def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.section_end = '$end'
self.delimiter = ' ' # how we're breaking up each line
self.section_parsers = {\
'mast' : self.parse_mast_section,
'structure' : self.parse_structure_section,
'scaling' : self.parse_scaling_section,
'ingredients' : self.parse_ingredients_section,
'defects' : self.parse_defects_section,
'recipe' : self.parse_recipe_section,
'neb' : self.parse_neb_section,
'chemical_potentials' : self.parse_chemical_potentials_section,
'summary' : self.parse_summary_section,
'personal_recipe' : self.parse_personal_recipe_section
}
scratchpath = dirutil.get_mast_scratch_path()
inputlocation = os.path.dirname(self.keywords['inputfile'])
if (inputlocation == ""):
self.logger = loggerutils.get_mast_logger("mast input parser")
elif scratchpath not in inputlocation:
self.logger = loggerutils.get_mast_logger("mast input parser")
else:
self.logger = loggerutils.get_mast_logger("mast input parser %s" %
inputlocation)
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.recdir = self.keywords['recdir']
self.input_options = None
self.timestamp=""
self.asctime=""
self.recipe_plan = None
self.logger = loggerutils.initialize_short_logger(os.path.join(get_mast_control_path(),"mast.log"))
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.indeploop = "indeploop"
self.loop_delim = ","
self.loop_start = "("
self.loop_end = ")"
self.baseinput = MASTFile(self.keywords['inputfile'])
self.pegloop1 = "pegloop1"
self.pegloop2 = "pegloop2"
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.recdir = self.keywords['recdir']
self.input_options = None
self.timestamp = ""
self.asctime = ""
self.recipe_plan = None
self.logger = loggerutils.initialize_short_logger(
os.path.join(get_mast_control_path(), "mast.log"))
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.indeploop = "indeploop"
self.loop_delim = ","
self.loop_start = "("
self.loop_end = ")"
self.baseinput = MASTFile(self.keywords['inputfile'])
self.pegloop1 = "pegloop1"
self.pegloop2 = "pegloop2"
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.recipe_file = self.keywords['recipeFile']
self.input_options = self.keywords['inputOptions']
self.structure = self.keywords['structure']
self.work_dir = self.keywords['workingDirectory']
self.logger = loggerutils.get_mast_logger("recipe setup %s" % self.work_dir)
self.metafile = Metadata(metafile='%s/metadata.txt' % self.work_dir)
self.logger.debug('Setting up the recipe based on the personal recipe contents passed in self.recipe_file')
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.input_options = self.keywords["inputOptions"]
self.template_file = self.keywords["templateFile"]
self.personal_recipe = self.keywords["personalRecipe"]
self.ingredient_list = list()
self.metafile = Metadata(metafile="%s/metadata.txt" % self.keywords["working_directory"])
self.chunks = list()
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.input_options = self.keywords['inputOptions']
self.template_file = self.keywords['templateFile']
self.personal_recipe = self.keywords['personalRecipe']
self.ingredient_list = list()
self.metafile = Metadata(metafile='%s/metadata.txt' %
self.keywords['working_directory'])
self.chunks = list()
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.input_options = None
self.origin_dir=""
self.timestamp=""
self.asctime=""
self.working_directory=""
self.sysname=""
self.recipe_plan = None
self.logger = loggerutils.initialize_short_logger(os.path.join(get_mast_control_path(),"mast_input.log"))
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.input_options = None
self.origin_dir = ""
self.timestamp = ""
self.asctime = ""
self.working_directory = ""
self.sysname = ""
self.recipe_plan = None
self.logger = loggerutils.initialize_short_logger(
os.path.join(get_mast_control_path(), "mast_input.log"))
def __init__(self, allowed_keys, **kwargs):
allowed_keys_base = dict()
allowed_keys_base.update(allowed_keys)
MASTObj.__init__(self, allowed_keys_base, **kwargs)
work_dir = '/'.join(self.keywords['name'].split('/')[:-1])
topmeta = Metadata(metafile='%s/metadata.txt' % work_dir)
data = topmeta.read_data(self.keywords['name'].split('/')[-1])
self.meta_dict = dict()
if data:
for datum in data.split(';'):
self.meta_dict[datum.split(':')[0]] = datum.split(':')[1].strip()
self.metafile = Metadata(metafile='%s/metadata.txt' % self.keywords['name'])
self.program = self.keywords['program_keys']['mast_program'].lower()
self.logger = loggerutils.get_mast_logger(self.keywords['name'])
sdir=os.path.join(os.path.dirname(self.keywords['name']),"structure_index_files")
if os.path.exists(sdir):
self.atomindex = AtomIndex(structure_index_directory=sdir)
else:
self.atomindex = None
if self.program == 'vasp':
self.checker = VaspChecker(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
self.errhandler = VaspError(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
elif self.program == 'vasp_neb':
self.checker = VaspNEBChecker(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
self.errhandler = VaspNEBError(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
elif self.program == 'phon':
self.checker = PhonChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = PhonError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
elif self.program == 'lammps':
self.checker = LammpsChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
elif self.program =='structopt':
self.checker = StructoptChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
else:
allowed_keys={'name','program_keys','structure'}
self.checker = GenericChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.recipe_file = self.keywords['recipeFile']
self.input_options = self.keywords['inputOptions']
self.structure = self.keywords['structure']
self.work_dir = self.keywords['workingDirectory']
self.logger = loggerutils.get_mast_logger("recipe setup %s" %
self.work_dir)
