def set_up_recipe_plan(self, fulldir, verbose=0):
"""Set up a recipe plan from the recipe directory.
Args:
fulldir <str>: full path of recipe directory
verbose <int>: verbosity
"""
self.logger.info("--------------------------------")
self.logger.info("Setting up recipe plan for %s" % fulldir)
self.logger.info("--------------------------------")
os.chdir(fulldir) #need to change directories in order to submit jobs?
myipparser = InputParser(inputfile=os.path.join(fulldir, 'input.inp'))
myinputoptions = myipparser.parse()
input_options_keys = myinputoptions.get_sections()
key = 'personal_recipe'
if key in input_options_keys:
self.logger.debug("Key - personal recipe was found")
personal_recipe_contents = myinputoptions.get_item('personal_recipe', 'personal_recipe_list')
rsetup = RecipeSetup(recipeFile=personal_recipe_contents,
inputOptions=myinputoptions,
structure=myinputoptions.get_item('structure','structure'),
workingDirectory=fulldir)
recipe_plan_obj = rsetup.start()
recipe_plan_obj.get_statuses_from_file()
self.logger.debug("Returning recipe plan object to calling method.")
return recipe_plan_obj
def set_up_recipe_plan(self, fulldir, verbose=0):
"""Set up a recipe plan from the recipe directory.
Args:
fulldir <str>: full path of recipe directory
verbose <int>: verbosity
"""
self.logger.info("--------------------------------")
self.logger.info("Setting up recipe plan for %s" % fulldir)
self.logger.info("--------------------------------")
os.chdir(fulldir) #need to change directories in order to submit jobs?
myipparser = InputParser(inputfile=os.path.join(fulldir, 'input.inp'))
myinputoptions = myipparser.parse()
input_options_keys = myinputoptions.get_sections()
key = 'personal_recipe'
if key in input_options_keys:
self.logger.debug("Key - personal recipe was found")
personal_recipe_contents = myinputoptions.get_item(
'personal_recipe', 'personal_recipe_list')
rsetup = RecipeSetup(recipeFile=personal_recipe_contents,
inputOptions=myinputoptions,
structure=myinputoptions.get_item(
'structure', 'structure'),
workingDirectory=fulldir)
recipe_plan_obj = rsetup.start()
recipe_plan_obj.get_statuses_from_file()
self.logger.debug("Returning recipe plan object to calling method.")
return recipe_plan_obj
def check_recipe_dir(self, fulldir, verbose):
"""Check a recipe directory.
Args:
fulldir <str>: full path of recipe directory
verbose <int>: verbosity
"""
shortdir = os.path.basename(fulldir) #only the recipe directory name
if not os.path.exists(fulldir):
raise MASTError(self.__class__.__name__, "No recipe directory at %s" % fulldir)
if os.path.exists(os.path.join(fulldir, "MAST_SKIP")):
self.logger.warning("Skipping recipe %s due to the presence of a MAST_SKIP file in the recipe directory." % shortdir)
return
if os.path.exists(os.path.join(fulldir, "MAST_ERROR")):
self.logger.error("ATTENTION!: Skipping recipe %s due to the presence of a MAST_ERROR file in the recipe directory." % shortdir)
return
self.logger.info("--------------------------------")
self.logger.info("Processing recipe %s" % shortdir)
self.logger.info("--------------------------------")
os.chdir(fulldir) #need to change directories in order to submit jobs?
