def create_recipe_plan(self):
"""Creates a recipe object which has the ingredients and dependency information
"""
import inspect
#'GRJ DEBUG: %s.%s' % (self.__class__.__name__, inspect.stack()[0][3])
[how_to_update, parents_to_check, how_to_run] = ru.read_recipe(self.recipe_file)
recipe_obj = RecipePlan(self.work_dir)
ingredlist = how_to_run.keys()
for ingred in ingredlist:
self.update_top_meta_for_ingred(ingred)
ingredtype = how_to_run[ingred]
recipe_obj.ingredients[ingred]="I" #set all to initialized
recipe_obj.ingred_input_options[ingred] = self.get_my_ingredient_options(ingred, ingredtype)
if not os.path.isdir(os.path.join(self.work_dir, ingred)):
self.create_ingredient(recipe_obj.ingred_input_options[ingred])
recipe_obj.write_methods[ingred] = self.get_method_list(ingredtype, "mast_write_method")
recipe_obj.ready_methods[ingred] = self.get_method_list(ingredtype, "mast_ready_method")
recipe_obj.run_methods[ingred] = self.get_method_list(ingredtype, "mast_run_method")
recipe_obj.complete_methods[ingred] = self.get_method_list(ingredtype, "mast_complete_method")
recipe_obj.update_methods[ingred] = dict()
for ichild in how_to_update[ingred].keys():
updingredtype = how_to_update[ingred][ichild]
recipe_obj.update_methods[ingred][ichild] = self.get_method_list(updingredtype, "mast_update_children_method")
recipe_obj.parents_to_check = dict(parents_to_check)
recipe_obj.summary_options = self.get_summary_options()
return recipe_obj
def create_recipe_plan(self):
"""Creates a recipe object which has the ingredients and dependency information
"""
import inspect
#'GRJ DEBUG: %s.%s' % (self.__class__.__name__, inspect.stack()[0][3])
[how_to_update, parents_to_check,
how_to_run] = ru.read_recipe(self.recipe_file)
recipe_obj = RecipePlan(self.work_dir)
ingredlist = how_to_run.keys()
for ingred in ingredlist:
self.update_top_meta_for_ingred(ingred)
ingredtype = how_to_run[ingred]
recipe_obj.ingredients[ingred] = "I" #set all to initialized
recipe_obj.ingred_input_options[
ingred] = self.get_my_ingredient_options(ingred, ingredtype)
if not os.path.isdir(os.path.join(self.work_dir, ingred)):
self.create_ingredient(recipe_obj.ingred_input_options[ingred])
recipe_obj.write_methods[ingred] = self.get_method_list(
ingredtype, "mast_write_method")
recipe_obj.ready_methods[ingred] = self.get_method_list(
ingredtype, "mast_ready_method")
recipe_obj.run_methods[ingred] = self.get_method_list(
ingredtype, "mast_run_method")
recipe_obj.complete_methods[ingred] = self.get_method_list(
ingredtype, "mast_complete_method")
recipe_obj.update_methods[ingred] = dict()
for ichild in how_to_update[ingred].keys():
updingredtype = how_to_update[ingred][ichild]
recipe_obj.update_methods[ingred][
ichild] = self.get_method_list(
updingredtype, "mast_update_children_method")
recipe_obj.parents_to_check = dict(parents_to_check)
recipe_obj.summary_options = self.get_summary_options()
return recipe_obj
def test_read_recipe(self):
fss_recipe = MASTFile(os.path.join(testdir, "fss_recipe.txt"))
fss_recipe_lines = fss_recipe.data
fss_recipe_lines.pop(0) # remove recipe name
[htu, ptc, htr] = recipeutility.read_recipe(fss_recipe_lines)
self.assertEqual(htu["defect_2x2x3_int1_opt"]["neb_2x2x3_int1-int2_opt"], "relax_to_neb")
self.assertItemsEqual(ptc["neb_1x2x4_int1-int2_opt"], ["defect_1x2x4_int1_opt", "defect_1x2x4_int2_opt"])
self.assertEqual(htr["phonon_1x1x2_int1-int2_w0"], "phonon")
def test_read_recipe(self):
file_contents = MASTFile(os.path.join(testdir,'neb_int_personalized'))
[htu, ptc,htr]=recipeutility.read_recipe(file_contents.data)
#print htu
#print ptc
#print htr
#print rname
self.assertEqual(htu['neb_group1-group3_q=n1_opt2']['neb_group1-group3_q=n1_stat'],'neb_to_nebstat')
self.assertItemsEqual(ptc['neb_group1-group3_q=n1_opt1'],['defect_group1_q=n1_stat','defect_group3_q=n1_stat'])
self.assertEqual(htr['neb_group1-group3_q=n1_stat'],'nebstat_to_nebphonon')
def test_read_recipe(self):
fss_recipe = MASTFile(os.path.join(testdir, 'fss_recipe.txt'))
fss_recipe_lines = fss_recipe.data
fss_recipe_lines.pop(0) #remove recipe name
[htu, ptc, htr] = recipeutility.read_recipe(fss_recipe_lines)
self.assertEqual(
htu['defect_2x2x3_int1_opt']['neb_2x2x3_int1-int2_opt'],
'relax_to_neb')
self.assertItemsEqual(
ptc['neb_1x2x4_int1-int2_opt'],
['defect_1x2x4_int1_opt', 'defect_1x2x4_int2_opt'])
self.assertEqual(htr['phonon_1x1x2_int1-int2_w0'], 'phonon')
def test_read_recipe(self):
file_contents = MASTFile(os.path.join(testdir, 'neb_int_personalized'))
[htu, ptc, htr] = recipeutility.read_recipe(file_contents.data)
#print htu
#print ptc
#print htr
#print rname
self.assertEqual(
htu['neb_group1-group3_q=n1_opt2']['neb_group1-group3_q=n1_stat'],
'neb_to_nebstat')
self.assertItemsEqual(
ptc['neb_group1-group3_q=n1_opt1'],
['defect_group1_q=n1_stat', 'defect_group3_q=n1_stat'])
self.assertEqual(htr['neb_group1-group3_q=n1_stat'],
'nebstat_to_nebphonon')
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 _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
