def __init__(self, **kwargs):
"""
Valid keyword arguments for a Component are:
*ucp_a*: unit cell property along a axis
*ucp_b*: unit cell property along b axis
*d001*: unit cell length c (aka d001)
*default_c*: default c-value
*delta_c*: the variation in basal spacing due to defects
*layer_atoms*: ObjectListStore of layer Atoms
*interlayer_atoms*: ObjectListStore of interlayer Atoms
*atom_relations*: ObjectListStore of AtomRelations
*inherit_ucp_a*: whether or not to inherit the ucp_a property from
the linked component (if linked)
*inherit_ucp_b*: whether or not to inherit the ucp_b property from
the linked component (if linked)
*inherit_d001*: whether or not to inherit the d001 property from
the linked component (if linked)
*inherit_default_c*: whether or not to inherit the default_c
property from the linked component (if linked)
*inherit_delta_c*: whether or not to inherit the delta_c
property from the linked component (if linked)
*inherit_layer_atoms*: whether or not to inherit the layer_atoms
property from the linked component (if linked)
*inherit_interlayer_atoms*: whether or not to inherit the
interlayer_atoms property from the linked component (if linked)
*inherit_atom_relations*: whether or not to inherit the
atom_relations property from the linked component (if linked)
*linked_with_uuid*: the UUID for the component this one is linked
with
Deprecated, but still supported:
*linked_with_index*: the index of the component this one is
linked with in the ObjectListStore of the parent based on phase.
"""
my_kwargs = self.pop_kwargs(
kwargs, "data_name", "data_layer_atoms", "data_interlayer_atoms",
"data_atom_relations", "data_atom_ratios", "data_d001",
"data_default_c", "data_delta_c", "lattice_d", "data_cell_a",
"data_ucp_a", "data_cell_b", "data_ucp_b", "linked_with_uuid",
"linked_with_index", "inherit_cell_a", "inherit_cell_b", *[
names[0]
for names in type(self).Meta.get_local_storable_properties()
])
super(Component, self).__init__(**kwargs)
kwargs = my_kwargs
# Setup signals:
self.atoms_changed = HoldableSignal()
# Set up data object
self._data_object = ComponentData(d001=0.0, delta_c=0.0)
# Set attributes:
self.name = self.get_kwarg(kwargs, "", "name", "data_name")
# Load lists:
self.layer_atoms = self.get_list(kwargs, [],
"layer_atoms",
"data_layer_atoms",
parent=self)
self.interlayer_atoms = self.get_list(kwargs, [],
"interlayer_atoms",
"data_interlayer_atoms",
parent=self)
self.atom_relations = self.get_list(kwargs, [],
"atom_relations",
"data_atom_relations",
parent=self)
# Add all atom ratios to the AtomRelation list
for atom_ratio in self.get_list(kwargs, [],
"atom_ratios",
"data_atom_ratios",
parent=self):
self.atom_relations.append(atom_ratio)
# Observe the inter-layer atoms, and make sure they get stretched
for atom in self.interlayer_atoms:
atom.stretch_values = True
self.observe_model(atom)
# Observe the layer atoms
for atom in self.layer_atoms:
self.observe_model(atom)
# Resolve their relations and observe the atom relations
for relation in self.atom_relations:
relation.resolve_relations()
self.observe_model(relation)
# Connect signals to lists and dicts:
self._layer_atoms_observer = ListObserver(self._on_layer_atom_inserted,
self._on_layer_atom_removed,
prop_name="layer_atoms",
model=self)
self._interlayer_atoms_observer = ListObserver(
self._on_interlayer_atom_inserted,
self._on_interlayer_atom_removed,
prop_name="interlayer_atoms",
model=self)
self._atom_relations_observer = ListObserver(
self._on_atom_relation_inserted,
self._on_atom_relation_removed,
prop_name="atom_relations",
model=self)
# Update lattice values:
self.d001 = self.get_kwarg(kwargs, self._d001, "d001", "data_d001")
self._default_c = float(
self.get_kwarg(kwargs, self._d001, "default_c", "data_default_c"))
self.delta_c = float(
self.get_kwarg(kwargs, self._delta_c, "delta_c", "data_delta_c"))
self.update_lattice_d()
# Set/Create & observe unit cell properties:
ucp_a = self.get_kwarg(kwargs, None, "ucp_a", "data_ucp_a",
"data_cell_a")
if isinstance(ucp_a, float):
ucp_a = UnitCellProperty(name="cell length a",
value=ucp_a,
parent=self)
self._ucp_a = self.parse_init_arg(ucp_a,
UnitCellProperty,
child=True,
default_is_class=True,
name="Cell length a [nm]",
parent=self)
self.observe_model(self._ucp_a)
ucp_b = self.get_kwarg(kwargs, None, "ucp_b", "data_ucp_b",
"data_cell_b")
if isinstance(ucp_b, float):
ucp_b = UnitCellProperty(name="cell length b",
value=ucp_b,
parent=self)
self._ucp_b = self.parse_init_arg(ucp_b,
UnitCellProperty,
child=True,
default_is_class=True,
name="Cell length b [nm]",
parent=self)
self.observe_model(self._ucp_b)
# Set links:
self._linked_with_uuid = self.get_kwarg(kwargs, "", "linked_with_uuid")
self._linked_with_index = self.get_kwarg(kwargs, -1,
"linked_with_index")
# Set inherit flags:
self.inherit_d001 = self.get_kwarg(kwargs, False, "inherit_d001")
self.inherit_ucp_a = self.get_kwarg(kwargs, False, "inherit_ucp_a",
"inherit_cell_a")
self.inherit_ucp_b = self.get_kwarg(kwargs, False, "inherit_ucp_b",
"inherit_cell_b")
self.inherit_default_c = self.get_kwarg(kwargs, False,
"inherit_default_c")
self.inherit_delta_c = self.get_kwarg(kwargs, False, "inherit_delta_c")
self.inherit_layer_atoms = self.get_kwarg(kwargs, False,
"inherit_layer_atoms")
self.inherit_interlayer_atoms = self.get_kwarg(
kwargs, False, "inherit_interlayer_atoms")
self.inherit_atom_relations = self.get_kwarg(kwargs, False,
"inherit_atom_relations")
class Component(DataModel, Storable, RefinementGroup):
# MODEL INTEL:
__metaclass__ = PyXRDRefinableMeta
class Meta(DataModel.Meta):
properties = [
PropIntel(name="name", data_type=unicode, label="Name", is_column=True, has_widget=True, storable=True),
PropIntel(name="linked_with", data_type=object, label="Linked with", widget_type='custom', is_column=True, has_widget=True),
PropIntel(name="d001", data_type=float, label="Cell length c [nm]", is_column=True, has_widget=True, storable=True, refinable=True, minimum=0.0, maximum=5.0, inh_name="inherit_d001", stor_name="_d001", inh_from="linked_with"),
PropIntel(name="lattice_d", data_type=float, label="Lattice c length [nm]"),
PropIntel(name="default_c", data_type=float, label="Default c length [nm]", is_column=True, has_widget=True, storable=True, minimum=0.0, maximum=5.0, inh_name="inherit_default_c", stor_name="_default_c", inh_from="linked_with"),
PropIntel(name="delta_c", data_type=float, label="C length dev. [nm]", is_column=True, has_widget=True, storable=True, refinable=True, minimum=0.0, maximum=0.05, inh_name="inherit_delta_c", stor_name="_delta_c", inh_from="linked_with"),
PropIntel(name="ucp_a", data_type=object, label="Cell length a [nm]", is_column=True, has_widget=True, storable=True, refinable=True, inh_name="inherit_ucp_a", stor_name="_ucp_a", inh_from="linked_with"),
PropIntel(name="ucp_b", data_type=object, label="Cell length b [nm]", is_column=True, has_widget=True, storable=True, refinable=True, inh_name="inherit_ucp_b", stor_name="_ucp_b", inh_from="linked_with"),
PropIntel(name="inherit_d001", data_type=bool, label="Inh. cell length c", is_column=True, has_widget=True, storable=True),
PropIntel(name="inherit_ucp_b", data_type=bool, label="Inh. cell length b", is_column=True, has_widget=True, storable=True),