self.metafile = Metadata(metafile='%s/metadata.txt' % self.work_dir)
self.logger.debug(
'Setting up the recipe based on the personal recipe contents passed in self.recipe_file'
)
def __init__(self, **kwargs):
allowed_keys = {
'input_options': (InputOptions, None, 'Input options'),
'structure_index_directory': (str, "structure_index_files", "Structure index directory")
}
MASTObj.__init__(self, allowed_keys, **kwargs)
self.logger = loggerutils.get_mast_logger("atom_indexing")
self.sdir = self.keywords['structure_index_directory']
self.input_options = self.keywords['input_options']
if self.input_options == None:
return
self.scaling = self.input_options.get_item('scaling')
self.logger.info("Scaling: %s" % self.scaling)
if self.scaling == None:
self.scaling = dict()
self.startstr = self.input_options.get_item('structure','structure')
self.atomcount=1
return
def __init__(self, **kwargs):
allowed_keys = {
'input_options': (InputOptions, None, 'Input options'),
'structure_index_directory':
(str, "structure_index_files", "Structure index directory")
}
MASTObj.__init__(self, allowed_keys, **kwargs)
self.logger = loggerutils.get_mast_logger("atom_indexing")
self.sdir = self.keywords['structure_index_directory']
self.input_options = self.keywords['input_options']
if self.input_options == None:
return
self.scaling = self.input_options.get_item('scaling')
self.logger.info("Scaling: %s" % self.scaling)
if self.scaling == None:
self.scaling = dict()
self.startstr = self.input_options.get_item('structure', 'structure')
self.atomcount = 1
return
def __init__(self, **kwargs):
allowed_keys = {
"struc_work1": (
Structure,
None,
"First working Pymatgen Structure object (e.g. create a defect, or use work1 and work2 to interpolate positions)",
),
"struc_work2": (Structure, None, "Second working Pymatgen Structure object"),
"struc_init": (Structure, None, "Initial structure at the beginning of the MAST recipe"),
"scaling_size": (str, None, "Scaling size"),
"name": (str, get_mast_control_path(), "Name of ingredient"),
}
MASTObj.__init__(self, allowed_keys, **kwargs)
rname = os.path.dirname(self.keywords["name"])
self.logger = loggerutils.get_mast_logger(rname)
self.metafile = Metadata(metafile="%s/metadata.txt" % self.keywords["name"])
self.scaleinput = ""
self.transform_scaling_size()
return
def __init__(self, **kwargs):
allowed_keys = {
'struc_work1':
(Structure, None,
'First working Pymatgen Structure object (e.g. create a defect, or use work1 and work2 to interpolate positions)'
),
'struc_work2':
(Structure, None, 'Second working Pymatgen Structure object'),
'struc_init':
(Structure, None,
'Initial structure at the beginning of the MAST recipe'),
'scaling_size': (str, None, 'Scaling size'),
'name': (str, get_mast_control_path(), 'Name of ingredient')
}
MASTObj.__init__(self, allowed_keys, **kwargs)
rname = os.path.dirname(self.keywords['name'])
self.logger = loggerutils.get_mast_logger(rname)
self.metafile = Metadata(metafile='%s/metadata.txt' %
self.keywords['name'])
self.scaleinput = ""
self.transform_scaling_size()
return
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.section_end = '$end'
self.delimiter = ' ' # how we're breaking up each line
self.section_parsers = {\
'mast' : self.parse_mast_section,
'structure' : self.parse_structure_section,
'scaling' : self.parse_scaling_section,
'ingredients' : self.parse_ingredients_section,
'defects' : self.parse_defects_section,
'recipe' : self.parse_recipe_section,
'neb' : self.parse_neb_section,
'chemical_potentials' : self.parse_chemical_potentials_section,
'summary' : self.parse_summary_section,
'personal_recipe' : self.parse_personal_recipe_section
}
scratchpath = dirutil.get_mast_scratch_path()
inputlocation = os.path.dirname(self.keywords['inputfile'])
if (inputlocation == ""):
self.logger = loggerutils.get_mast_logger("mast input parser")
elif scratchpath not in inputlocation:
self.logger = loggerutils.get_mast_logger("mast input parser")
else:
self.logger = loggerutils.get_mast_logger("mast input parser %s" % inputlocation)
def __init__(self, allowed_keys, **kwargs):
allowed_keys_base = dict()
allowed_keys_base.update(allowed_keys)
MASTObj.__init__(self, allowed_keys_base, **kwargs)
self.logger = loggerutils.get_mast_logger(self.keywords['name'])
def __init__(self, allowed_keys, **kwargs):
allowed_keys_base = dict()
allowed_keys_base.update(allowed_keys)
MASTObj.__init__(self, allowed_keys_base, **kwargs)
work_dir = '/'.join(self.keywords['name'].split('/')[:-1])
topmeta = Metadata(metafile='%s/metadata.txt' % work_dir)
data = topmeta.read_data(self.keywords['name'].split('/')[-1])
self.meta_dict = dict()
if data:
for datum in data.split(';'):
self.meta_dict[datum.split(':')[0]] = datum.split(
':')[1].strip()
self.metafile = Metadata(metafile='%s/metadata.txt' %
self.keywords['name'])
self.program = self.keywords['program_keys']['mast_program'].lower()
self.logger = loggerutils.get_mast_logger(self.keywords['name'])
sdir = os.path.join(os.path.dirname(self.keywords['name']),
"structure_index_files")
if os.path.exists(sdir):
self.atomindex = AtomIndex(structure_index_directory=sdir)
else:
self.atomindex = None
if self.program == 'vasp':
self.checker = VaspChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = VaspError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'vasp_neb':
self.checker = VaspNEBChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = VaspNEBError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'phon':
self.checker = PhonChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = PhonError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'lammps':
self.checker = LammpsChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'structopt':
self.checker = StructoptChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
else:
allowed_keys = {'name', 'program_keys', 'structure'}
self.checker = GenericChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)