def __init__(self, universe, name, units,
data=None, dtype=None, element_shape=None):
api.validate_type(universe, Universe, "universe")
self._universe = universe
api.validate_label(name, "name")
self._name = name
api.validate_units(units, "units")
self._units = units
if data is None:
if dtype is None:
dtype = N.float64
if dtype not in self._allowed_dtypes:
raise ValueError("dtype must be " +
" or ".join(str(t)
for t in self._allowed_dtypes))
if element_shape is None:
element_shape = ()
array_shape = (self._number_of_values(),) + element_shape
self._data = N.empty(array_shape, dtype)
else:
api.validate_array(data, None, self._allowed_dtypes, "data")
if dtype is not None and data.dtype != dtype:
raise ValueError("elements of data array do not have "
"the requested type")
if data.shape[0] != self._number_of_values():
raise ValueError("data array has incorrect shape")
if element_shape is not None and data.shape[1:] != element_shape:
raise ValueError("elements of data array do not have "
"the requested shape")
self._data = data
def __init__(self, universe, indices, selection_type):
api.validate_type(universe, Universe, "universe")
api.validate_array(indices, None,
[N.uint8, N.uint16, N.uint32, N.uint64], "indices")
api.validate_value(selection_type, self._allowed_types,
"selection_type")
self._universe = universe
self._indices = indices
self._type = selection_type
def __init__(self, universe, positions, cell_parameters):
api.validate_type(universe, Universe, "universe")
api.validate_array(positions, (universe.number_of_sites, 3),
self._allowed_dtypes, "positions")
api.validate_array(cell_parameters,
universe._cell_parameter_array_shapes
[universe.cell_shape],
[positions.dtype], "cell_parameters")
self._universe = universe
self._positions = positions
self._cell_parameters = cell_parameters
def __init__(self, universe, name, units, data, property_type):
api.validate_type(universe, Universe, "universe")
api.validate_label(name, "name")
api.validate_units(units, "units")
api.validate_array(data, None, self._allowed_dtypes, "data")
api.validate_value(property_type, self._allowed_types, "property_type")
self._universe = universe
self._name = name
self._units = units
self._data = data
self._type = property_type
def __init__(self, universe, name, units, data):
api.validate_type(universe, Universe, "universe")
self._universe = universe
api.validate_label(name, "name")
self._name = name
api.validate_units(units, "units")
self._units = units
api.validate_array(data, None, self._allowed_dtypes, "data")
if data.shape[0] != self._number_of_values():
raise ValueError("data array has incorrect shape")
self._data = data
def __init__(self, universe, positions, cell_parameters):
api.validate_type(universe, Universe, "universe")
cell_param_shape = universe.cell_parameter_array_shape
nsites = universe.number_of_sites
# Allow cell_parameters=None for universes that don't
# need cell parameters.
if cell_parameters is None and cell_param_shape == (0,):
cell_parameters = IN.zeros(cell_param_shape, positions.dtype)
# At this point, positions and cell_parameters must be arrays
# of the required shapes.
api.validate_array(positions, (nsites, 3), self._allowed_dtypes, "positions")
api.validate_array(cell_parameters, cell_param_shape, self._allowed_dtypes, "cell_parameters")
if positions.dtype != cell_parameters.dtype:
raise ValueError("positions and cell parameters must have" " the same element type")
self._universe = universe
self._positions = positions
self._cell_parameters = cell_parameters
def __init__(self, universe, positions=None, cell_parameters=None,
dtype=None):
api.validate_type(universe, Universe, "universe")
cell_param_shape = universe.cell_parameter_array_shape
nsites = universe.number_of_sites
if positions is None and cell_parameters is None:
if dtype is None:
dtype = N.float64
if dtype not in self._allowed_dtypes:
raise ValueError("dtype must be " +
" or ".join(str(t)
for t in self._allowed_dtypes))
positions = N.empty((nsites, 3), dtype)
cell_parameters = N.empty(cell_param_shape, dtype)
else:
# Allow cell_parameters=None for universes that don't
# need cell parameters.
if positions is not None and cell_parameters is None \
and cell_param_shape == (0,):
cell_parameters = N.empty(cell_param_shape,
positions.dtype)
# Require both positions and cell parameters, or neither
if positions is None or cell_parameters is None:
raise ValueError("configuration requires both "
"positions and cell parameters")
# At this point, positions and cell_parameters must be arrays
# of the required shapes.
api.validate_array(positions, (nsites, 3),
self._allowed_dtypes, "positions")
api.validate_array(cell_parameters, cell_param_shape,
self._allowed_dtypes, "cell_parameters")
if positions.dtype != cell_parameters.dtype:
raise ValueError("positions and cell parameters must have"
" the same element type")
# If an explicit dtype is given, check arrays for conformance
if dtype is not None:
if positions.dtype != dtype:
raise ValueError("arrays don't have the requested"
" element type " + str(dtype))
self._universe = universe
self._positions = positions
self._cell_parameters = cell_parameters