def registerAtomType(self, parameters):
"""Register a new atom type. """
name = parameters['name']
if name in self._atomTypes:
raise ValueError('Found multiple definitions for atom type: '+name)
atomClass = parameters['class']
mass = _convertParameterToNumber(parameters['mass'])
element = None
if 'element' in parameters:
element = self._create_element(parameters['element'], mass)
self.non_element_types[element.name] = element
self._atomTypes[name] = self.__class__._AtomType(name, atomClass, mass, element)
if atomClass in self._atomClasses:
typeSet = self._atomClasses[atomClass]
else:
typeSet = set()
self._atomClasses[atomClass] = typeSet
typeSet.add(name)
self._atomClasses[''].add(name)
name = parameters['name']
if 'def' in parameters:
self.atomTypeDefinitions[name] = parameters['def']
if 'overrides' in parameters:
overrides = set(parameters['overrides'].split(","))
if overrides:
self.atomTypeOverrides[name] = overrides
if 'des' in parameters:
self.atomTypeDesc[name] = parameters['desc']
if 'doi' in parameters:
self.atomTypeRefs[name] = parameters['doi']
def registerAtomType(self, parameters):
"""Register a new atom type. """
name = parameters['name']
if name in self._atomTypes:
raise ValueError('Found multiple definitions for atom type: ' + name)
atom_class = parameters['class']
mass = _convertParameterToNumber(parameters['mass'])
element = None
if 'element' in parameters:
element, custom = self._create_element(parameters['element'], mass)
if custom:
self.non_element_types[element.symbol] = element
self._atomTypes[name] = self.__class__._AtomType(name, atom_class, mass, element)
if atom_class in self._atomClasses:
type_set = self._atomClasses[atom_class]
else:
type_set = set()
self._atomClasses[atom_class] = type_set
type_set.add(name)
self._atomClasses[''].add(name)
name = parameters['name']
if 'def' in parameters:
self.atomTypeDefinitions[name] = parameters['def']
if 'overrides' in parameters:
overrides = set(parameters['overrides'].split(","))
if overrides:
self.atomTypeOverrides[name] = overrides
if 'des' in parameters:
self.atomTypeDesc[name] = parameters['desc']
if 'doi' in parameters:
self.atomTypeRefs[name] = parameters['doi']
def registerAtomType(self, parameters):
"""Register a new atom type. """
name = parameters['name']
if name in self._atomTypes:
raise ValueError('Found multiple definitions for atom type: ' +
name)
atomClass = parameters['class']
mass = _convertParameterToNumber(parameters['mass'])
element = None
if 'element' in parameters:
element = parameters['element']
if not isinstance(element, elem.Element):
try:
element = elem.get_by_symbol(element)
except KeyError:
# Enables support for non-atomistic "element types"
if element not in self.non_element_types:
warnings.warn(
'Non-atomistic element type detected. '
'Creating custom element for {}'.format(element))
element = elem.Element(number=0,
mass=parameters['mass'],
name=element,
symbol=element)
self.non_element_types[element.name] = element
self._atomTypes[name] = self.__class__._AtomType(
name, atomClass, mass, element)
if atomClass in self._atomClasses:
typeSet = self._atomClasses[atomClass]
else:
typeSet = set()
self._atomClasses[atomClass] = typeSet
typeSet.add(name)
self._atomClasses[''].add(name)
name = parameters['name']
if 'def' in parameters:
self._atomTypeDefinitions[name] = parameters['def']
if 'overrides' in parameters:
overrides = set(parameters['overrides'].split(","))
if overrides:
self._atomTypeOverrides[name] = overrides
if 'des' in parameters:
self._atomTypeDesc[name] = parameters['desc']
def registerAtomType(self, parameters):
"""Register a new atom type. """
name = parameters['name']
if name in self._atomTypes:
raise ValueError('Found multiple definitions for atom type: '+name)
atomClass = parameters['class']
mass = _convertParameterToNumber(parameters['mass'])
element = None
if 'element' in parameters:
element = parameters['element']
if not isinstance(element, elem.Element):
try:
element = elem.get_by_symbol(element)
except KeyError:
# Enables support for non-atomistic "element types"
if element not in self.non_element_types:
warnings.warn('Non-atomistic element type detected. '
'Creating custom element for {}'.format(element))
element = elem.Element(number=0,
mass=parameters['mass'],
name=element,
symbol=element)
self.non_element_types[element.name] = element
self._atomTypes[name] = self.__class__._AtomType(name, atomClass, mass, element)
if atomClass in self._atomClasses:
typeSet = self._atomClasses[atomClass]
else:
typeSet = set()
self._atomClasses[atomClass] = typeSet
typeSet.add(name)
self._atomClasses[''].add(name)
name = parameters['name']
if 'def' in parameters:
self._atomTypeDefinitions[name] = parameters['def']
if 'overrides' in parameters:
overrides = set(parameters['overrides'].split(","))
if overrides:
self._atomTypeOverrides[name] = overrides
if 'des' in parameters:
self._atomTypeDesc[name] = parameters['desc']
