def explore_defect(defect, host, **kwargs):
""" Diagnostic tool to determine defect from defect calculation and host.
:Parameters:
defect : `pylada.vasp.ExtractDFT`
Extraction object for the vasp calculation of the defect structure.
The defect structure should be a supercell of the host. Its unit cell
must be an exact multiple of the host unit cell. Atoms may have moved
around, however.
host : `pylada.vasp.ExtractDFT`
Extraction object for the vasp calculation of the host structure.
kwargs
Passed on to `reindex_sites`.
:return:
Dictionary containing three items:
- 'vacancy': a list of atoms from the host *missing* in the defect
structure. The position of these atoms correspond to the missing atom
in the supercell (not the translational equivalent of the unit-cell).
- 'substitution': list of indices referring to atoms in the defect
structure with substituted types (w.r.t. the host).
- 'intersititial': list of indices referring to atoms in the defect
structure with no counterpart in the host structure.
:note: The results may be incorrect if the defects incur too much relaxation.
"""
from copy import deepcopy
from pylada.crystal.defects import reindex_sites
from pylada.crystal import structure_to_lattice
dstr = defect.structure.copy()
hstr = host.structure
# modified by Haowei: using the p1 structure for reindexing and potential_alignment
hlat_p1 = structure_to_lattice(hstr, primitive=False)
reindex_sites(dstr, hlat_p1, **kwargs)
result = {'interstitial': [], 'substitution': [], 'vacancy': []}
# looks for intersitials and substitutionals.
for i, atom in enumerate(dstr.atoms):
if atom.site == -1:
result['interstitial'].append(i)
elif atom.type != hstr.atoms[atom.site].type:
result['substitution'].append(i)
# looks for vacancies.
filled = hlat_p1.to_structure(dstr.cell)
reindex_sites(filled, dstr, **kwargs)
for atom in filled.atoms:
if atom.site != -1: continue
result['vacancy'].append(deepcopy(atom))
return result
def explore_defect(defect, host, **kwargs):
""" Diagnostic tool to determine defect from defect calculation and host.
:Parameters:
defect : `pylada.vasp.ExtractDFT`
Extraction object for the vasp calculation of the defect structure.
The defect structure should be a supercell of the host. Its unit cell
must be an exact multiple of the host unit cell. Atoms may have moved
around, however.
host : `pylada.vasp.ExtractDFT`
Extraction object for the vasp calculation of the host structure.
kwargs
Passed on to `reindex_sites`.
:return:
Dictionary containing three items:
- 'vacancy': a list of atoms from the host *missing* in the defect
structure. The position of these atoms correspond to the missing atom
in the supercell (not the translational equivalent of the unit-cell).
- 'substitution': list of indices referring to atoms in the defect
structure with substituted types (w.r.t. the host).
- 'intersititial': list of indices referring to atoms in the defect
structure with no counterpart in the host structure.
:note: The results may be incorrect if the defects incur too much relaxation.
"""
from copy import deepcopy
from pylada.crystal.defects import reindex_sites
from pylada.crystal import structure_to_lattice
dstr = defect.structure.copy()
hstr = host.structure
# modified by Haowei: using the p1 structure for reindexing and potential_alignment
hlat_p1 = structure_to_lattice(hstr, primitive=False)
reindex_sites(dstr, hlat_p1, **kwargs)
result = {'interstitial': [], 'substitution': [], 'vacancy': []}
# looks for intersitials and substitutionals.
for i, atom in enumerate(dstr.atoms):
if atom.site == -1:
result['interstitial'].append(i)
elif atom.type != hstr.atoms[atom.site].type:
result['substitution'].append(i)
# looks for vacancies.
filled = hlat_p1.to_structure(dstr.cell)
reindex_sites(filled, dstr, **kwargs)
for atom in filled.atoms:
if atom.site != -1: continue
result['vacancy'].append(deepcopy(atom))
return result
def potential_alignment(defect, host, maxdiff=None, first_shell=False, tolerance=0.25):
""" Returns potential alignment correction.
:Parameters:
defect
An output extraction object as returned by the vasp functional when
computing the defect of interest.
host
An output extraction object as returned by the vasp functional when
computing the host matrix.
maxdiff : float or None, in eV(?)
Maximum difference between the electrostatic potential of an atom and
the equivalent host electrostatic potential beyond which that atom is
considered pertubed by the defect.
If None or negative, then differences in electrostatice potentials
are not considered.
Default 0.5.
first_shell : bool
If true then removes from potential alignment the first neighbor of
defect atoms.
Default False.
tolerance
Passed on to `reindex_sites`.
Default 0.25.
:return: The potential alignment in eV (without charge factor).
Returns average difference of the electrostatic potential of the
unperturbed atoms in the defect structure with respect to the host.
*Perturbed* atoms are those flagged as defect by `explore_defect`, their
first coordination shell if ''first_shell'' is true, and atoms for which
the electrostatic potential differ to far from the average electrostatic
potential for each lattice site (parameterized by maxdiff).
