def Extract(self, jobdir):
from pylada.vasp import MassExtract
extract = MassExtract(jobdir)
success={}
for name in self.names:
success[name]=MassExtract(jobdir+'/'+name).success
success=all(success.values())
extract.success=success
return extract
def Extract(self, jobdir):
extract = MassExtract(jobdir)
success = {}
for name in self.names:
#import pdb; pdb.set_trace()
success[name] = Extract(jobdir + '/' + name).success
success = all(success.values())
extract.success = success
return extract
def Extract(self, jobdir):
extract = MassExtract(jobdir)
success = {}
last = self.names[-1]
lasts = [last, os.path.join('bottom', last), os.path.join('top', last)]
folders = self.names[self.to_run:] + [
os.path.join('bottom', x) for x in self.names
] + [os.path.join('top', x) for x in self.names]
for name in folders:
#import pdb; pdb.set_trace()
success[name] = Extract(jobdir + '/' + name).success
success = all(success.values())
extract.success = success
return extract
def __init__(self, path=None, epsilon = 1e0, pa_maxdiff=0.5, Extractor=None, **kwargs):
""" Initializes an enthalpy function. """
from pylada.vasp import MassExtract
super(PointDefectMassExtractor, self).__init__(**kwargs)
self.Extractor = Extractor
""" Class for extracting data from a single defect. """
if self.Extractor is None: self.Extractor = PointDefectExtractor
self.massextract = MassExtract(path, unix_re=False, excludes=[".*relax_*"])
""" Mass extraction object from which all results are pulled. """
self.host = self._get_host()
""" Result of host calculations. """
# must be last. Can't use porperty setter.
self._epsilon = epsilon
self._pa_maxdiff = pa_maxdiff
class PointDefectMassExtractorImpl(AbstractMassExtract):
""" Enthalpy for a series of defects for a given material and lattice. """
def __init__(self, path=None, epsilon = 1e0, pa_maxdiff=0.5, Extractor=None, **kwargs):
""" Initializes an enthalpy function. """
from pylada.vasp import MassExtract
super(PointDefectMassExtractor, self).__init__(**kwargs)
self.Extractor = Extractor
""" Class for extracting data from a single defect. """
if self.Extractor is None: self.Extractor = PointDefectExtractor
self.massextract = MassExtract(path, unix_re=False, excludes=[".*relax_*"])
""" Mass extraction object from which all results are pulled. """
self.host = self._get_host()
""" Result of host calculations. """
# must be last. Can't use porperty setter.
self._epsilon = epsilon
self._pa_maxdiff = pa_maxdiff
@property
def epsilon(self):
""" Dimensionless dielectric constant. """
return self._epsilon
@epsilon.setter
def epsilon(self, value):
self._epsilon = value
for v in self.itervalues(): v.epsilon = self._epsilon
@property
def pa_maxdiff(self):
""" Dimensionless dielectric constant. """
return self._pa_maxdiff
@pa_maxdiff.setter
def pa_maxdiff(self, value):
self._pa_maxdiff = value
for v in self.itervalues(): v.pa_maxdiff = self._pa_maxdiff
@property
def rootdir(self):
""" Path to the root-directory containing the poin-defects. """
return self.massextract.rootdir
@rootdir.setter
def rootdir(self, value): self.massextract.rootdir = value
def _get_host(self):
""" Returns extraction object towards the host. """
from operator import itemgetter
host = self.massextract.copy(excludes=[".*PointDefects"])
host.excludes.extend(self.massextract.excludes)
lowest = sorted(host.total_energies.iteritems(), key=itemgetter(1))[0][0]
host = [u for u in host[lowest].itervalues()]
assert len(host) == 1
return host[0]
def __iter_alljobs__(self):
""" Walks through point-defects only. """
for child in self.massextract["PointDefects"].children:
# looks for site_n
if len(child["site_\d+"].jobs) != 0:
assert len(child["site_\d+"].jobs) == len(child.jobs),\
RuntimeError("Don't understand directory structure of {0}.".format(child.view))
for site in child.children: # should site specific defects.
result = self.Extractor(site, self.epsilon, self.host, self.pa_maxdiff)
# checks this is a point-defect.
if result.is_interstitial or result.is_vacancy or result.is_substitution:
yield site.view, result
else:
result = self.Extractor(child, host=self.host, pa_maxdiff=self.pa_maxdiff,\
epsilon = self.epsilon)
# checks if this is a valid point-defect.
if result.is_interstitial or result.is_vacancy or result.is_substitution:
yield child.view, result
def ordered_items(self):
""" Returns items ordered by substitution, vacancy, and interstitial. """
from operator import itemgetter
interstitials = (u for u in self.iteritems() if u[1].is_interstitial)
substitution = (u for u in self.iteritems() if u[1].is_substitution)
vacancy = (u for u in self.iteritems() if u[1].is_vacancy)
result = sorted(substitution, key = itemgetter(0))
result.extend(sorted(vacancy, key = itemgetter(0)))
result.extend(sorted(interstitials, key = itemgetter(0)))
return result
def ordered_keys(self):
""" Returns keys ordered by substitution, vacancy, and interstitial. """
return [u[0] for u in self.ordered_items()]
def ordered_values(self):
""" Returns values ordered by substitution, vacancy, and interstitial. """
return [u[1] for u in self.ordered_items()]
def __str__(self):
""" Prints out all energies and corrections. """
return "".join( str(value) for value in self.ordered_values() )