PropIntel(name="inherit_ucp_a", data_type=bool, label="Inh. cell length a", is_column=True, has_widget=True, storable=True),
PropIntel(name="inherit_default_c", data_type=bool, label="Inh. default length c", is_column=True, has_widget=True, storable=True),
PropIntel(name="inherit_delta_c", data_type=bool, label="Inh. c length dev.", is_column=True, has_widget=True, storable=True),
PropIntel(name="inherit_layer_atoms", data_type=bool, label="Inh. layer atoms", is_column=True, has_widget=True, storable=True),
PropIntel(name="inherit_interlayer_atoms", data_type=bool, label="Inh. interlayer atoms", is_column=True, has_widget=True, storable=True),
PropIntel(name="inherit_atom_relations", data_type=bool, label="Inh. atom relations", is_column=True, has_widget=True, storable=True),
PropIntel(name="atom_relations", data_type=object, label="Atom relations", is_column=True, has_widget=True, storable=True, widget_type="custom", refinable=True, inh_name="inherit_atom_relations", stor_name="_atom_relations", inh_from="linked_with", class_type=AtomRelation),
PropIntel(name="layer_atoms", data_type=object, label="Layer atoms", is_column=True, has_widget=True, storable=True, widget_type="custom", inh_name="inherit_layer_atoms", stor_name="_layer_atoms", inh_from="linked_with", class_type=Atom),
PropIntel(name="interlayer_atoms", data_type=object, label="Interlayer atoms", is_column=True, has_widget=True, storable=True, widget_type="custom", inh_name="inherit_interlayer_atoms", stor_name="_interlayer_atoms", inh_from="linked_with", class_type=Atom),
PropIntel(name="atoms_changed", data_type=object, is_column=False, storable=False, has_widget=False)
]
store_id = "Component"
_data_object = None
@property
def data_object(self):
weight = 0.0
self._data_object.layer_atoms = [None] * len(self.layer_atoms)
for i, atom in enumerate(self.layer_atoms):
self._data_object.layer_atoms[i] = atom.data_object
weight += atom.weight
self._data_object.interlayer_atoms = [None] * len(self.interlayer_atoms)
for i, atom in enumerate(self.interlayer_atoms):
self._data_object.interlayer_atoms[i] = atom.data_object
weight += atom.weight
self._data_object.volume = self.get_volume()
self._data_object.weight = weight
self._data_object.d001 = self.d001
self._data_object.default_c = self.default_c
self._data_object.delta_c = self.delta_c
self._data_object.lattice_d = self._lattice_d
return self._data_object
phase = property(DataModel.parent.fget, DataModel.parent.fset)
# SIGNALS:
atoms_changed = None
# UNIT CELL DIMENSION SHORTCUTS:
@property
def cell_a(self):
return self._ucp_a.value
@property
def cell_b(self):
return self._ucp_b.value
@property
def cell_c(self):
return self.d001
# PROPERTIES:
_name = ""
def get_name(self): return self._name
def set_name(self, value):
self._name = value
self.visuals_changed.emit()
def get_inherit_ucp_a(self):
return self._ucp_a.inherited
def set_inherit_ucp_a(self, value):
self._ucp_a.inherited = value
def get_inherit_ucp_b(self):
return self._ucp_b.inherited
def set_inherit_ucp_b(self, value):
self._ucp_b.inherited = value
def _set_float_data_property(self, name, value):
try: value = float(value)
except ValueError: return # ignore faulty values
setattr(self._data_object, name, value)
self.data_changed.emit()
def _set_bool_property(self, name, value):
try: value = bool(value)
except ValueError: return # ignore faulty values
if getattr(self, "_%s" % name) != value:
with self.data_changed.hold_and_emit():
setattr(self, "_%s" % name, value)
_inherit_d001 = False
def get_inherit_d001(self): return self._inherit_d001
def set_inherit_d001(self, value): self._set_bool_property("inherit_d001", value)
_inherit_default_c = False
def get_inherit_default_c(self): return self._inherit_default_c
def set_inherit_default_c(self, value): self._set_bool_property("inherit_default_c", value)
_inherit_delta_c = False
def get_inherit_delta_c(self): return self._inherit_delta_c
def set_inherit_delta_c(self, value): self._set_bool_property("inherit_delta_c", value)
_inherit_layer_atoms = False
def get_inherit_layer_atoms(self): return self._inherit_layer_atoms
def set_inherit_layer_atoms(self, value): self._set_bool_property("inherit_layer_atoms", value)
_inherit_interlayer_atoms = False
def get_inherit_interlayer_atoms(self): return self._inherit_interlayer_atoms
def set_inherit_interlayer_atoms(self, value): self._set_bool_property("inherit_interlayer_atoms", value)
_inherit_atom_relations = False
def get_inherit_atom_relations(self): return self._inherit_atom_relations
def set_inherit_atom_relations(self, value): self._set_bool_property("inherit_atom_relations", value)
_linked_with = None
_linked_with_index = None
_linked_with_uuid = None
def get_linked_with(self): return self._linked_with
def set_linked_with(self, value):
if value != self._linked_with:
if self._linked_with is not None:
self.relieve_model(self._linked_with)
self._linked_with = value
if self._linked_with is not None:
self.observe_model(self._linked_with)
else:
for prop in self.Meta.get_inheritable_properties():
setattr(self, "inherit_%s" % prop, False)
self.data_changed.emit()
# Lattice d-value
__lattice_d = 0.0
@property
def _lattice_d(self):
return self.__lattice_d;
@_lattice_d.setter
def _lattice_d(self, value):
try: value = float(value)
except ValueError: return # ignore faulty values
if self.__lattice_d != value:
self.__lattice_d = value
self.data_changed.emit()
def get_lattice_d(self): return self._lattice_d
# INHERITABLE PROPERTIES:
def _set_inheritable_property_value(self, name, value):
current = getattr(self, "_%s" % name)
if current != value:
with self.data_changed.hold_and_emit():
if name.startswith("ucp_"):
if current is not None:
self.relieve_model(current)
setattr(self, "_%s" % name, value)
if name.startswith("ucp_"):
if value is not None:
self.observe_model(value)
_ucp_a = None
def get_ucp_a(self): return self._get_inheritable_property_value("ucp_a")
def set_ucp_a(self, value): self._set_inheritable_property_value("ucp_a", value)
_ucp_b = None
def get_ucp_b(self): return self._get_inheritable_property_value("ucp_b")
def set_ucp_b(self, value): self._set_inheritable_property_value("ucp_b", value)
_d001 = 1.0
def get_d001(self): return self._get_inheritable_property_value("d001")
def set_d001(self, value): self._set_inheritable_property_value("d001", float(value))
_default_c = 1.0
def get_default_c(self): return self._get_inheritable_property_value("default_c")
def set_default_c(self, value): self._set_inheritable_property_value("default_c", float(value))
_delta_c = 0.0
def get_delta_c(self): return self._get_inheritable_property_value("delta_c")
def set_delta_c(self, value): self._set_inheritable_property_value("delta_c", float(value))
_layer_atoms = []
def get_layer_atoms(self): return self._get_inheritable_property_value("layer_atoms")
def set_layer_atoms(self, value):
with self.data_changed.hold_and_emit():
self._layer_atoms = value
_interlayer_atoms = []
def get_interlayer_atoms(self): return self._get_inheritable_property_value("interlayer_atoms")
def set_interlayer_atoms(self, value):
with self.data_changed.hold_and_emit():
self._interlayer_atoms = value
_atom_relations = []
def get_atom_relations(self): return self._get_inheritable_property_value("atom_relations")
def set_atom_relations(self, value):
with self.data_changed.hold_and_emit():
