recommendations[def_type] = []
recommendations[def_type].append(charge)
return recommendations
def solve_for_fermi_energy(self, temperature, chemical_potentials, bulk_dos):
"""
Solve for the Fermi energy self-consistently as a function of T
Observations are Defect concentrations, electron and hole conc
Args:
temperature: Temperature to equilibrate fermi energies for
chemical_potentials: dict of chemical potentials to use for calculation fermi level
bulk_dos: bulk system dos (pymatgen Dos object)
Returns:
Fermi energy dictated by charge neutrality
"""
fdos = FermiDos(bulk_dos, bandgap=self.band_gap)
_, fdos_vbm = fdos.get_cbm_vbm()
def _get_total_q(ef):
qd_tot = sum(
[
d["charge"] * d["conc"]
for d in self.defect_concentrations(
chemical_potentials=chemical_potentials,
temperature=temperature,
fermi_level=ef,
)
]
)
qd_tot += fdos.get_doping(fermi_level=ef + fdos_vbm, temperature=temperature)
return qd_tot
return bisect(_get_total_q, -1.0, self.band_gap + 1.0)
def solve_for_non_equilibrium_fermi_energy(self, temperature, quench_temperature, chemical_potentials, bulk_dos):
"""
Solve for the Fermi energy after quenching in the defect concentrations at a higher
temperature (the quench temperature),
as outlined in P. Canepa et al (2017) Chemistry of Materials (doi: 10.1021/acs.chemmater.7b02909)
Args:
temperature: Temperature to equilibrate fermi energy at after quenching in defects
quench_temperature: Temperature to equilibrate defect concentrations at (higher temperature)
chemical_potentials: dict of chemical potentials to use for calculation fermi level
bulk_dos: bulk system dos (pymatgen Dos object)
Returns:
Fermi energy dictated by charge neutrality with respect to frozen in defect concentrations
"""
high_temp_fermi_level = self.solve_for_fermi_energy(quench_temperature, chemical_potentials, bulk_dos)
fixed_defect_charge = sum(
[
d["charge"] * d["conc"]
for d in self.defect_concentrations(
chemical_potentials=chemical_potentials,
temperature=quench_temperature,
fermi_level=high_temp_fermi_level,
)
]
)
fdos = FermiDos(bulk_dos, bandgap=self.band_gap)
_, fdos_vbm = fdos.get_cbm_vbm()
def _get_total_q(ef):
qd_tot = fixed_defect_charge
qd_tot += fdos.get_doping(fermi_level=ef + fdos_vbm, temperature=temperature)
return qd_tot
return bisect(_get_total_q, -1.0, self.band_gap + 1.0)
def get_dopability_limits(self, chemical_potentials):
"""
Find Dopability limits for a given chemical potential.
This is defined by the defect formation energies which first cross zero
in formation energies.
This determine bounds on the fermi level.
Does this by computing formation energy for every stable defect with non-zero charge.
If the formation energy value changes sign on either side of the band gap, then
compute the fermi level value where the formation energy is zero
(formation energies are lines and basic algebra shows: x_crossing = x1 - (y1 / q)
for fermi level, x1, producing formation energy y1)
Args:
chemical_potentials: dict of chemical potentials to use for calculation fermi level
Returns:
lower dopability limit, upper dopability limit
(returns None if no limit exists for upper or lower i.e. no negative defect
crossing before +/- 20 of band edges OR defect formation energies are entirely zero)
"""
min_fl_range = -20.0
max_fl_range = self.band_gap + 20.0
lower_lim = None
upper_lim = None
for def_entry in self.all_stable_entries:
min_fl_formen = def_entry.formation_energy(
chemical_potentials=chemical_potentials, fermi_level=min_fl_range
)
max_fl_formen = def_entry.formation_energy(
chemical_potentials=chemical_potentials, fermi_level=max_fl_range
)
if min_fl_formen < 0.0 and max_fl_formen < 0.0:
logger.error(
"Formation energy is negative through entire gap for entry {} q={}."
" Cannot return dopability limits.".format(def_entry.name, def_entry.charge)
)
return None, None
if np.sign(min_fl_formen) != np.sign(max_fl_formen):
x_crossing = min_fl_range - (min_fl_formen / def_entry.charge)
if min_fl_formen < 0.0:
if lower_lim is None or lower_lim < x_crossing:
lower_lim = x_crossing
else:
if upper_lim is None or upper_lim > x_crossing:
upper_lim = x_crossing
return lower_lim, upper_lim
def plot(
self,
mu_elts=None,
xlim=None,
ylim=None,
ax_fontsize=1.3,
lg_fontsize=1.0,
lg_position=None,
fermi_level=None,
title=None,
saved=False,
):
"""
Produce defect Formation energy vs Fermi energy plot
Args:
mu_elts:
a dictionnary of {Element:value} giving the chemical
potential of each element
xlim:
Tuple (min,max) giving the range of the x (fermi energy) axis
ylim:
Tuple (min,max) giving the range for the formation energy axis
ax_fontsize:
float multiplier to change axis label fontsize
lg_fontsize:
float multiplier to change legend label fontsize
lg_position:
Tuple (horizontal-position, vertical-position) giving the position
to place the legend.
