def test_volume(base_box):
assert isclose(base_box.volume, np.product(base_box.L))
for L in np.linspace(1, 10, 10):
box = Box.cube(L)
assert isclose(box.volume, L**3)
box = Box(L, L + 1, L + 2)
assert isclose(box.volume, L * (L + 1) * (L + 2))
def box(self):
"""hoomd.Box: The current simulation box.
Editing the box directly is not allowed. For example
``state.box.scale(1.1)`` would not scale the state's box. To set the
state's box to a new box ``state.box = new_box`` must be used.
"""
b = Box._from_cpp(self._cpp_sys_def.getParticleData().getGlobalBox())
return Box.from_box(b)
def box(self):
"""hoomd.Box: A copy of the current simulation box.
Note:
The `box` property cannot be set. Call `set_box` to set a new
simulation box.
"""
b = Box._from_cpp(self._cpp_sys_def.getParticleData().getGlobalBox())
return Box.from_box(b)
def test_lattice_vectors(base_box):
expected_vectors = np.array([[1, 0, 0], [2, 2, 0], [6, 9, 3]],
dtype=np.float64)
assert np.allclose(base_box.lattice_vectors, expected_vectors)
box = Box.cube(4)
lattice_vectors = np.array([[4, 0, 0], [0, 4, 0], [0, 0, 4]])
assert np.allclose(box.lattice_vectors, lattice_vectors)
def set_box(self, box):
"""Set a new simulation box.
Args:
box (Box): New simulation box.
Note:
All particles must be inside the new box. `set_box` does not change
any particle properties.
See Also:
`hoomd.update.BoxResize.update`
"""
if self._in_context_manager:
raise RuntimeError(
"Cannot set system box within local snapshot context manager.")
try:
box = Box.from_box(box)
except Exception:
raise ValueError('{} is not convertable to hoomd.Box using '
'hoomd.Box.from_box'.format(box))
if box.dimensions != self._cpp_sys_def.getNDimensions():
self._simulation.device._cpp_msg.warning(
"Box changing dimensions from {} to {}."
"".format(self._cpp_sys_def.getNDimensions(), box.dimensions))
self._cpp_sys_def.setNDimensions(box.dimensions)
self._cpp_sys_def.getParticleData().setGlobalBox(box._cpp_obj)
def test_from_matrix(new_box_matrix_dict):
box = Box.from_matrix(new_box_matrix_dict['matrix'])
assert np.allclose(new_box_matrix_dict['matrix'], box.matrix)
assert np.allclose(box.L, [new_box_matrix_dict['Lx'],
new_box_matrix_dict['Ly'],
new_box_matrix_dict['Lz']])
assert np.allclose(box.tilts, [new_box_matrix_dict['xy'],
new_box_matrix_dict['xz'],
new_box_matrix_dict['yz']])
def box(self, value):
if self._in_context_manager:
raise RuntimeError(
"Cannot set system box within local snapshot context manager.")
try:
value = Box.from_box(value)
except Exception:
raise ValueError('{} is not convertable to hoomd.Box using '
'hoomd.Box.from_box'.format(value))
if value.dimensions != self._cpp_sys_def.getNDimensions():
self._simulation.device._cpp_msg.warning(
"Box changing dimensions from {} to {}."
"".format(self._cpp_sys_def.getNDimensions(),
value.dimensions))
self._cpp_sys_def.setNDimensions(value.dimensions)
self._cpp_sys_def.getParticleData().setGlobalBox(value._cpp_obj)
def get_box(self, timestep):
"""Get the box for a given timestep.
Args:
timestep (int): The timestep to use for determining the resized
box.
Returns:
Box: The box used at the given timestep.
"""
if self._attached:
timestep = int(timestep)
if timestep < 0:
raise ValueError("Timestep must be a non-negative integer.")
return Box._from_cpp(self._cpp_obj.get_current_box(timestep))
else:
return None
def base_box(box_dict):
return Box(**box_dict)
def test_neq(base_box, box_dict):
box2 = Box(**box_dict)
assert not base_box != box2
box2.Lx = 2
assert base_box != box2
def test_square():
for L in np.linspace(1, 100, 10):
box = Box.square(L)
assert all(box.L == [L, L, 0])
assert box.Lx == box.Ly == L and box.Lz == 0
def test_base_constructor(box_dict):
box = Box(**box_dict)
for key in box_dict:
assert getattr(box, key) == box_dict[key]
def test_cube():
for L in np.linspace(1, 100, 10):
box = Box.cube(L)
assert all(box.L == L)
assert box.Lx == box.Ly == box.Lz == L