"""
from itertools import chain
from numpy import abs, array, mean, any
from quantities import eV
from . import reindex_sites, first_shell as ffirst_shell
from pylada.crystal import structure_to_lattice
dstr = defect.structure
hstr = host.structure
# modified by Haowei: uring the p1 structure for potential alignment
# this is necessary for two reasons:
# 1, the host unit cell may be a *supercell* due to the magnetic structure
# 2, in the conventional defect calculations, we run the calculation for host using the same supercell as defect calculations
# but this should not be a problem if the calculations are converged very well
hlat_p1 = structure_to_lattice(hstr, primitive=False)
reindex_sites(dstr, hlat_p1, tolerance=tolerance)
defects = explore_defect(defect, host, tolerance=tolerance)
acceptable = [True for a in dstr.atoms]
# make interstitials and substitutionals unaceptable.
for i in chain(defects['interstitial'], defects['substitution']):
acceptable[i] = False
if first_shell:
for n in ffirst_shell(dstr, dstr.atoms[i].pos, tolerance=tolerance):
acceptable[n.index] = False
# makes vacancies unacceptable.
if first_shell:
for atom in defects['vacancy']:
for n in ffirst_shell(dstr, atom.pos, tolerance=tolerance):
acceptable[n.index] = False
# make a deepcopy for backup
raw_acceptable = list(acceptable)
if maxdiff != None and maxdiff > 0.0:
# directly compare the atomic site between the host and defect cell/supercell
diff_dh = [ (0.0 * eV if not ok else abs(e - host.electropot[a.site]).rescale(eV)) \
for e, a, ok in zip(defect.electropot, dstr.atoms, acceptable) ]
for ixx in range(len(acceptable)):
if acceptable[ixx] == False: pass
elif float(diff_dh[ixx].magnitude) > maxdiff: acceptable[ixx] = False
if not any(acceptable):
# if some one try to use maxdiff = 0.0000000001, @&#(@&#(#@^@
print "WARNING: maxdiff is too small! Jump to maxdiff=None"
# return to the default one, which accept all the atomic sites except the defect sites
acceptable = list(raw_acceptable)
iterable = zip(defect.electropot, dstr.atoms, acceptable)
return mean([ (e - host.electropot[a.site]).rescale(eV).magnitude\
for e, a, ok in iterable if ok ]) * eV
def potential_alignment(defect,
host,
maxdiff=None,
first_shell=False,
tolerance=0.25):
""" Returns potential alignment correction.
:Parameters:
defect
An output extraction object as returned by the vasp functional when
computing the defect of interest.
host
An output extraction object as returned by the vasp functional when
computing the host matrix.
maxdiff : float or None, in eV(?)
Maximum difference between the electrostatic potential of an atom and
the equivalent host electrostatic potential beyond which that atom is
considered pertubed by the defect.
If None or negative, then differences in electrostatice potentials
are not considered.
Default 0.5.
first_shell : bool
If true then removes from potential alignment the first neighbor of
defect atoms.
Default False.
tolerance
Passed on to `reindex_sites`.
Default 0.25.
:return: The potential alignment in eV (without charge factor).
Returns average difference of the electrostatic potential of the
unperturbed atoms in the defect structure with respect to the host.
*Perturbed* atoms are those flagged as defect by `explore_defect`, their
first coordination shell if ''first_shell'' is true, and atoms for which
the electrostatic potential differ to far from the average electrostatic
potential for each lattice site (parameterized by maxdiff).
"""
from itertools import chain
from numpy import abs, array, mean, any
from quantities import eV
from . import reindex_sites, first_shell as ffirst_shell
from pylada.crystal import structure_to_lattice
dstr = defect.structure
hstr = host.structure
# modified by Haowei: uring the p1 structure for potential alignment
# this is necessary for two reasons:
# 1, the host unit cell may be a *supercell* due to the magnetic structure
# 2, in the conventional defect calculations, we run the calculation for host using the same supercell as defect calculations
# but this should not be a problem if the calculations are converged very well
hlat_p1 = structure_to_lattice(hstr, primitive=False)
reindex_sites(dstr, hlat_p1, tolerance=tolerance)
defects = explore_defect(defect, host, tolerance=tolerance)
acceptable = [True for a in dstr.atoms]
# make interstitials and substitutionals unaceptable.
for i in chain(defects['interstitial'], defects['substitution']):
acceptable[i] = False
if first_shell:
for n in ffirst_shell(dstr, dstr.atoms[i].pos,
tolerance=tolerance):
acceptable[n.index] = False
# makes vacancies unacceptable.
if first_shell:
for atom in defects['vacancy']:
for n in ffirst_shell(dstr, atom.pos, tolerance=tolerance):
acceptable[n.index] = False
# make a deepcopy for backup
raw_acceptable = list(acceptable)
if maxdiff != None and maxdiff > 0.0:
# directly compare the atomic site between the host and defect cell/supercell
diff_dh = [ (0.0 * eV if not ok else abs(e - host.electropot[a.site]).rescale(eV)) \
for e, a, ok in zip(defect.electropot, dstr.atoms, acceptable) ]
for ixx in range(len(acceptable)):
if acceptable[ixx] == False: pass
elif float(diff_dh[ixx].magnitude) > maxdiff:
acceptable[ixx] = False
if not any(acceptable):
# if some one try to use maxdiff = 0.0000000001, @&#(@&#(#@^@
print "WARNING: maxdiff is too small! Jump to maxdiff=None"
# return to the default one, which accept all the atomic sites except the defect sites
acceptable = list(raw_acceptable)
iterable = zip(defect.electropot, dstr.atoms, acceptable)
return mean([ (e - host.electropot[a.site]).rescale(eV).magnitude\
for e, a, ok in iterable if ok ]) * eV