myipparser = InputParser(inputfile=os.path.join(fulldir, 'input.inp'))
myinputoptions = myipparser.parse()
input_options_keys = myinputoptions.get_sections()
key = 'personal_recipe'
if key in input_options_keys:
self.logger.debug("Key - personal recipe was found")
personal_recipe_contents = myinputoptions.get_item('personal_recipe', 'personal_recipe_list')
rsetup = RecipeSetup(recipeFile=personal_recipe_contents,
inputOptions=myinputoptions,
structure=myinputoptions.get_item('structure','structure'),
workingDirectory=fulldir)
recipe_plan_obj = rsetup.start()
recipe_plan_obj.get_statuses_from_file()
try:
recipe_plan_obj.check_recipe_status(verbose)
except Exception:
import sys,traceback
#ex_type, ex, trbck = sys.exc_info()
errortext = traceback.format_exc()
#del trbck
errorfile = open(os.path.join(fulldir, "MAST_ERROR"), "ab")
errorfile.write("ERROR LOGGED %s\n" % time.asctime())
errorfile.write("%s\n" % errortext)
errorfile.close()
self.logger.warning("ERROR in recipe %s. Check MAST_ERROR file in the %s directory." % (shortdir, fulldir))
#raise MASTError(self.__class__.__name__,"Error in recipe %s as follows: %s %s %s" % (shortdir, ex_type, ex, errortext))
os.chdir(self.scratch)
if recipe_plan_obj.status == "C":
shutil.move(fulldir, self._ARCHIVE)
summarypath = "%s/%s/SUMMARY.txt" % (self._ARCHIVE, shortdir)
if os.path.isfile(summarypath):
self.logger.info("Recipe %s completed." % shortdir)
self.logger.info("SUMMARY.txt below:")
summarytext = MASTFile(summarypath)
for myline in summarytext.data:
self.logger.info(myline.strip())
self.logger.info("-----------------------------")
self.logger.info("Recipe %s processed." % shortdir)
self.logger.info("-----------------------------")
def create_recipe_plan(self):
"""Create the recipe plan object, and print its status.
"""
personal_recipe_contents = self.input_options.get_item('personal_recipe', 'personal_recipe_list')
setup_obj = RecipeSetup(recipeFile=personal_recipe_contents,
inputOptions=self.input_options,
structure=self.input_options.get_item('structure','structure'),
workingDirectory=self.recdir
)
self.recipe_plan = setup_obj.start()
self.recipe_plan.print_status()
return
def create_recipe_plan(self):
"""Create the recipe plan object, and print its status.
"""
personal_recipe_contents = self.input_options.get_item(
'personal_recipe', 'personal_recipe_list')
setup_obj = RecipeSetup(recipeFile=personal_recipe_contents,
inputOptions=self.input_options,
structure=self.input_options.get_item(
'structure', 'structure'),
workingDirectory=self.recdir)
self.recipe_plan = setup_obj.start()
self.recipe_plan.print_status()
return
def test_start(self):
#rfile=os.path.join(testdir,'personalized')
wdir=os.path.join(testdir,'workdir')
struc=None
iopt=MAST.parsers.inputparser.InputParser(inputfile='input.inp').parse()
rfile = iopt.get_item('personal_recipe', 'personal_recipe_list')
myrs=RecipeSetup(recipeFile=rfile, workingDirectory=wdir, inputOptions=iopt, structure=struc)
myrs.start()
compare_metadata=MASTFile('compare_metadata.txt')
myrs_metadata=MASTFile(os.path.join(wdir,'metadata.txt'))
self.assertEqual(myrs_metadata.data, compare_metadata.data)
dirlist=MAST.utility.dirutil.walkdirs(wdir)
print dirlist
compare_dirlist=list()
compare_dirlist.append('defect_1nn_q=p0_opt1')
compare_dirlist.append('defect_1nn_q=p0_opt2')
compare_dirlist.append('defect_1nn_q=p0_stat')
compare_dirlist.append('defect_purefin_q=p0_opt1')
compare_dirlist.append('defect_purefin_q=p0_opt2')
compare_dirlist.append('defect_purefin_q=p0_stat')
compare_dirlist.append('defect_pureinit_q=p0_opt1')
compare_dirlist.append('defect_pureinit_q=p0_opt2')
compare_dirlist.append('defect_pureinit_q=p0_stat')
compare_dirlist.append('defect_solute_q=p0_opt1')
compare_dirlist.append('defect_solute_q=p0_opt2')
compare_dirlist.append('defect_solute_q=p0_stat')
compare_dirlist.append('diffcoeff_utility')
compare_dirlist.append('inducedefect_1nn')
compare_dirlist.append('inducedefect_purefin')
compare_dirlist.append('inducedefect_pureinit')
compare_dirlist.append('inducedefect_solute')
compare_dirlist.append('neb_1nn-solute_q=p0_opt1')
compare_dirlist.append('neb_1nn-solute_q=p0_opt2')
compare_dirlist.append('neb_1nn-solute_q=p0_stat')
compare_dirlist.append('neb_pureinit-purefin_q=p0_opt1')
compare_dirlist.append('neb_pureinit-purefin_q=p0_opt2')