self._atom_relations = value
# Instance flag indicating whether or not linked_with & inherit flags should be saved
save_links = True
# Class flag indicating whether or not atom types in the component should be
# exported using their name rather then their project-uuid.
export_atom_types = False
# REFINEMENT GROUP IMPLEMENTATION:
@property
def refine_title(self):
return self.name
@property
def refine_descriptor_data(self):
return dict(
phase_name=self.phase.refine_title,
component_name=self.refine_title
)
# ------------------------------------------------------------
# Initialization and other internals
# ------------------------------------------------------------
def __init__(self, **kwargs):
"""
Valid keyword arguments for a Component are:
*ucp_a*: unit cell property along a axis
*ucp_b*: unit cell property along b axis
*d001*: unit cell length c (aka d001)
*default_c*: default c-value
*delta_c*: the variation in basal spacing due to defects
*layer_atoms*: ObjectListStore of layer Atoms
*interlayer_atoms*: ObjectListStore of interlayer Atoms
*atom_relations*: ObjectListStore of AtomRelations
*inherit_ucp_a*: whether or not to inherit the ucp_a property from
the linked component (if linked)
*inherit_ucp_b*: whether or not to inherit the ucp_b property from
the linked component (if linked)
*inherit_d001*: whether or not to inherit the d001 property from
the linked component (if linked)
*inherit_default_c*: whether or not to inherit the default_c
property from the linked component (if linked)
*inherit_delta_c*: whether or not to inherit the delta_c
property from the linked component (if linked)
*inherit_layer_atoms*: whether or not to inherit the layer_atoms
property from the linked component (if linked)
*inherit_interlayer_atoms*: whether or not to inherit the
interlayer_atoms property from the linked component (if linked)
*inherit_atom_relations*: whether or not to inherit the
atom_relations property from the linked component (if linked)
*linked_with_uuid*: the UUID for the component this one is linked
with
Deprecated, but still supported:
*linked_with_index*: the index of the component this one is
linked with in the ObjectListStore of the parent based on phase.
"""
my_kwargs = self.pop_kwargs(kwargs,
"data_name", "data_layer_atoms", "data_interlayer_atoms", "data_atom_relations",
"data_atom_ratios", "data_d001", "data_default_c", "data_delta_c",
"data_cell_a", "data_ucp_a", "data_cell_b", "data_ucp_b",
"linked_with_uuid", "linked_with_index", "inherit_cell_a", "inherit_cell_b",
*[names[0] for names in type(self).Meta.get_local_storable_properties()]
)
super(Component, self).__init__(**kwargs)
kwargs = my_kwargs
# Setup signals:
self.atoms_changed = HoldableSignal()
# Set up data object
self._data_object = ComponentData(
d001=0.0,
delta_c=0.0
)
# Set attributes:
self.name = self.get_kwarg(kwargs, "", "name", "data_name")
# Load lists:
self.layer_atoms = self.get_list(kwargs, [], "layer_atoms", "data_layer_atoms", parent=self)
self.interlayer_atoms = self.get_list(kwargs, [], "interlayer_atoms", "data_interlayer_atoms", parent=self)
self.atom_relations = self.get_list(kwargs, [], "atom_relations", "data_atom_relations", parent=self)
# Add all atom ratios to the AtomRelation list
for atom_ratio in self.get_list(kwargs, [], "atom_ratios", "data_atom_ratios", parent=self):
self.atom_relations.append(atom_ratio)
# Observe the inter-layer atoms, and make sure they get stretched
for atom in self.interlayer_atoms:
atom.stretch_values = True
self.observe_model(atom)
# Observe the layer atoms
for atom in self.layer_atoms:
self.observe_model(atom)
# Resolve their relations and observe the atom relations
for relation in self.atom_relations:
relation.resolve_relations()
self.observe_model(relation)
# Connect signals to lists and dicts:
self._layer_atoms_observer = ListObserver(
self._on_layer_atom_inserted,
self._on_layer_atom_removed,
prop_name="layer_atoms",
model=self
)
self._interlayer_atoms_observer = ListObserver(
self._on_interlayer_atom_inserted,
self._on_interlayer_atom_removed,
prop_name="interlayer_atoms",
model=self
)
self._atom_relations_observer = ListObserver(
self._on_atom_relation_inserted,
self._on_atom_relation_removed,
prop_name="atom_relations",
model=self
)
# Update lattice values:
self.d001 = self.get_kwarg(kwargs, self._d001, "d001", "data_d001")
self._default_c = float(self.get_kwarg(kwargs, self._d001, "default_c", "data_default_c"))
self.delta_c = float(self.get_kwarg(kwargs, self._delta_c, "delta_c", "data_delta_c"))
self.update_lattice_d()
# Set/Create & observe unit cell properties:
ucp_a = self.get_kwarg(kwargs, None, "ucp_a", "data_ucp_a", "data_cell_a")
if isinstance(ucp_a, float):
ucp_a = UnitCellProperty(name="cell length a", value=ucp_a, parent=self)
self._ucp_a = self.parse_init_arg(
ucp_a, UnitCellProperty, child=True,
default_is_class=True, name="Cell length a [nm]", parent=self
)
self.observe_model(self._ucp_a)
ucp_b = self.get_kwarg(kwargs, None, "ucp_b", "data_ucp_b", "data_cell_b")
if isinstance(ucp_b, float):
ucp_b = UnitCellProperty(name="cell length b", value=ucp_b, parent=self)
self._ucp_b = self.parse_init_arg(
ucp_b, UnitCellProperty, child=True,
default_is_class=True, name="Cell length b [nm]", parent=self
)
self.observe_model(self._ucp_b)
# Set links:
self._linked_with_uuid = self.get_kwarg(kwargs, "", "linked_with_uuid")
self._linked_with_index = self.get_kwarg(kwargs, -1, "linked_with_index")
# Set inherit flags:
self.inherit_d001 = self.get_kwarg(kwargs, False, "inherit_d001")
self.inherit_ucp_a = self.get_kwarg(kwargs, False, "inherit_ucp_a", "inherit_cell_a")
self.inherit_ucp_b = self.get_kwarg(kwargs, False, "inherit_ucp_b", "inherit_cell_b")
self.inherit_default_c = self.get_kwarg(kwargs, False, "inherit_default_c")
self.inherit_delta_c = self.get_kwarg(kwargs, False, "inherit_delta_c")
self.inherit_layer_atoms = self.get_kwarg(kwargs, False, "inherit_layer_atoms")
self.inherit_interlayer_atoms = self.get_kwarg(kwargs, False, "inherit_interlayer_atoms")
self.inherit_atom_relations = self.get_kwarg(kwargs, False, "inherit_atom_relations")
def __repr__(self):
return "Component(name='%s', linked_with=%r)" % (self.name, self.linked_with)
# ------------------------------------------------------------
# Notifications of observable properties
# ------------------------------------------------------------
@DataModel.observe("data_changed", signal=True)
def _on_data_model_changed(self, model, prop_name, info):