Example: (0.5,-0.75) will likely put it below the x-axis.
saved:
Returns:
a matplotlib object
"""
if xlim is None:
xlim = (-0.5, self.band_gap + 0.5)
xy = {}
lower_cap = -100.0
upper_cap = 100.0
y_range_vals = [] # for finding max/min values on y-axis based on x-limits
for defnom, def_tl in self.transition_level_map.items():
xy[defnom] = [[], []]
if def_tl:
org_x = sorted(def_tl.keys()) # list of transition levels
# establish lower x-bound
first_charge = max(def_tl[org_x[0]])
for chg_ent in self.stable_entries[defnom]:
if chg_ent.charge == first_charge:
form_en = chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=lower_cap)
fe_left = chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=xlim[0])
xy[defnom][0].append(lower_cap)
xy[defnom][1].append(form_en)
y_range_vals.append(fe_left)
# iterate over stable charge state transitions
for fl in org_x:
charge = max(def_tl[fl])
for chg_ent in self.stable_entries[defnom]:
if chg_ent.charge == charge:
form_en = chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=fl)
xy[defnom][0].append(fl)
xy[defnom][1].append(form_en)
y_range_vals.append(form_en)
# establish upper x-bound
last_charge = min(def_tl[org_x[-1]])
for chg_ent in self.stable_entries[defnom]:
if chg_ent.charge == last_charge:
form_en = chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=upper_cap)
fe_right = chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=xlim[1])
xy[defnom][0].append(upper_cap)
xy[defnom][1].append(form_en)
y_range_vals.append(fe_right)
else:
# no transition - just one stable charge
chg_ent = self.stable_entries[defnom][0]
for x_extrem in [lower_cap, upper_cap]:
xy[defnom][0].append(x_extrem)
xy[defnom][1].append(chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=x_extrem))
for x_window in xlim:
y_range_vals.append(chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=x_window))
if ylim is None:
window = max(y_range_vals) - min(y_range_vals)
spacer = 0.1 * window
ylim = (min(y_range_vals) - spacer, max(y_range_vals) + spacer)
if len(xy) <= 8:
colors = cm.Dark2(np.linspace(0, 1, len(xy))) # pylint: disable=E1101
else:
colors = cm.gist_rainbow(np.linspace(0, 1, len(xy))) # pylint: disable=E1101
plt.figure()
plt.clf()
width = 12
# plot formation energy lines
for_legend = []
for cnt, defnom in enumerate(xy.keys()):
plt.plot(xy[defnom][0], xy[defnom][1], linewidth=3, color=colors[cnt])
for_legend.append(self.stable_entries[defnom][0].copy())
# plot transtition levels
for cnt, defnom in enumerate(xy.keys()):
x_trans, y_trans = [], []
for x_val, chargeset in self.transition_level_map[defnom].items():
x_trans.append(x_val)
for chg_ent in self.stable_entries[defnom]:
if chg_ent.charge == chargeset[0]:
form_en = chg_ent.formation_energy(chemical_potentials=mu_elts, fermi_level=x_val)
y_trans.append(form_en)
if len(x_trans):
plt.plot(
x_trans,
y_trans,
marker="*",
color=colors[cnt],
markersize=12,
fillstyle="full",
)
# get latex-like legend titles
legends_txt = []
for dfct in for_legend:
flds = dfct.name.split("_")
if flds[0] == "Vac":
base = "$Vac"
sub_str = "_{" + flds[1] + "}$"
elif flds[0] == "Sub":
flds = dfct.name.split("_")
base = "$" + flds[1]
sub_str = "_{" + flds[3] + "}$"
elif flds[0] == "Int":
base = "$" + flds[1]
sub_str = "_{inter}$"
else:
base = dfct.name
sub_str = ""
legends_txt.append(base + sub_str)
if not lg_position:
plt.legend(legends_txt, fontsize=lg_fontsize * width, loc=0)
else:
plt.legend(
legends_txt,
fontsize=lg_fontsize * width,
ncol=3,
loc="lower center",
bbox_to_anchor=lg_position,
)
plt.ylim(ylim)
plt.xlim(xlim)
plt.plot([xlim[0], xlim[1]], [0, 0], "k-") # black dashed line for Eformation = 0
plt.axvline(x=0.0, linestyle="--", color="k", linewidth=3) # black dashed lines for gap edges
plt.axvline(x=self.band_gap, linestyle="--", color="k", linewidth=3)
if fermi_level is not None:
plt.axvline(x=fermi_level, linestyle="-.", color="k", linewidth=2) # smaller dashed lines for gap edges
plt.xlabel("Fermi energy (eV)", size=ax_fontsize * width)
plt.ylabel("Defect Formation\nEnergy (eV)", size=ax_fontsize * width)
if title:
plt.title("{}".format(title), size=ax_fontsize * width)
if saved:
plt.savefig(str(title) + "FreyplnravgPlot.pdf")
else:
return plt
return None