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 test_set_structure_from_inputs(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
compare_struct = pymatgen.io.vaspio.Poscar.from_file(
"nebphononsposcar").structure
self.assertEqual(myoptions.options['structure']['structure'],
compare_struct)
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 test_parse(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
print myoptions.options.keys()
self.assertItemsEqual(
myoptions.options.keys(),
['mast', 'structure', 'defects', 'recipe', 'ingredients', 'neb'])
def test_perform_element_mapping(self):
myip = InputParser(inputfile="element_mapping.inp")
myoptions = myip.parse()
self.assertItemsEqual(myoptions.options.keys(), [
'mast', 'structure', 'defects', 'recipe', 'ingredients', 'neb',
'chemical_potentials'
])
self.assertEqual(
myoptions.options['defects']['defects']['group1']['subdefect_1']
['symbol'], 'Xe')
self.assertEqual(
myoptions.options['defects']['defects']['group1']['subdefect_2']
['symbol'], 'Ar')
self.assertEqual(
myoptions.options['defects']['defects']['group2']['subdefect_1']
['symbol'], 'Ar')
self.assertEqual(
myoptions.options['defects']['defects']['group2']['subdefect_2']
['symbol'], 'Xe')
self.assertEqual(
myoptions.options['neb']['nebs']['group1-group2']['lines'][0][0],
'Ar')
self.assertEqual(
myoptions.options['neb']['nebs']['group1-group2']['lines'][1][0],
'Xe')
def test_parse_defect_formation(self):
myip = InputParser(inputfile="defect_formation_energy.inp")
myoptions = myip.parse()
print myoptions.options.keys()
self.assertItemsEqual(myoptions.options.keys(), [
'mast', 'structure', 'defects', 'recipe', 'ingredients',
'chemical_potentials', 'summary'
])
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 test_perform_element_mapping(self):
myip = InputParser(inputfile="element_mapping.inp")
myoptions = myip.parse()
self.assertItemsEqual(myoptions.options.keys(),['mast','structure','defects','recipe','ingredients','neb','chemical_potentials'])
self.assertEqual(myoptions.options['defects']['defects']['group1']['subdefect_1']['symbol'],'Xe')
self.assertEqual(myoptions.options['defects']['defects']['group1']['subdefect_2']['symbol'],'Ar')
self.assertEqual(myoptions.options['defects']['defects']['group2']['subdefect_1']['symbol'],'Ar')
self.assertEqual(myoptions.options['defects']['defects']['group2']['subdefect_2']['symbol'],'Xe')
self.assertEqual(myoptions.options['neb']['nebs']['group1-group2']['lines'][0][0],'Ar')
self.assertEqual(myoptions.options['neb']['nebs']['group1-group2']['lines'][1][0],'Xe')
def test_parse_defect_formation(self):
myip = InputParser(inputfile="defect_formation_energy.inp")
myoptions = myip.parse()
print myoptions.options.keys()
self.assertItemsEqual(myoptions.options.keys(),['mast','structure','defects','recipe','ingredients','chemical_potentials','summary'])
def test_parse(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
print myoptions.options.keys()
self.assertItemsEqual(myoptions.options.keys(),['mast','structure','defects','recipe','ingredients','neb'])
def test_set_structure_from_inputs(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
compare_struct = pymatgen.io.vaspio.Poscar.from_file("nebphononsposcar").structure
self.assertEqual(myoptions.options['structure']['structure'],compare_struct)
def test_validate_execs(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
myoptions.options['ingredients']['global'].pop('mast_exec')
myoptions.options['ingredients']['diffcoeff'].pop('mast_exec')
self.assertRaises(MASTError,myip.validate_execs,myoptions)
def test_validate_execs(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
myoptions = myip.parse()
myoptions.options['ingredients']['global'].pop('mast_exec')
myoptions.options['ingredients']['diffcoeff'].pop('mast_exec')
self.assertRaises(MASTError, myip.validate_execs, myoptions)