# Check whether the changed model is an AtomRelation or Atom, if so
# re-apply the atom_relations.
with self.data_changed.hold():
if isinstance(model, AtomRelation) or isinstance(model, Atom):
self._apply_atom_relations()
self._update_ucp_values()
if isinstance(model, UnitCellProperty):
self.data_changed.emit() # propagate signal
@DataModel.observe("removed", signal=True)
def _on_data_model_removed(self, model, prop_name, info):
# Check whether the removed component is linked with this one, if so
# clears the link and emits the data_changed signal.
if model != self and self.linked_with is not None and self.linked_with == model:
with self.data_changed.hold_and_emit():
self.linked_with = None
def _on_layer_atom_inserted(self, atom):
"""Sets the atoms parent and stretch_values property,
updates the components lattice d-value, and emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
atom.parent = self
atom.stretch_values = False
self.observe_model(atom)
self.update_lattice_d()
def _on_layer_atom_removed(self, atom):
"""Clears the atoms parent, updates the components lattice d-value, and
emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
self.relieve_model(atom)
atom.parent = None
self.update_lattice_d()
def _on_interlayer_atom_inserted(self, atom):
"""Sets the atoms parent and stretch_values property,
and emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
atom.stretch_values = True
atom.parent = self
def _on_interlayer_atom_removed(self, atom):
"""Clears the atoms parent property,
and emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
atom.parent = None
def _on_atom_relation_inserted(self, item):
item.parent = self
self.observe_model(item)
self._apply_atom_relations()
def _on_atom_relation_removed(self, item):
self.relieve_model(item)
item.parent = None
self._apply_atom_relations()
# ------------------------------------------------------------
# Input/Output stuff
# ------------------------------------------------------------
def resolve_json_references(self):
for atom in self.layer_atoms:
atom.resolve_json_references()
for atom in self.interlayer_atoms:
atom.resolve_json_references()
self._ucp_a.resolve_json_references()
self._ucp_a.update_value()
self._ucp_b.resolve_json_references()
self._ucp_b.update_value()
if getattr(self, "_linked_with_uuid", None):
self.linked_with = type(type(self)).object_pool.get_object(self._linked_with_uuid)
del self._linked_with_uuid
elif getattr(self, "_linked_with_index", None) and self._linked_with_index != -1:
warn("The use of object indeces is deprected since version 0.4. Please switch to using object UUIDs.", DeprecationWarning)
self.linked_with = self.parent.based_on.components.get_user_from_index(self._linked_with_index)
del self._linked_with_index
@classmethod
def save_components(cls, components, filename):
"""
Saves multiple components to a single file.
"""
Component.export_atom_types = True
for comp in components:
comp.save_links = False
with zipfile.ZipFile(filename, 'w', compression=COMPRESSION) as zfile:
for component in components:
zfile.writestr(component.uuid, component.dump_object())
for comp in components:
comp.save_links = True
Component.export_atom_types = False
# After export we change all the UUID's
# This way, we're sure that we're not going to import objects with
# duplicate UUID's!
type(cls).object_pool.change_all_uuids()
@classmethod
def load_components(cls, filename, parent=None):
"""
Returns multiple components loaded from a single file.
"""
# Before import, we change all the UUID's
# This way we're sure that we're not going to import objects
# with duplicate UUID's!
type(cls).object_pool.change_all_uuids()
if zipfile.is_zipfile(filename):
with zipfile.ZipFile(filename, 'r') as zfile:
for uuid in zfile.namelist():
yield cls.load_object(zfile.open(uuid), parent=parent)
else:
yield cls.load_object(filename, parent=parent)
def json_properties(self):
if self.phase == None or not self.save_links:
retval = Storable.json_properties(self)
for prop in self.Meta.all_properties:
if prop.inh_name:
retval[prop.inh_name] = False
else:
retval = Storable.json_properties(self)
retval["linked_with_uuid"] = self.linked_with.uuid if self.linked_with is not None else ""
return retval
# ------------------------------------------------------------
# Methods & Functions
# ------------------------------------------------------------
def get_factors(self, range_stl):
"""
Get the structure factor for the given range of sin(theta)/lambda values.
:param range_stl: A 1D numpy ndarray
"""
return get_factors(range_stl, self.data_object)
def get_interlayer_stretch_factors(self):
z_factor = (self.cell_c - self.lattice_d) / (self.default_c - self.lattice_d)
return self.lattice_d, z_factor
def update_lattice_d(self):
"""
Updates the lattice_d attribute for this :class:`~.Component`.
Should normally not be called from outside the component.
"""
for atom in self.layer_atoms:
self._lattice_d = float(max(self.lattice_d, atom.default_z))
def _apply_atom_relations(self):
"""
Applies the :class:`~..atom_relations.AtomRelation` objects
in this component. Should normally not be called from outside the component.
"""
with self.data_changed.hold_and_emit():
for relation in self.atom_relations:
# Clear the 'driven by' flags:
relation.driven_by_other = False
for relation in self.atom_relations:
# Apply the relations, will also take care of flag setting:
relation.apply_relation()
def _update_ucp_values(self):
"""
Updates the :class:`~..unit_cell_prop.UnitCellProperty` objects in this
component. Should normally not be called from outside the component.
"""
with self.data_changed.hold():
for ucp in [self._ucp_a, self._ucp_b]:
ucp.update_value()
def get_volume(self):
"""
Get the volume for this :class:`~.Component`.
Will always return a value >= 1e-25, to prevent division-by-zero
errors in calculation code.
"""
return max(self.cell_a * self.cell_b * self.cell_c, 1e-25)
def get_weight(self):
"""
Get the total atomic weight for this
:class:`~.Component`.
