def create_state_from_snapshot(self, snapshot):
"""Create the simulations state from a `Snapshot`.
Args:
snapshot (Snapshot or gsd.hoomd.Snapshot): Snapshot to initialize
the state from. A `gsd.hoomd.Snapshot` will first be
converted to a `hoomd.Snapshot`.
When `timestep` is `None` before calling, `create_state_from_snapshot`
sets `timestep` to 0.
"""
if self.state is not None:
raise RuntimeError("Cannot initialize more than once\n")
if isinstance(snapshot, Snapshot):
# snapshot is hoomd.Snapshot
self._state = State(self, snapshot)
elif _match_class_path(snapshot, 'gsd.hoomd.Snapshot'):
# snapshot is gsd.hoomd.Snapshot
snapshot = Snapshot.from_gsd_snapshot(snapshot,
self._device.communicator)
self._state = State(self, snapshot)
else:
raise TypeError(
"Snapshot must be a hoomd.Snapshot or gsd.hoomd.Snapshot.")
step = 0
if self.timestep is not None:
step = self.timestep
self._init_system(step)
def test_from_gsd_snapshot_populated(s, device):
if s.exists:
s.configuration.box = [10, 12, 7, 0.1, 0.4, 0.2]
for section in ('particles', 'bonds', 'angles', 'dihedrals',
'impropers', 'pairs'):
setattr(getattr(s, section), 'N', 5)
setattr(getattr(s, section), 'types', ['A', 'B'])
for prop in ('angmom', 'body', 'charge', 'diameter', 'image', 'mass',
'moment_inertia', 'orientation', 'position', 'typeid',
'velocity'):
attr = getattr(s.particles, prop)
if attr.dtype == numpy.float64:
attr[:] = numpy.random.rand(*attr.shape)
else:
attr[:] = numpy.random.randint(3, size=attr.shape)
for section in ('bonds', 'angles', 'dihedrals', 'impropers', 'pairs'):
for prop in ('group', 'typeid'):
attr = getattr(getattr(s, section), prop)
attr[:] = numpy.random.randint(3, size=attr.shape)
s.constraints.N = 3
for prop in ('group', 'value'):
attr = getattr(s.constraints, prop)
if attr.dtype == numpy.float64:
attr[:] = numpy.random.rand(*attr.shape)
else:
attr[:] = numpy.random.randint(3, size=attr.shape)
gsd_snap = make_gsd_snapshot(s)
hoomd_snap = Snapshot.from_gsd_snapshot(gsd_snap, device.communicator)
assert_equivalent_snapshots(gsd_snap, hoomd_snap)
def create_state_from_snapshot(self,
snapshot,
domain_decomposition=(None, None, None)):
"""Create the simulation state from a `Snapshot`.
Args:
snapshot (Snapshot or gsd.hoomd.Snapshot): Snapshot to initialize
the state from. A `gsd.hoomd.Snapshot` will first be
converted to a `hoomd.Snapshot`.
domain_decomposition (tuple): Choose how to distribute the state
across MPI ranks with domain decomposition. Provide a tuple
of 3 integers indicating the number of evenly spaced domains in
the x, y, and z directions (e.g. ``(8,4,2)``). Provide a tuple
of 3 lists of floats to set the fraction of the simulation box
to include in each domain. The sum of each list of floats must
be 1.0 (e.g. ``([0.25, 0.75], [0.2, 0.8], [1.0])``).
When `timestep` is `None` before calling, `create_state_from_snapshot`
sets `timestep` to 0.
Note:
Set any or all of the ``domain_decomposition`` tuple elements to
`None` and `create_state_from_gsd` will select a value that
minimizes the surface area between the domains (e.g.
``(2,None,None)``). The domains are spaced evenly along each
automatically selected direction. The default value of ``(None,
None, None)`` will automatically select the number of domains in all
directions.
See Also:
`State.get_snapshot`
`State.set_snapshot`
"""
if self._state is not None:
raise RuntimeError("Cannot initialize more than once\n")
if isinstance(snapshot, Snapshot):
# snapshot is hoomd.Snapshot
self._state = State(self, snapshot, domain_decomposition)
elif _match_class_path(snapshot, 'gsd.hoomd.Snapshot'):
# snapshot is gsd.hoomd.Snapshot
snapshot = Snapshot.from_gsd_snapshot(snapshot,
self._device.communicator)
self._state = State(self, snapshot, domain_decomposition)
else:
raise TypeError(
"Snapshot must be a hoomd.Snapshot or gsd.hoomd.Snapshot.")
step = 0
if self.timestep is not None:
step = self.timestep
self._init_system(step)
def test_from_gsd_snapshot_empty(s, device):
gsd_snap = make_gsd_snapshot(s)
hoomd_snap = Snapshot.from_gsd_snapshot(gsd_snap, device.communicator)
assert_equivalent_snapshots(gsd_snap, hoomd_snap)