def __init__(self, inputtxt="", plot_threshold=0.01):
"""Initialize defect formation energy ingredient
Args:
inputtxt <str>: Input text file, containing:
dfe_label1=perfect_label defected_label
dfe_label2=perfect_label defected_label
dfe_label3=perfect_label defected_label etc.
bandgap_lda_or_gga=<float>
bandgap_hse_or_expt=<float>
plot_threshold <float>: Plotting threshold value
"""
self.logger = loggerutils.get_mast_logger("DFE ingredient")
self.ingdir = os.getcwd() #Should be run in current directory
self.recdir = os.path.dirname(self.ingdir)
self.plot_threshold = plot_threshold
ipdir = os.path.join(self.recdir, 'input.inp')
os.chdir(self.recdir) #change to recipe directory
ipparser = InputParser(inputfile=ipdir)
self.input_options = ipparser.parse()
os.chdir(self.ingdir) #change back to ingredient directory
self.dirs = dict()
self.bandgap_lda_or_gga = 0.0
self.bandgap_hse_or_expt = 0.0
self.read_input_file(inputtxt)
self.e_defects = dict()
def test_parse(self):
#ipfile='small_workflow_with_scaling.inp'
ipfile = 'phonon_with_neb.inp'
workdir = os.path.join(testdir, 'workdir')
shutil.copy(os.path.join(testdir, ipfile), workdir)
input_file = os.path.join(workdir, ipfile)
parser_obj = InputParser(inputfile=input_file)
input_options = parser_obj.parse()
recipe_file_contents = input_options.get_item('recipe', 'recipe_file')
myrtp = RecipeTemplateParser(inputOptions=input_options,
working_directory=workdir,
templateFile=recipe_file_contents,
personalRecipe=input_file)
parsed_lines = myrtp.parse()
output_parsed = MASTFile()
output_parsed.data = list(parsed_lines)
output_parsed.to_file('workdir/personal_recipe_test_output.txt')
self.assertEquals(len(myrtp.chunks), 5)
#mypr = MASTFile(pr)
#for line in mypr.data:
# print line.rstrip()
compare_pr = MASTFile(
os.path.join(testdir, 'compare',
'personal_recipe_test_output.txt'))
self.assertEquals(parsed_lines, compare_pr.data)
def __init__(self, inputtxt="", plot_threshold=0.01):
"""Initialize defect formation energy ingredient
Args:
inputtxt <str>: Input text file, containing:
dfe_label1=perfect_label defected_label
dfe_label2=perfect_label defected_label
dfe_label3=perfect_label defected_label etc.
bandgap_lda_or_gga=<float>
bandgap_hse_or_expt=<float>
plot_threshold <float>: Plotting threshold value
"""
self.logger = loggerutils.get_mast_logger("DFE ingredient")
self.ingdir = os.getcwd() #Should be run in current directory
self.recdir = os.path.dirname(self.ingdir)
self.plot_threshold = plot_threshold
ipdir = os.path.join(self.recdir,'input.inp')
os.chdir(self.recdir) #change to recipe directory
ipparser = InputParser(inputfile=ipdir)
self.input_options = ipparser.parse()
os.chdir(self.ingdir) #change back to ingredient directory
self.dirs = dict()
self.bandgap_lda_or_gga = 0.0
self.bandgap_hse_or_expt = 0.0
self.read_input_file(inputtxt)
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_inputpythoncreator(self):
raise SkipTest
myip = InputParser(inputfile='mast.inp')
myoptions=myip.parse()
myipc = InputPythonCreator(input_options=myoptions)
mylines=myipc.print_input_options()
myfile = MASTFile()
myfile.data = mylines
myfile.to_file("./input_python_created")
#print mylines
self.assertTrue(filecmp.cmp("input_python_created","test_input_python_created"))
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_parse(self):
#ipfile='small_workflow_with_scaling.inp'
ipfile='phonon_with_neb.inp'
workdir = os.path.join(testdir,'workdir')
shutil.copy(os.path.join(testdir,ipfile),workdir)
input_file = os.path.join(workdir,ipfile)
parser_obj = InputParser(inputfile=input_file)
input_options = parser_obj.parse()
recipe_file_contents = input_options.get_item('recipe','recipe_file')
myrtp = RecipeTemplateParser(inputOptions=input_options,
working_directory=workdir,
templateFile=recipe_file_contents,
personalRecipe=input_file)
parsed_lines = myrtp.parse()
output_parsed = MASTFile()
output_parsed.data = list(parsed_lines)
output_parsed.to_file('workdir/personal_recipe_test_output.txt')
self.assertEquals(len(myrtp.chunks),5)
#mypr = MASTFile(pr)
#for line in mypr.data:
# print line.rstrip()
compare_pr = MASTFile(os.path.join(testdir,'compare','personal_recipe_test_output.txt'))
self.assertEquals(parsed_lines, compare_pr.data)
def test_inputparser(self):
raise SkipTest
myip = InputParser(inputfile='mast.inp')
myoptions=myip.parse()
print myoptions
self.assertEqual(True,True)
def set_input_options(self):
"""Set input options.
"""
parser_obj = InputParser(inputfile=self.keywords['inputfile'])
self.input_options = parser_obj.parse()
def set_input_options(self):
"""Set input options.
"""
parser_obj = InputParser(inputfile=self.keywords['inputfile'])
self.input_options = parser_obj.parse()