"""
weight = 0
for atom in (self.layer_atoms + self.interlayer_atoms):
weight += atom.weight
return weight
# ------------------------------------------------------------
# AtomRelation list related
# ------------------------------------------------------------
def move_atom_relation_up(self, relation):
"""
Move the passed :class:`~..atom_relations.AtomRelation`
up one slot
"""
index = self.atom_relations.index(relation)
del self.atom_relations[index]
self.atom_relations.insert(max(index - 1, 0), relation)
def move_atom_relation_down(self, relation):
"""
Move the passed :class:`~..atom_relations.AtomRelation`
down one slot
"""
index = self.atom_relations.index(relation)
del self.atom_relations[index]
self.atom_relations.insert(min(index + 1, len(self.atom_relations)), relation)
pass # end of class
class Component(RefinementGroup, DataModel, Storable):
# MODEL INTEL:
__metaclass__ = PyXRDRefinableMeta
class Meta(DataModel.Meta):
properties = [
PropIntel(name="name",
data_type=unicode,
label="Name",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="linked_with",
data_type=object,
label="Linked with",
widget_type='custom',
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="d001",
data_type=float,
label="Cell length c [nm]",
is_column=True,
has_widget=True,
storable=True,
refinable=True,
minimum=0.0,
maximum=5.0,
inh_name="inherit_d001",
stor_name="_d001",
inh_from="linked_with"),
PropIntel(name="lattice_d",
data_type=float,
label="Lattice c length [nm]"),
PropIntel(name="default_c",
data_type=float,
label="Default c length [nm]",
is_column=True,
has_widget=True,
storable=True,
minimum=0.0,
maximum=5.0,
inh_name="inherit_default_c",
stor_name="_default_c",
inh_from="linked_with"),
PropIntel(name="delta_c",
data_type=float,
label="C length dev. [nm]",
is_column=True,
has_widget=True,
storable=True,
refinable=True,
minimum=0.0,
maximum=0.05,
inh_name="inherit_delta_c",
stor_name="_delta_c",
inh_from="linked_with"),
PropIntel(name="ucp_a",
data_type=object,
label="Cell length a [nm]",
is_column=True,
has_widget=True,
storable=True,
refinable=True,
inh_name="inherit_ucp_a",
stor_name="_ucp_a",
inh_from="linked_with"),
PropIntel(name="ucp_b",
data_type=object,
label="Cell length b [nm]",
is_column=True,
has_widget=True,
storable=True,
refinable=True,
inh_name="inherit_ucp_b",
stor_name="_ucp_b",
inh_from="linked_with"),
PropIntel(name="inherit_d001",
data_type=bool,
label="Inh. cell length c",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="inherit_ucp_b",
data_type=bool,
label="Inh. cell length b",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="inherit_ucp_a",
data_type=bool,
label="Inh. cell length a",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="inherit_default_c",
data_type=bool,
label="Inh. default length c",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="inherit_delta_c",
data_type=bool,
label="Inh. c length dev.",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="inherit_layer_atoms",
data_type=bool,
label="Inh. layer atoms",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="inherit_interlayer_atoms",
data_type=bool,
label="Inh. interlayer atoms",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="inherit_atom_relations",
data_type=bool,
label="Inh. atom relations",
is_column=True,
has_widget=True,
storable=True),
PropIntel(name="atom_relations",
data_type=object,
label="Atom relations",
is_column=True,
has_widget=True,
storable=True,
widget_type="custom",
refinable=True,
inh_name="inherit_atom_relations",
stor_name="_atom_relations",
inh_from="linked_with",
class_type=AtomRelation),
PropIntel(name="layer_atoms",
data_type=object,
label="Layer atoms",
is_column=True,
has_widget=True,
storable=True,
widget_type="custom",
inh_name="inherit_layer_atoms",
stor_name="_layer_atoms",
inh_from="linked_with",
class_type=Atom),
PropIntel(name="interlayer_atoms",
data_type=object,
label="Interlayer atoms",
is_column=True,
has_widget=True,
storable=True,
widget_type="custom",
inh_name="inherit_interlayer_atoms",
stor_name="_interlayer_atoms",
inh_from="linked_with",
class_type=Atom),
PropIntel(name="atoms_changed",
data_type=object,
is_column=False,
storable=False,
has_widget=False)
]
store_id = "Component"
_data_object = None
@property
def data_object(self):
weight = 0.0
self._data_object.layer_atoms = [None] * len(self.layer_atoms)
for i, atom in enumerate(self.layer_atoms):
self._data_object.layer_atoms[i] = atom.data_object
weight += atom.weight
self._data_object.interlayer_atoms = [None] * len(
self.interlayer_atoms)
for i, atom in enumerate(self.interlayer_atoms):
self._data_object.interlayer_atoms[i] = atom.data_object
weight += atom.weight
self._data_object.volume = self.get_volume()
self._data_object.weight = weight
self._data_object.d001 = self.d001
self._data_object.default_c = self.default_c
self._data_object.delta_c = self.delta_c
self._data_object.lattice_d = self._lattice_d
return self._data_object
phase = property(DataModel.parent.fget, DataModel.parent.fset)
# SIGNALS:
atoms_changed = None
# UNIT CELL DIMENSION SHORTCUTS:
@property
def cell_a(self):
return self._ucp_a.value
@property
def cell_b(self):
return self._ucp_b.value
@property
def cell_c(self):
return self.d001
# PROPERTIES:
_name = ""
def get_name(self):
return self._name
def set_name(self, value):
self._name = value
self.visuals_changed.emit()
def get_inherit_ucp_a(self):
return self._ucp_a.inherited
def set_inherit_ucp_a(self, value):
self._ucp_a.inherited = value
def get_inherit_ucp_b(self):
return self._ucp_b.inherited
def set_inherit_ucp_b(self, value):
self._ucp_b.inherited = value
def _set_float_data_property(self, name, value):
try:
value = float(value)
except ValueError:
return # ignore faulty values
setattr(self._data_object, name, value)
self.data_changed.emit()
def _set_bool_property(self, name, value):
try:
value = bool(value)
except ValueError:
return # ignore faulty values
if getattr(self, "_%s" % name) != value:
with self.data_changed.hold_and_emit():
setattr(self, "_%s" % name, value)
_inherit_d001 = False
def get_inherit_d001(self):
return self._inherit_d001
def set_inherit_d001(self, value):
self._set_bool_property("inherit_d001", value)
_inherit_default_c = False
def get_inherit_default_c(self):
return self._inherit_default_c
def set_inherit_default_c(self, value):
self._set_bool_property("inherit_default_c", value)
_inherit_delta_c = False
def get_inherit_delta_c(self):
return self._inherit_delta_c
def set_inherit_delta_c(self, value):
self._set_bool_property("inherit_delta_c", value)
_inherit_layer_atoms = False
def get_inherit_layer_atoms(self):
return self._inherit_layer_atoms
def set_inherit_layer_atoms(self, value):
self._set_bool_property("inherit_layer_atoms", value)
_inherit_interlayer_atoms = False
def get_inherit_interlayer_atoms(self):
return self._inherit_interlayer_atoms
def set_inherit_interlayer_atoms(self, value):
self._set_bool_property("inherit_interlayer_atoms", value)
_inherit_atom_relations = False
def get_inherit_atom_relations(self):
return self._inherit_atom_relations
def set_inherit_atom_relations(self, value):
self._set_bool_property("inherit_atom_relations", value)
_linked_with = None
_linked_with_index = None
_linked_with_uuid = None
def get_linked_with(self):
return self._linked_with
def set_linked_with(self, value):
if value != self._linked_with:
if self._linked_with is not None:
self.relieve_model(self._linked_with)
self._linked_with = value
if self._linked_with is not None:
self.observe_model(self._linked_with)
else:
for prop in self.Meta.get_inheritable_properties():
setattr(self, "inherit_%s" % prop, False)
self.data_changed.emit()
# Lattice d-value
__lattice_d = 0.0
@property
def _lattice_d(self):
return self.__lattice_d
@_lattice_d.setter
def _lattice_d(self, value):
try:
value = float(value)
except ValueError:
return # ignore faulty values
if self.__lattice_d != value:
self.__lattice_d = value
self.data_changed.emit()
def get_lattice_d(self):
return self._lattice_d
# INHERITABLE PROPERTIES:
def _set_inheritable_property_value(self, name, value):
current = getattr(self, "_%s" % name)
if current != value:
with self.data_changed.hold_and_emit():