compare_dirlist.append('neb_pureinit-purefin_q=p0_stat')
compare_dirlist.append('perfect_opt1')
compare_dirlist.append('perfect_opt2')
compare_dirlist.append('perfect_stat')
compare_dirlist.append('phonon_1nn-solute_q=p0_movingsolute')
compare_dirlist.append('phonon_1nn_q=p0_solute')
compare_dirlist.append('phonon_pureinit-purefin_q=p0_movingsolvent')
compare_dirlist.append('phonon_pureinit_q=p0_solvent')
compare_dirlist_withpath=list()
for diritem in compare_dirlist:
compare_dirlist_withpath.append(os.path.join(wdir,diritem))
mdiff=self.maxDiff
self.maxDiff=None
self.assertItemsEqual(dirlist,compare_dirlist_withpath)
self.maxDiff=mdiff
def __init__(self, directory=None, plot_threshold=0.01):
self.directory = directory
self.plot_threshold = plot_threshold
ipparser = InputParser(
inputfile=os.path.join(self.directory, 'input.inp'))
self.input_options = ipparser.parse()
#pm = PickleManager(self.directory + '/input_options.pickle')
#self.input_options = pm.load_variable()
self.recipe_setup = RecipeSetup(inputOptions=self.input_options,
recipeFile=self.input_options.get_item(
"personal_recipe",
"personal_recipe_list"),
workingDirectory=self.directory)
self.recipe_plan = self.recipe_setup.start()
self.e_defects = dict()
def __init__(self, directory=None, plot_threshold=0.01):
self.directory = directory
self.plot_threshold = plot_threshold
ipparser = InputParser(inputfile=os.path.join(self.directory,'input.inp'))
self.input_options = ipparser.parse()
#pm = PickleManager(self.directory + '/input_options.pickle')
#self.input_options = pm.load_variable()
self.recipe_setup = RecipeSetup(inputOptions=self.input_options,recipeFile=self.input_options.get_item("personal_recipe","personal_recipe_list"),workingDirectory=self.directory)
self.recipe_plan = self.recipe_setup.start()
self.e_defects = dict()
def test_get_my_ingredient_options(self):
raise SkipTest
#rfile=os.path.join(testdir,'personalized')
wdir=os.path.join(testdir,'workdir')
struc=None
iopt=MAST.parsers.inputparser.InputParser(inputfile='input.inp').parse()
rfile = iopt.get_item('personal_recipe', 'personal_recipe_list')
myrs=RecipeSetup(recipeFile=rfile, workingDirectory=wdir, inputOptions=iopt, structure=struc)
print iopt
self.assertEqual(type(myrs.metafile),MAST.utility.metadata.Metadata)
class DefectFormationEnergy:
"""Class for calculating the defect formation energy for a completed MAST
run.
"""
def __init__(self, directory=None, plot_threshold=0.01):
self.directory = directory
self.plot_threshold = plot_threshold
ipparser = InputParser(inputfile=os.path.join(self.directory,'input.inp'))
self.input_options = ipparser.parse()
#pm = PickleManager(self.directory + '/input_options.pickle')
#self.input_options = pm.load_variable()
self.recipe_setup = RecipeSetup(inputOptions=self.input_options,recipeFile=self.input_options.get_item("personal_recipe","personal_recipe_list"),workingDirectory=self.directory)
self.recipe_plan = self.recipe_setup.start()
self.e_defects = dict()
def _calculate_defect_formation_energies(self,scsize):
perf_dirs = []
ingredients = self.recipe_plan.ingredients.keys()
for i in range(len(ingredients)):
if 'perfect' in ingredients[i]:
perf_dirs.append(ingredients[i])
if len(perf_dirs)==0:
raise MASTError(self.__class__.__name__, "A perfect final directory (has no children and has the word 'perfect' in its name) could not be found. Check recipe %s for a perfect directory." % self.directory)
def_dir = ru.read_recipe(self.input_options.get_item("personal_recipe","personal_recipe_list"))[1]['madelung_utility']
defects = self.input_options.get_item('defects', 'defects')
chempot = self.input_options.get_item('chemical_potentials')
for i in range(len(perf_dirs)):
perf_meta = Metadata(metafile='%s/%s/metadata.txt' % (self.directory, perf_dirs[i]))
if scsize == perf_meta.read_data('scaling_size'): perf_dir = perf_dirs[i]
perfpath = os.path.join(self.directory, perf_dir)
if os.path.isfile(os.path.join(perfpath,"vasprun.xml")):
e_perf = pmg.io.vaspio.vasp_output.Vasprun(os.path.join(perfpath, "vasprun.xml")).final_energy
else:
e_perf = float(open(os.path.join(perfpath, "OSZICAR")).readlines()[-1].split('E0=')[1].split()[0])
efermi = self.get_fermi_energy(perf_dir)
struct_perf = self.get_structure(perf_dir)
perf_species = dict()
for site in struct_perf:
if (str(site.specie) not in perf_species):
perf_species[str(site.specie)] = 1
else:
perf_species[str(site.specie)] += 1
#print 'Perfect composition: ', perf_species
#First Loop through the conditions for the defects
for conditions, potentials in chempot.items():
self.e_defects[conditions] = dict()
# Loop through each defect
for ddir in sorted(def_dir):
def_meta = Metadata(metafile='%s/%s/metadata.txt' % (self.directory, ddir))
if scsize == def_meta.read_data('scaling_size'):
label = def_meta.read_data('defect_label')+'_q='+def_meta.read_data('charge')
charge = int(def_meta.read_data('charge'))
if os.path.isfile(os.path.join(self.directory, ddir, "vasprun.xml")):
energy = pmg.io.vaspio.vasp_output.Vasprun(self.directory+'/'+ddir+'/vasprun.xml').final_energy
else:
energy = float(open(self.directory+'/'+ddir+'/OSZICAR').readlines()[-1].split('E0=')[1].split()[0])
structure = self.get_structure(ddir)
#if (label not in self.e_defects[conditions]):
# self.e_defects[conditions][label] = list()
# Find out how many atoms of each type are in the defects
def_species = dict()
for site in structure.sites:
if (site.specie not in def_species):
def_species[site.specie] = 1
else:
def_species[site.specie] += 1
# Find the differences in the number of each atom type
# between the perfect and the defect
struct_diff = dict()
for specie, number in def_species.items():
try:
nperf = perf_species[str(specie)]
except KeyError:
nperf = 0
struct_diff[str(specie)] = number - nperf
# Get the potential alignment correction
alignment = self.get_potential_alignment(perf_dir, ddir)
# Calculate the base DFE energy
e_def = energy - e_perf # E_defect - E_perf
for specie, number in struct_diff.items():
mu = potentials[str(specie)]
e_def -= (number * mu)
e_def += charge * (efermi + alignment) # Add in the shift here!
#print '%-15s%-5i%12.5f%12.5f%12.5f%12.5f' % (label.split('_')[1], charge, energy, e_perf, efermi, alignment)
#print 'DFE = %f' % e_def
self.e_defects[conditions][label] = e_def
def get_total_energy(self, directory):
"""Returns the total energy from a directory"""
abspath = '%s/%s/' % (self.directory, directory)
if ('vasprun.xml' in os.listdir(abspath)):
# Modified from the PyMatGen Vasprun.final_energy() function to return E_0
return Vasprun('%s/vasprun.xml' % abspath).ionic_steps[-1]["electronic_steps"][-1]["e_0_energy"]
def get_fermi_energy(self, directory):
"""Returns the Fermi energy from a directory"""
abspath = '%s/%s/' % (self.directory, directory)
if ('vasprun.xml' in os.listdir(abspath)):
return Vasprun('%s/vasprun.xml' % abspath).efermi
elif ('OUTCAR' in os.listdir(abspath)):
return Outcar('%s/OUTCAR' % abspath).efermi
def get_structure(self, directory):
"""Returns the final structure from an optimization"""
abspath = '%s/%s/' % (self.directory, directory)
if ('vasprun.xml' in os.listdir(abspath)):
return Vasprun('%s/vasprun.xml' % abspath).final_structure
elif ('CONTCAR' in os.listdir(abspath)):
return pmg.read_structure('%s/CONTCAR' % abspath)
def get_potential_alignment(self, perf_dir, def_dir):
"""Returns the potential alignment correction used in charge defects"""
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
abs_path_perf = '%s/%s/' % (self.directory, perf_dir)
abs_path_def = '%s/%s/' % (self.directory, def_dir)
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
pa = PotentialAlignment()
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
if ('OUTCAR' in os.listdir(abs_path_perf)):
perfect_info = pa.read_outcar('%s/%s' % (abs_path_perf, 'OUTCAR'))
defect_info = pa.read_outcar('%s/%s' % (abs_path_def, 'OUTCAR'))
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
return pa.get_potential_alignment(perfect_info, defect_info)
def get_defect_formation_energies(self,scsize):
if not self.e_defects:
self._calculate_defect_formation_energies(scsize)
return self.e_defects
@property
def defect_formation_energies(self):
return self.get_defect_formation_energies(scsize)
@property
def dfe(self):
return self.get_defect_formation_energies(scsize)
def print_table(self,scsize):
if not self.e_defects:
self._calculate_defect_formation_energies(scsize)
myfile = MASTFile()
for conditions, defects in self.e_defects.items():
myfile.data.append('\n\nDefect formation energies for %s conditions.\n' % conditions.upper())
