def test_get_nameless_cuds_component(self):
c = CUDS()
c.add([self.nameless_cuds_1])
component = c.get(self.nameless_cuds_1.uid)
self.assertEqual(component, self.nameless_cuds_1)
self.assertRaises(TypeError, c.get_by_name, component.name)
def test_get_named_cuds_component(self):
c = CUDS()
c.add([self.named_cuds_1])
self.assertEqual(c.get_by_name(self.named_cuds_1.name),
self.named_cuds_1)
self.assertEqual(c.get(self.named_cuds_1.uid), self.named_cuds_1)
def test_add_nameless_cuds_component(self):
c = CUDS()
c.add([self.nameless_cuds_1])
self.assertEqual(c.get(self.nameless_cuds_1.uid),
self.nameless_cuds_1)
self.assertRaises(TypeError, c.get_by_name, self.nameless_cuds_1.name)
def test_get_named_cuds_component(self):
c = CUDS()
c.add([self.named_cuds_1])
self.assertEqual(c.get_by_name(self.named_cuds_1.name),
self.named_cuds_1)
self.assertEqual(c.get(self.named_cuds_1.uid),
self.named_cuds_1)
def test_add_nameless_component_several_times(self):
c = CUDS()
c.add([self.nameless_cuds_1])
c.add([self.nameless_cuds_1])
component = c.get(self.nameless_cuds_1.uid)
self.assertEqual(component,
self.nameless_cuds_1)
self.assertRaises(TypeError, c.get_by_name, component.name)
def test_cuds_update(self):
component = api.Box(name='a box')
c = CUDS()
c.add([component])
component.name = 'updated box'
c.update([component])
updated_component = c.get(component.uid)
self.assertEqual(updated_component.name, 'updated box')
def read_data_file(filename, atom_style=None, name=None):
""" Reads LAMMPS data file and create CUDS objects
Reads LAMMPS data file and create a Particles and CUDS. The CUDS
will contain a material for each atom type (e.g. CUBA.MATERIAL_TYPE).
The attributes for each particle are based upon what atom-style
the file contains (i.e. "sphere" means that particles in addition to having
CUBA.VELOCITY will also have a CUBA.RADIUS and CUBA.MASS). See
'atom_style' for more details.
Parameters
----------
filename : str
filename of lammps data file
atom_style : AtomStyle, optional
type of atoms in the file. If None, then an attempt of
interpreting the atom-style in the file is performed.
name : str, optional
name to be given to returned Particles. If None, then filename is
used.
Returns
-------
particles : Particles
particles
SD : CUDS
SD containing materials
"""
handler = LammpsSimpleDataHandler()
parser = LammpsDataFileParser(handler=handler)
parser.parse(filename)
if atom_style is None:
atom_style = (
get_atom_style(handler.get_atom_type())
if handler.get_atom_type()
else AtomStyle.ATOMIC)
types = (atom_t for atom_t in
range(1, handler.get_number_atom_types() + 1))
atoms = handler.get_atoms()
velocities = handler.get_velocities()
masses = handler.get_masses()
box_origin = handler.get_box_origin()
box_vectors = handler.get_box_vectors()
type_to_material_map = {}
statedata = CUDS()
# set up a Material for each different type
for atom_type in types:
material = Material()
description = "Material for lammps atom type (originally '{}')".format(
atom_type
)
material.description = description
type_to_material_map[atom_type] = material.uid
statedata.add([material])
# add masses to materials
for atom_type, mass in masses.iteritems():
material = statedata.get(type_to_material_map[atom_type])
material.data[CUBA.MASS] = mass
statedata.update([material])
def convert_atom_type_to_material(atom_type):
return type_to_material_map[atom_type]
interpreter = LammpsDataLineInterpreter(atom_style,
convert_atom_type_to_material)
# create particles
particles = Particles(name=name if name else filename)
data = particles.data
data.update({CUBA.ORIGIN: box_origin,
CUBA.VECTOR: box_vectors})
particles.data = data
# add each particle
for lammps_id, values in atoms.iteritems():
coordinates, data = interpreter.convert_atom_values(values)
data.update(interpreter.convert_velocity_values(velocities[lammps_id]))
p = Particle(coordinates=coordinates, data=data)
particles.add([p])
return particles, statedata