if name.startswith("ucp_"):
if current is not None:
self.relieve_model(current)
setattr(self, "_%s" % name, value)
if name.startswith("ucp_"):
if value is not None:
self.observe_model(value)
_ucp_a = None
def get_ucp_a(self):
return self._get_inheritable_property_value("ucp_a")
def set_ucp_a(self, value):
self._set_inheritable_property_value("ucp_a", value)
_ucp_b = None
def get_ucp_b(self):
return self._get_inheritable_property_value("ucp_b")
def set_ucp_b(self, value):
self._set_inheritable_property_value("ucp_b", value)
_d001 = 1.0
def get_d001(self):
return self._get_inheritable_property_value("d001")
def set_d001(self, value):
self._set_inheritable_property_value("d001", float(value))
_default_c = 1.0
def get_default_c(self):
return self._get_inheritable_property_value("default_c")
def set_default_c(self, value):
self._set_inheritable_property_value("default_c", float(value))
_delta_c = 0.0
def get_delta_c(self):
return self._get_inheritable_property_value("delta_c")
def set_delta_c(self, value):
self._set_inheritable_property_value("delta_c", float(value))
_layer_atoms = []
def get_layer_atoms(self):
return self._get_inheritable_property_value("layer_atoms")
def set_layer_atoms(self, value):
with self.data_changed.hold_and_emit():
self._layer_atoms = value
_interlayer_atoms = []
def get_interlayer_atoms(self):
return self._get_inheritable_property_value("interlayer_atoms")
def set_interlayer_atoms(self, value):
with self.data_changed.hold_and_emit():
self._interlayer_atoms = value
_atom_relations = []
def get_atom_relations(self):
return self._get_inheritable_property_value("atom_relations")
def set_atom_relations(self, value):
with self.data_changed.hold_and_emit():
self._atom_relations = value
# Instance flag indicating whether or not linked_with & inherit flags should be saved
save_links = True
# Class flag indicating whether or not atom types in the component should be
# exported using their name rather then their project-uuid.
export_atom_types = False
# REFINEMENT GROUP IMPLEMENTATION:
@property
def refine_title(self):
return self.name
@property
def refine_descriptor_data(self):
return dict(phase_name=self.phase.refine_title,
component_name=self.refine_title)
# ------------------------------------------------------------
# Initialization and other internals
# ------------------------------------------------------------
def __init__(self, **kwargs):
"""
Valid keyword arguments for a Component are:
*ucp_a*: unit cell property along a axis
*ucp_b*: unit cell property along b axis
*d001*: unit cell length c (aka d001)
*default_c*: default c-value
*delta_c*: the variation in basal spacing due to defects
*layer_atoms*: ObjectListStore of layer Atoms
*interlayer_atoms*: ObjectListStore of interlayer Atoms
*atom_relations*: ObjectListStore of AtomRelations
*inherit_ucp_a*: whether or not to inherit the ucp_a property from
the linked component (if linked)
*inherit_ucp_b*: whether or not to inherit the ucp_b property from
the linked component (if linked)
*inherit_d001*: whether or not to inherit the d001 property from
the linked component (if linked)
*inherit_default_c*: whether or not to inherit the default_c
property from the linked component (if linked)
*inherit_delta_c*: whether or not to inherit the delta_c
property from the linked component (if linked)
*inherit_layer_atoms*: whether or not to inherit the layer_atoms
property from the linked component (if linked)
*inherit_interlayer_atoms*: whether or not to inherit the
interlayer_atoms property from the linked component (if linked)
*inherit_atom_relations*: whether or not to inherit the
atom_relations property from the linked component (if linked)
*linked_with_uuid*: the UUID for the component this one is linked
with
Deprecated, but still supported:
*linked_with_index*: the index of the component this one is
linked with in the ObjectListStore of the parent based on phase.
"""
my_kwargs = self.pop_kwargs(
kwargs, "data_name", "data_layer_atoms", "data_interlayer_atoms",
"data_atom_relations", "data_atom_ratios", "data_d001",
"data_default_c", "data_delta_c", "lattice_d", "data_cell_a",
"data_ucp_a", "data_cell_b", "data_ucp_b", "linked_with_uuid",
"linked_with_index", "inherit_cell_a", "inherit_cell_b", *[
names[0]
for names in type(self).Meta.get_local_storable_properties()
])
super(Component, self).__init__(**kwargs)
kwargs = my_kwargs
# Setup signals:
self.atoms_changed = HoldableSignal()
# Set up data object
self._data_object = ComponentData(d001=0.0, delta_c=0.0)
# Set attributes:
self.name = self.get_kwarg(kwargs, "", "name", "data_name")
# Load lists:
self.layer_atoms = self.get_list(kwargs, [],
"layer_atoms",
"data_layer_atoms",
parent=self)
self.interlayer_atoms = self.get_list(kwargs, [],
"interlayer_atoms",
"data_interlayer_atoms",
parent=self)
self.atom_relations = self.get_list(kwargs, [],
"atom_relations",
"data_atom_relations",
parent=self)
# Add all atom ratios to the AtomRelation list
for atom_ratio in self.get_list(kwargs, [],
"atom_ratios",
"data_atom_ratios",
parent=self):
self.atom_relations.append(atom_ratio)
# Observe the inter-layer atoms, and make sure they get stretched
for atom in self.interlayer_atoms:
atom.stretch_values = True
self.observe_model(atom)
# Observe the layer atoms
for atom in self.layer_atoms:
self.observe_model(atom)
# Resolve their relations and observe the atom relations
for relation in self.atom_relations:
relation.resolve_relations()
self.observe_model(relation)
# Connect signals to lists and dicts:
self._layer_atoms_observer = ListObserver(self._on_layer_atom_inserted,
self._on_layer_atom_removed,
prop_name="layer_atoms",
model=self)
self._interlayer_atoms_observer = ListObserver(
self._on_interlayer_atom_inserted,
self._on_interlayer_atom_removed,
prop_name="interlayer_atoms",
model=self)
self._atom_relations_observer = ListObserver(
self._on_atom_relation_inserted,
self._on_atom_relation_removed,
prop_name="atom_relations",
model=self)
# Update lattice values:
self.d001 = self.get_kwarg(kwargs, self._d001, "d001", "data_d001")
self._default_c = float(
self.get_kwarg(kwargs, self._d001, "default_c", "data_default_c"))
self.delta_c = float(
self.get_kwarg(kwargs, self._delta_c, "delta_c", "data_delta_c"))
self.update_lattice_d()
# Set/Create & observe unit cell properties:
ucp_a = self.get_kwarg(kwargs, None, "ucp_a", "data_ucp_a",
"data_cell_a")
if isinstance(ucp_a, float):
ucp_a = UnitCellProperty(name="cell length a",
value=ucp_a,
parent=self)
self._ucp_a = self.parse_init_arg(ucp_a,
UnitCellProperty,
child=True,
default_is_class=True,
name="Cell length a [nm]",
parent=self)
self.observe_model(self._ucp_a)
ucp_b = self.get_kwarg(kwargs, None, "ucp_b", "data_ucp_b",
"data_cell_b")
if isinstance(ucp_b, float):
ucp_b = UnitCellProperty(name="cell length b",
value=ucp_b,
parent=self)
self._ucp_b = self.parse_init_arg(ucp_b,
UnitCellProperty,
child=True,
default_is_class=True,
name="Cell length b [nm]",
parent=self)
self.observe_model(self._ucp_b)
# Set links:
self._linked_with_uuid = self.get_kwarg(kwargs, "", "linked_with_uuid")
self._linked_with_index = self.get_kwarg(kwargs, -1,
"linked_with_index")
# Set inherit flags:
self.inherit_d001 = self.get_kwarg(kwargs, False, "inherit_d001")
self.inherit_ucp_a = self.get_kwarg(kwargs, False, "inherit_ucp_a",
"inherit_cell_a")
self.inherit_ucp_b = self.get_kwarg(kwargs, False, "inherit_ucp_b",
"inherit_cell_b")
self.inherit_default_c = self.get_kwarg(kwargs, False,
"inherit_default_c")
self.inherit_delta_c = self.get_kwarg(kwargs, False, "inherit_delta_c")
self.inherit_layer_atoms = self.get_kwarg(kwargs, False,
"inherit_layer_atoms")
self.inherit_interlayer_atoms = self.get_kwarg(
kwargs, False, "inherit_interlayer_atoms")
self.inherit_atom_relations = self.get_kwarg(kwargs, False,
"inherit_atom_relations")
def __repr__(self):
return "Component(name='%s', linked_with=%r)" % (self.name,
self.linked_with)
# ------------------------------------------------------------
# Notifications of observable properties
# ------------------------------------------------------------
@DataModel.observe("data_changed", signal=True)
def _on_data_model_changed(self, model, prop_name, info):