myfile.data.append('%-20s | %10s\n' % ('Defect', 'DFE'))
myfile.data.append('---------------------------------\n')
for defect, energies in defects.items():
for energy in energies:
myfile.data.append('%-14s(q=%2i) | %8.4f\n' % (defect, energy[0], energy[1]))
myfile.data.append(str()) # Add a blank line here
myfile.data.append('---------------------------------\n')
myfile.to_file(os.path.join(os.getcwd(),"dfe.txt"))
for line in myfile.data:
print line.strip()
class DefectFormationEnergy:
"""Class for calculating the defect formation energy for a completed MAST
run.
"""
def __init__(self, directory=None, plot_threshold=0.01):
self.directory = directory
self.plot_threshold = plot_threshold
ipparser = InputParser(
inputfile=os.path.join(self.directory, 'input.inp'))
self.input_options = ipparser.parse()
#pm = PickleManager(self.directory + '/input_options.pickle')
#self.input_options = pm.load_variable()
self.recipe_setup = RecipeSetup(inputOptions=self.input_options,
recipeFile=self.input_options.get_item(
"personal_recipe",
"personal_recipe_list"),
workingDirectory=self.directory)
self.recipe_plan = self.recipe_setup.start()
self.e_defects = dict()
def _calculate_defect_formation_energies(self, scsize):
perf_dirs = []
ingredients = self.recipe_plan.ingredients.keys()
for i in range(len(ingredients)):
if 'perfect' in ingredients[i]:
perf_dirs.append(ingredients[i])
if len(perf_dirs) == 0:
raise MASTError(
self.__class__.__name__,
"A perfect final directory (has no children and has the word 'perfect' in its name) could not be found. Check recipe %s for a perfect directory."
% self.directory)
def_dir = ru.read_recipe(
self.input_options.get_item(
"personal_recipe",
"personal_recipe_list"))[1]['madelung_utility']
defects = self.input_options.get_item('defects', 'defects')
chempot = self.input_options.get_item('chemical_potentials')
for i in range(len(perf_dirs)):
perf_meta = Metadata(metafile='%s/%s/metadata.txt' %
(self.directory, perf_dirs[i]))
if scsize == perf_meta.read_data('scaling_size'):
perf_dir = perf_dirs[i]
perfpath = os.path.join(self.directory, perf_dir)
if os.path.isfile(os.path.join(perfpath, "vasprun.xml")):
e_perf = pmg.io.vaspio.vasp_output.Vasprun(
os.path.join(perfpath, "vasprun.xml")).final_energy
else:
e_perf = float(
open(os.path.join(
perfpath,
"OSZICAR")).readlines()[-1].split('E0=')[1].split()[0])
efermi = self.get_fermi_energy(perf_dir)
struct_perf = self.get_structure(perf_dir)
perf_species = dict()
for site in struct_perf:
if (str(site.specie) not in perf_species):
perf_species[str(site.specie)] = 1
else:
perf_species[str(site.specie)] += 1
#print 'Perfect composition: ', perf_species
#First Loop through the conditions for the defects
for conditions, potentials in chempot.items():
self.e_defects[conditions] = dict()
# Loop through each defect
for ddir in sorted(def_dir):
def_meta = Metadata(metafile='%s/%s/metadata.txt' %
(self.directory, ddir))
if scsize == def_meta.read_data('scaling_size'):
label = def_meta.read_data(
'defect_label') + '_q=' + def_meta.read_data('charge')
charge = int(def_meta.read_data('charge'))
if os.path.isfile(
os.path.join(self.directory, ddir, "vasprun.xml")):
energy = pmg.io.vaspio.vasp_output.Vasprun(
self.directory + '/' + ddir +
'/vasprun.xml').final_energy
else:
energy = float(
open(self.directory + '/' + ddir +
'/OSZICAR').readlines()[-1].split('E0=')
[1].split()[0])
structure = self.get_structure(ddir)
#if (label not in self.e_defects[conditions]):
# self.e_defects[conditions][label] = list()
# Find out how many atoms of each type are in the defects
def_species = dict()
for site in structure.sites:
if (site.specie not in def_species):
def_species[site.specie] = 1
else:
def_species[site.specie] += 1
# Find the differences in the number of each atom type
# between the perfect and the defect
struct_diff = dict()
for specie, number in def_species.items():
try:
nperf = perf_species[str(specie)]
except KeyError:
nperf = 0
struct_diff[str(specie)] = number - nperf
# Get the potential alignment correction
alignment = self.get_potential_alignment(perf_dir, ddir)
# Calculate the base DFE energy
e_def = energy - e_perf # E_defect - E_perf
for specie, number in struct_diff.items():
mu = potentials[str(specie)]
e_def -= (number * mu)
e_def += charge * (efermi + alignment
) # Add in the shift here!
