def __init__(self, hdf5_group_or_filename, universe=None,
author_name='unknown', author_email=None,
file_mode=None,
float_type=np.float32,
mosaic_data = {}):
"""
:param hdf5_group_or_filename: a group in an open HDF5 file,
or a string interpreted as a file name
:type hdf5_group_or_filename: str or ``h5py.Group``
:param file_mode: ``'r'`` or ``'w'``, used only with a filename argument
:type file_mode: str
:param universe: the universe associated with the trajectory
:type universe: :class:`mosaic.api.MosaicUniverse`
:param mosaic_data: additional MOSAIC data items to be stored
"""
if isstring(hdf5_group_or_filename):
if file_mode is None:
file_mode = 'r'
self.root = h5py.File(hdf5_group_or_filename, file_mode)
self._close = True
else:
api.validate_value(file_mode, [None], "file_mode")
self.root = hdf5_group_or_filename
self._close = False
self.float_type = float_type
self._mosaic_group(universe, mosaic_data)
self._create_h5md_group(author_name, author_email)
self._create_particles_group()
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, name, strings, label_type):
api.validate_type(universe, Universe, "universe")
api.validate_label(name, "name")
api.validate_sequence(strings, str, "strings")
api.validate_value(label_type, self._allowed_types, "label_type")
self._universe = universe
self._name = name
self._string_array = N.array(list('\0'.join(strings) + '\0'),
dtype='S')
self._type = label_type
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, args):
cell_shape, molecules, symmetry_transformations, convention = args
api.validate_type(cell_shape, str, "cell_shape")
api.validate_value(cell_shape, list(self._cell_parameter_array_shapes.keys()), "cell_shape")
api.validate_sequence(
molecules,
ImmutableTuple,
"molecules",
(
(lambda p: len(p) == 3, "must have length 3"),
(
lambda p: isinstance(p[0], Fragment) and isascii(p[1]) and isinstance(p[2], int),
"elements must be (fragment, label, count) " "triples",
),
),
)
api.validate_sequence(
symmetry_transformations,
ImmutableTuple,
"symmetry_transformations",
(
(lambda p: len(p) == 2, "must have length 2"),
(
lambda p: hasattr(p[0], "shape") and p[0].shape == (3, 3) and p[0].dtype == N.float64,
"rotation matrix must be float64 " "and have shape (3,3)",
),
(
lambda p: hasattr(p[1], "shape") and p[1].shape == (3,) and p[0].dtype == N.float64,
"translation vector must be float64 " "and have shape (3,)",
),
),
)
if cell_shape == "infinite" and len(symmetry_transformations) > 0:
raise ValueError("Symmetry transformations are allowed " "only in periodic universes")
api.validate_label(convention, "Universe.convention")
self._cell_shape = cell_shape
self._molecules = ImmutableTuple(
ImmutableTuple((FragmentRef(label, fragment), count)) for fragment, label, count in molecules
)
self._symmetry_transformations = symmetry_transformations
self._convention = convention
self._fragments = ImmutableTuple(ImmutableTuple((f, l)) for f, l, c in molecules)
self._molecule_counts = ImmutableTuple(c for f, l, c in molecules)
self._atom_counts = ImmutableTuple(f.number_of_atoms for f, l, c in molecules)
self._site_counts = ImmutableTuple(f.number_of_sites for f, l, c in molecules)
self._bond_counts = ImmutableTuple(f.number_of_bonds for f, l, c in molecules)
def __init__(self, hdf5_group_or_filename, file_mode=None):
"""
:param hdf5_group_or_filename: a group in an open HDF5 file,
or a string interpreted as a file name
:type hdf5_group_or_filename: str or ``h5py.Group``
:param file_mode: ``'r'`` or ``'w'``, used only with a filename argument
:type file_mode: str
"""
if isstring(hdf5_group_or_filename):
if file_mode is None:
file_mode = 'r'
self.root = h5py.File(hdf5_group_or_filename, file_mode)
self._close = True
else:
api.validate_value(file_mode, [None], "file_mode")
self.root = hdf5_group_or_filename
self._close = False
self._path_map = weakref.WeakKeyDictionary()
self._data_map = weakref.WeakValueDictionary()
self._factory = mosaic.array_model.Factory()
def __init__(self, args):
species, fragments, atoms, bonds = args
api.validate_label(species, "species")
self.species = species
labels = set()
api.validate_sequence(fragments, ImmutableTuple, "fragments", ((lambda p: len(p) == 2, "must have length 2"),))
for label, fragment in fragments:
api.validate_label(label, "fragment label")
if label in labels:
raise ValueError("label %s occurs more than once" % label)
labels.add(label)
api.validate_type(fragment, Fragment, "fragment template")
self.fragments = fragments
api.validate_sequence(atoms, ImmutableTuple, "atoms", ((lambda p: len(p) == 2, "must have length 2"),))
for label, atom in atoms:
api.validate_label(label, "atom label")
if label in labels:
raise ValueError("label %s occurs more than once" % label)
labels.add(label)
api.validate_type(atom, Atom, "atom")
self.atoms = atoms
self.attrs = ImmutableDict(IT.chain(fragments, atoms))
api.validate_sequence(bonds, tuple, "bonds", ((lambda p: len(p) == 3, "must have length 3"),))
for a1, a2, order in bonds:
self._validate_bond_atom(a1)
self._validate_bond_atom(a2)
if a1.split(".")[0] == a2.split(".")[0]:
raise ValueError(
"bond between %s and %s must be defined " "in fragment %s" % (a1, a2, a1.split(".")[0])
)
api.validate_value(order, api.MosaicFragment._bond_orders, "bond order")
self.bonds = bonds
def cell_shape(self, new_cell_shape):
api.validate_type(new_cell_shape, str, "cell_shape")
api.validate_value(new_cell_shape,
self._cell_parameter_array_shapes.keys(),
"cell_shape")
self._cell_shape = new_cell_shape
def polymer_type(self, new_polymer_type):
api.validate_value(new_polymer_type, self._polymer_types,
'polymer_type')
self._polymer_type = new_polymer_type