# Check whether the changed model is an AtomRelation or Atom, if so
# re-apply the atom_relations.
with self.data_changed.hold():
if isinstance(model, AtomRelation) or isinstance(model, Atom):
self._apply_atom_relations()
self._update_ucp_values()
if isinstance(model, UnitCellProperty):
self.data_changed.emit() # propagate signal
@DataModel.observe("removed", signal=True)
def _on_data_model_removed(self, model, prop_name, info):
# Check whether the removed component is linked with this one, if so
# clears the link and emits the data_changed signal.
if model != self and self.linked_with is not None and self.linked_with == model:
with self.data_changed.hold_and_emit():
self.linked_with = None
def _on_layer_atom_inserted(self, atom):
"""Sets the atoms parent and stretch_values property,
updates the components lattice d-value, and emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
atom.parent = self
atom.stretch_values = False
self.observe_model(atom)
self.update_lattice_d()
def _on_layer_atom_removed(self, atom):
"""Clears the atoms parent, updates the components lattice d-value, and
emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
self.relieve_model(atom)
atom.parent = None
self.update_lattice_d()
def _on_interlayer_atom_inserted(self, atom):
"""Sets the atoms parent and stretch_values property,
and emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
atom.stretch_values = True
atom.parent = self
def _on_interlayer_atom_removed(self, atom):
"""Clears the atoms parent property,
and emits a data_changed signal"""
with self.data_changed.hold_and_emit():
with self.atoms_changed.hold_and_emit():
atom.parent = None
def _on_atom_relation_inserted(self, item):
item.parent = self
self.observe_model(item)
self._apply_atom_relations()
def _on_atom_relation_removed(self, item):
self.relieve_model(item)
item.parent = None
self._apply_atom_relations()
# ------------------------------------------------------------
# Input/Output stuff
# ------------------------------------------------------------
def resolve_json_references(self):
for atom in self.layer_atoms:
atom.resolve_json_references()
for atom in self.interlayer_atoms:
atom.resolve_json_references()
self._ucp_a.resolve_json_references()
self._ucp_a.update_value()
self._ucp_b.resolve_json_references()
self._ucp_b.update_value()
if getattr(self, "_linked_with_uuid", None):
self.linked_with = type(type(self)).object_pool.get_object(
self._linked_with_uuid)
del self._linked_with_uuid
elif getattr(self, "_linked_with_index",
None) and self._linked_with_index != -1:
warn(
"The use of object indeces is deprected since version 0.4. Please switch to using object UUIDs.",
DeprecationWarning)
self.linked_with = self.parent.based_on.components.get_user_from_index(
self._linked_with_index)
del self._linked_with_index
@classmethod
def save_components(cls, components, filename):
"""
Saves multiple components to a single file.
"""
Component.export_atom_types = True
for comp in components:
comp.save_links = False
with zipfile.ZipFile(filename, 'w', compression=COMPRESSION) as zfile:
for component in components:
zfile.writestr(component.uuid, component.dump_object())
for comp in components:
comp.save_links = True
Component.export_atom_types = False
# After export we change all the UUID's
# This way, we're sure that we're not going to import objects with
# duplicate UUID's!
type(cls).object_pool.change_all_uuids()
@classmethod
def load_components(cls, filename, parent=None):
"""
Returns multiple components loaded from a single file.
"""
# Before import, we change all the UUID's
# This way we're sure that we're not going to import objects
# with duplicate UUID's!
type(cls).object_pool.change_all_uuids()
if zipfile.is_zipfile(filename):
with zipfile.ZipFile(filename, 'r') as zfile:
for uuid in zfile.namelist():
obj = JSONParser.parse(zfile.open(uuid))
obj.parent = parent
yield obj
else:
obj = JSONParser.parse(filename)
obj.parent = parent
yield obj
def json_properties(self):
if self.phase == None or not self.save_links:
retval = Storable.json_properties(self)
for prop in self.Meta.all_properties:
if prop.inh_name:
retval[prop.inh_name] = False
else:
retval = Storable.json_properties(self)
retval[
"linked_with_uuid"] = self.linked_with.uuid if self.linked_with is not None else ""
return retval
# ------------------------------------------------------------
# Methods & Functions
# ------------------------------------------------------------
def get_factors(self, range_stl):
"""
Get the structure factor for the given range of sin(theta)/lambda values.
:param range_stl: A 1D numpy ndarray
"""
return get_factors(range_stl, self.data_object)
def get_interlayer_stretch_factors(self):
z_factor = (self.cell_c - self.lattice_d) / (self.default_c -
self.lattice_d)
return self.lattice_d, z_factor
def update_lattice_d(self):
"""
Updates the lattice_d attribute for this :class:`~.Component`.
Should normally not be called from outside the component.
"""
for atom in self.layer_atoms:
self._lattice_d = float(max(self.lattice_d, atom.default_z))
def _apply_atom_relations(self):
"""
Applies the :class:`~..atom_relations.AtomRelation` objects
in this component. Should normally not be called from outside the component.
"""
with self.data_changed.hold_and_emit():
for relation in self.atom_relations:
# Clear the 'driven by' flags:
relation.driven_by_other = False
for relation in self.atom_relations:
# Apply the relations, will also take care of flag setting:
relation.apply_relation()
def _update_ucp_values(self):
"""
Updates the :class:`~..unit_cell_prop.UnitCellProperty` objects in this
component. Should normally not be called from outside the component.