#print '%-15s%-5i%12.5f%12.5f%12.5f%12.5f' % (label.split('_')[1], charge, energy, e_perf, efermi, alignment)
#print 'DFE = %f' % e_def
self.e_defects[conditions][label] = e_def
def get_total_energy(self, directory):
"""Returns the total energy from a directory"""
abspath = '%s/%s/' % (self.directory, directory)
if ('vasprun.xml' in os.listdir(abspath)):
# Modified from the PyMatGen Vasprun.final_energy() function to return E_0
return Vasprun(
'%s/vasprun.xml' %
abspath).ionic_steps[-1]["electronic_steps"][-1]["e_0_energy"]
def get_fermi_energy(self, directory):
"""Returns the Fermi energy from a directory"""
abspath = '%s/%s/' % (self.directory, directory)
if ('vasprun.xml' in os.listdir(abspath)):
return Vasprun('%s/vasprun.xml' % abspath).efermi
elif ('OUTCAR' in os.listdir(abspath)):
return Outcar('%s/OUTCAR' % abspath).efermi
def get_structure(self, directory):
"""Returns the final structure from an optimization"""
abspath = '%s/%s/' % (self.directory, directory)
if ('vasprun.xml' in os.listdir(abspath)):
return Vasprun('%s/vasprun.xml' % abspath).final_structure
elif ('CONTCAR' in os.listdir(abspath)):
return pmg.read_structure('%s/CONTCAR' % abspath)
def get_potential_alignment(self, perf_dir, def_dir):
"""Returns the potential alignment correction used in charge defects"""
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
abs_path_perf = '%s/%s/' % (self.directory, perf_dir)
abs_path_def = '%s/%s/' % (self.directory, def_dir)
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
pa = PotentialAlignment()
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
if ('OUTCAR' in os.listdir(abs_path_perf)):
perfect_info = pa.read_outcar('%s/%s' % (abs_path_perf, 'OUTCAR'))
defect_info = pa.read_outcar('%s/%s' % (abs_path_def, 'OUTCAR'))
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
return pa.get_potential_alignment(perfect_info, defect_info)
def get_defect_formation_energies(self, scsize):
if not self.e_defects:
self._calculate_defect_formation_energies(scsize)
return self.e_defects
@property
def defect_formation_energies(self):
return self.get_defect_formation_energies(scsize)
@property
def dfe(self):
return self.get_defect_formation_energies(scsize)
def print_table(self, scsize):
if not self.e_defects:
self._calculate_defect_formation_energies(scsize)
myfile = MASTFile()
for conditions, defects in self.e_defects.items():
myfile.data.append(
'\n\nDefect formation energies for %s conditions.\n' %
conditions.upper())
myfile.data.append('%-20s | %10s\n' % ('Defect', 'DFE'))
myfile.data.append('---------------------------------\n')
for defect, energies in defects.items():
for energy in energies:
myfile.data.append('%-14s(q=%2i) | %8.4f\n' %
(defect, energy[0], energy[1]))
myfile.data.append(str()) # Add a blank line here
myfile.data.append('---------------------------------\n')
myfile.to_file(os.path.join(os.getcwd(), "dfe.txt"))
for line in myfile.data:
print line.strip()
