def _init_outcar(self, path):
"""Init with a filepath."""
self._parsed_data = {}
self._parsable_items = self.__class__.PARSABLE_ITEMS
self._data_obj = SingleFile(path=path)
# Since OUTCAR can be fairly large, we will parse it only
# once and store the parsevasp Outcar object.
try:
self._outcar = Outcar(file_path=path, logger=self._logger)
except SystemExit:
self._logger.warning('Parsevasp exited abruptly. Returning None.')
self._outcar = None
def outcar_parser(request, tmpdir_factory):
"""Load OUTCAR file.
"""
testdir = os.path.dirname(__file__)
outcarfile = testdir + '/OUTCAR'
tmpfile = str(tmpdir_factory.mktemp('data').join('OUTCAR'))
outcar_truncate(request.param, outcarfile, tmpfile)
outcar = Outcar(file_path=tmpfile)
return outcar
def outcar_parser(request):
"""A fixture that loads OUTCAR."""
try:
name = request.param
except AttributeError:
# Test not parametrized
name = 'OUTCAR'
testdir = os.path.dirname(__file__)
outcarfile = testdir + '/' + name
outcar = Outcar(file_path=outcarfile)
return outcar
def outcar_parser_file_objects(request, tmpdir_factory):
"""Load OUTCAR file from a file object.
"""
testdir = os.path.dirname(__file__)
outcarfile = testdir + '/OUTCAR'
tmpfile = str(tmpdir_factory.mktemp('data').join('OUTCAR'))
outcar_truncate(request.param, outcarfile, tmpfile)
outcar = None
with open(tmpfile) as file_handler:
outcar = Outcar(file_handler=file_handler)
return outcar
def outcar_parser_file_objects(request):
"""A fixture that loads OUTCAR using file object."""
try:
name = request.param
except AttributeError:
# Test not parametrized
name = 'OUTCAR'
testdir = os.path.dirname(__file__)
outcarfile = testdir + '/' + name
outcar = None
with open(outcarfile) as file_handler:
outcar = Outcar(file_handler=file_handler)
return outcar
def test_crashed_outcar(outcar_parser):
"""Test incomplete OUTCAR"""
testdir = os.path.dirname(__file__)
outcarfile = os.path.join(testdir, 'OUTCAR.crashed')
with pytest.raises(SystemExit):
outcar = Outcar(file_path=outcarfile)
class OutcarParser(BaseFileParser):
"""
Interface to parsevasp's OUTCAR parser.
The quantities listed here are not yet ejected in the xml file:
- symmetries
- elastic moduli
And we can thus not fully rely on the xml parser.
No possibilities to write OUTCAR files have been implemented.
"""
PARSABLE_ITEMS = {
'elastic_moduli': {
'inputs': [],
'name': 'elastic_moduli',
'prerequisites': []
},
'symmetries': {
'inputs': [],
'name': 'symmetries',
'prerequisites': []
},
'symmetries_extended': {
'inputs': [],
'name': 'symmetries',
'prerequisites': []
},
'magnetization': {
'inputs': [],
'name': 'magnetization',
'prerequisites': []
},
'site_magnetization': {
'inputs': [],
'name': 'site_magnetization',
'prerequisites': []
},
'run_stats': {
'inputs': [],
'name': 'run_stats',
'prerequisites': [],
}
}
def __init__(self, *args, **kwargs):
"""
Initialize OUTCAR parser
file_path : str
File path.
data : SingleFileData
AiiDA Data class install to store a single file.
settings : ParserSettings
"""
super(OutcarParser, self).__init__(*args, **kwargs)
self._outcar = None
self._settings = kwargs.get('settings', None)
if 'file_path' in kwargs:
self._init_outcar(kwargs['file_path'])
if 'data' in kwargs:
self._init_outcar(kwargs['data'].get_file_abs_path())
def _init_outcar(self, path):
"""Init with a filepath."""
self._parsed_data = {}
self._parsable_items = self.__class__.PARSABLE_ITEMS
self._data_obj = SingleFile(path=path)
# Since OUTCAR can be fairly large, we will parse it only
# once and store the parsevasp Outcar object.
try:
self._outcar = Outcar(file_path=path, logger=self._logger)
except SystemExit:
self._logger.warning('Parsevasp exited abruptly. Returning None.')
self._outcar = None
def _parse_file(self, inputs):
# Since all quantities will be returned by properties, we can't pass
# inputs as a parameter, so we store them in self._parsed_data
for key, value in inputs.items():
self._parsed_data[key] = value
quantities_to_parse = DEFAULT_OPTIONS.get('quantities_to_parse')
if self._settings is not None and self._settings.quantity_names_to_parse:
quantities_to_parse = self._settings.quantity_names_to_parse
result = {}
if self._outcar is None:
# parsevasp threw an exception, which means OUTCAR could not be parsed.
for quantity in quantities_to_parse:
if quantity in self.parsable_items:
result[quantity] = None
return result
for quantity in quantities_to_parse:
if quantity in self.parsable_items:
result[quantity] = getattr(self, quantity)
return result
@property
def run_stats(self):
"""Fetch the run statistics"""
return self._outcar.get_run_stats()
@property
def symmetries(self):
"""Fetch the symmetries, but only the point group (if it exists)."""
extended = self.symmetries_extended
sym = {
'point_group': extended['point_group'],
'primitive_translations': extended['primitive_translations'],
'num_space_group_operations': extended['num_space_group_operations']
}
return sym
@property
def symmetries_extended(self):
"""Fetch the symmetries, including operations etc."""
sym = self._outcar.get_symmetry()
# We do not want to store the site symmetry at origin
sym = {key: value for key, value in sym.items() if key != 'site_symmetry_at_origin'}
return sym
@property
def elastic_moduli(self):
"""Fetch the elastic moduli."""
return self._outcar.get_elastic_moduli()
@property
def magnetization(self):
"""Fetch the full cell magnetization."""
return self._outcar.get_magnetization()['full_cell']
@property
def site_magnetization(self):
"""Fetch the site dependent magnetization."""
return self._outcar.get_magnetization()