"""
with self.data_changed.hold():
for ucp in [self._ucp_a, self._ucp_b]:
ucp.update_value()
def get_volume(self):
"""
Get the volume for this :class:`~.Component`.
Will always return a value >= 1e-25, to prevent division-by-zero
errors in calculation code.
"""
return max(self.cell_a * self.cell_b * self.cell_c, 1e-25)
def get_weight(self):
"""
Get the total atomic weight for this
:class:`~.Component`.
"""
weight = 0
for atom in (self.layer_atoms + self.interlayer_atoms):
weight += atom.weight
return weight
# ------------------------------------------------------------
# AtomRelation list related
# ------------------------------------------------------------
def move_atom_relation_up(self, relation):
"""
Move the passed :class:`~..atom_relations.AtomRelation`
up one slot
"""
index = self.atom_relations.index(relation)
del self.atom_relations[index]
self.atom_relations.insert(max(index - 1, 0), relation)
def move_atom_relation_down(self, relation):
"""
Move the passed :class:`~..atom_relations.AtomRelation`
down one slot
"""
index = self.atom_relations.index(relation)
del self.atom_relations[index]
self.atom_relations.insert(min(index + 1, len(self.atom_relations)),
relation)
pass # end of class
def __init__(self, **kwargs):
"""
Valid keyword arguments for a Component are:
*ucp_a*: unit cell property along a axis
*ucp_b*: unit cell property along b axis
*d001*: unit cell length c (aka d001)
*default_c*: default c-value
*delta_c*: the variation in basal spacing due to defects
*layer_atoms*: ObjectListStore of layer Atoms
*interlayer_atoms*: ObjectListStore of interlayer Atoms
*atom_relations*: ObjectListStore of AtomRelations
*inherit_ucp_a*: whether or not to inherit the ucp_a property from
the linked component (if linked)
*inherit_ucp_b*: whether or not to inherit the ucp_b property from
the linked component (if linked)
*inherit_d001*: whether or not to inherit the d001 property from
the linked component (if linked)
*inherit_default_c*: whether or not to inherit the default_c
property from the linked component (if linked)
*inherit_delta_c*: whether or not to inherit the delta_c
property from the linked component (if linked)
*inherit_layer_atoms*: whether or not to inherit the layer_atoms
property from the linked component (if linked)
*inherit_interlayer_atoms*: whether or not to inherit the
interlayer_atoms property from the linked component (if linked)
*inherit_atom_relations*: whether or not to inherit the
atom_relations property from the linked component (if linked)
*linked_with_uuid*: the UUID for the component this one is linked
with
Deprecated, but still supported:
*linked_with_index*: the index of the component this one is
linked with in the ObjectListStore of the parent based on phase.
"""
my_kwargs = self.pop_kwargs(kwargs,
"data_name", "data_layer_atoms", "data_interlayer_atoms", "data_atom_relations",
"data_atom_ratios", "data_d001", "data_default_c", "data_delta_c",
"data_cell_a", "data_ucp_a", "data_cell_b", "data_ucp_b",
"linked_with_uuid", "linked_with_index", "inherit_cell_a", "inherit_cell_b",
*[names[0] for names in type(self).Meta.get_local_storable_properties()]
)
super(Component, self).__init__(**kwargs)
kwargs = my_kwargs
# Setup signals:
self.atoms_changed = HoldableSignal()
# Set up data object
self._data_object = ComponentData(
d001=0.0,
delta_c=0.0
)
# Set attributes:
self.name = self.get_kwarg(kwargs, "", "name", "data_name")
# Load lists:
self.layer_atoms = self.get_list(kwargs, [], "layer_atoms", "data_layer_atoms", parent=self)
self.interlayer_atoms = self.get_list(kwargs, [], "interlayer_atoms", "data_interlayer_atoms", parent=self)
self.atom_relations = self.get_list(kwargs, [], "atom_relations", "data_atom_relations", parent=self)
# Add all atom ratios to the AtomRelation list
for atom_ratio in self.get_list(kwargs, [], "atom_ratios", "data_atom_ratios", parent=self):
self.atom_relations.append(atom_ratio)
# Observe the inter-layer atoms, and make sure they get stretched
for atom in self.interlayer_atoms:
atom.stretch_values = True
self.observe_model(atom)
# Observe the layer atoms
for atom in self.layer_atoms:
self.observe_model(atom)
# Resolve their relations and observe the atom relations
for relation in self.atom_relations:
relation.resolve_relations()
self.observe_model(relation)
# Connect signals to lists and dicts:
self._layer_atoms_observer = ListObserver(
self._on_layer_atom_inserted,
self._on_layer_atom_removed,
prop_name="layer_atoms",
model=self
)
self._interlayer_atoms_observer = ListObserver(
self._on_interlayer_atom_inserted,
self._on_interlayer_atom_removed,
prop_name="interlayer_atoms",
model=self
)
self._atom_relations_observer = ListObserver(
self._on_atom_relation_inserted,
self._on_atom_relation_removed,
prop_name="atom_relations",
model=self
)
# Update lattice values:
self.d001 = self.get_kwarg(kwargs, self._d001, "d001", "data_d001")
self._default_c = float(self.get_kwarg(kwargs, self._d001, "default_c", "data_default_c"))
self.delta_c = float(self.get_kwarg(kwargs, self._delta_c, "delta_c", "data_delta_c"))
self.update_lattice_d()
# Set/Create & observe unit cell properties:
ucp_a = self.get_kwarg(kwargs, None, "ucp_a", "data_ucp_a", "data_cell_a")
if isinstance(ucp_a, float):
ucp_a = UnitCellProperty(name="cell length a", value=ucp_a, parent=self)
self._ucp_a = self.parse_init_arg(
ucp_a, UnitCellProperty, child=True,
default_is_class=True, name="Cell length a [nm]", parent=self
)
self.observe_model(self._ucp_a)
ucp_b = self.get_kwarg(kwargs, None, "ucp_b", "data_ucp_b", "data_cell_b")
if isinstance(ucp_b, float):
ucp_b = UnitCellProperty(name="cell length b", value=ucp_b, parent=self)
self._ucp_b = self.parse_init_arg(
ucp_b, UnitCellProperty, child=True,
default_is_class=True, name="Cell length b [nm]", parent=self
)
self.observe_model(self._ucp_b)
# Set links:
self._linked_with_uuid = self.get_kwarg(kwargs, "", "linked_with_uuid")
self._linked_with_index = self.get_kwarg(kwargs, -1, "linked_with_index")
# Set inherit flags:
self.inherit_d001 = self.get_kwarg(kwargs, False, "inherit_d001")
self.inherit_ucp_a = self.get_kwarg(kwargs, False, "inherit_ucp_a", "inherit_cell_a")
self.inherit_ucp_b = self.get_kwarg(kwargs, False, "inherit_ucp_b", "inherit_cell_b")
self.inherit_default_c = self.get_kwarg(kwargs, False, "inherit_default_c")
self.inherit_delta_c = self.get_kwarg(kwargs, False, "inherit_delta_c")
self.inherit_layer_atoms = self.get_kwarg(kwargs, False, "inherit_layer_atoms")
self.inherit_interlayer_atoms = self.get_kwarg(kwargs, False, "inherit_interlayer_atoms")
self.inherit_atom_relations = self.get_kwarg(kwargs, False, "inherit_atom_relations")
