def snapshot(self):
r"""hoomd.Snapshot: All data of a simulation's current microstate.
`State.snapshot` should be used when all of a simulation's state
information is desired in a single object. When accessed, data across
all MPI ranks and from GPUs is gathered on the root MPI rank's memory.
When accessing data in MPI simulations, it is recommended to use a
``if snapshot.exists:`` conditional to prevent attempting to access data
on a non-root rank.
This property can be set to replace the system state with the given
`hoomd.Snapshot` object. Example use cases in which a simulation's
state may be reset from a snapshot include Monte Carlo schemes
implemented at the Python script level, where the current snapshot is
passed to the Monte Carlo simulation before being passed back after
running some Monte Carlo steps.
Warning:
Using `State.snapshot` multiple times will gather data across MPI
ranks and GPUs every time. If the snapshot is needed for more than
one use, it is recommended to store it in a variable.
Note:
Setting or getting a snapshot is an order :math:`O(N_{particles}
+ N_{bonds} + \ldots)` operation.
"""
cpp_snapshot = self._cpp_sys_def.takeSnapshot_double()
return Snapshot._from_cpp_snapshot(cpp_snapshot,
self._simulation.device.communicator)
def get_snapshot(self):
"""Make a copy of the simulation current state.
`State.get_snapshot` makes a copy of the simulation state and
makes it available in a single object. `State.set_snapshot` resets
the internal state to that in the given snapshot. Use these methods
to implement techniques like hybrid MD/MC or umbrella sampling where
entire system configurations need to be reset to a previous one after a
rejected move.
Note:
Data across all MPI ranks and from GPUs is gathered on the root MPI
rank's memory. When accessing data in MPI simulations, use a ``if
snapshot.communicator.rank == 0:`` conditional to access data arrays
only on the root rank.
Note:
`State.get_snapshot` is an order :math:`O(N_{particles} + N_{bonds}
+ \\ldots)` operation.
See Also:
`set_snapshot`
Returns:
hoomd.Snapshot: The current simulation state
"""
cpp_snapshot = self._cpp_sys_def.takeSnapshot_double()
return Snapshot._from_cpp_snapshot(
cpp_snapshot, self._simulation.device.communicator)
def create_state_from_gsd(self, filename, frame=-1):
"""Create the simulation state from a GSD file.
Args:
filename (str): GSD file to read
frame (int): Index of the frame to read from the file. Negative
values index back from the last frame in the file.
"""
if self.state is not None:
raise RuntimeError("Cannot initialize more than once\n")
filename = _hoomd.mpi_bcast_str(filename, self.device._cpp_exec_conf)
# Grab snapshot and timestep
reader = _hoomd.GSDReader(self.device._cpp_exec_conf, filename,
abs(frame), frame < 0)
snapshot = Snapshot._from_cpp_snapshot(reader.getSnapshot(),
self.device.communicator)
step = reader.getTimeStep() if self.timestep is None else self.timestep
self._state = State(self, snapshot)
reader.clearSnapshot()
# Store System and Reader for Operations
self._cpp_sys = _hoomd.System(self.state._cpp_sys_def, step)
self._init_communicator()
self.operations._store_reader(reader)
def create_state_from_gsd(self,
filename,
frame=-1,
domain_decomposition=(None, None, None)):
"""Create the simulation state from a GSD file.
Args:
filename (str): GSD file to read
frame (int): Index of the frame to read from the file. Negative
values index back from the last frame in the file.
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_gsd`
sets `timestep` to the value in the selected GSD frame in the file.
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.
"""
if self._state is not None:
raise RuntimeError("Cannot initialize more than once\n")
filename = _hoomd.mpi_bcast_str(filename, self.device._cpp_exec_conf)
# Grab snapshot and timestep
reader = _hoomd.GSDReader(self.device._cpp_exec_conf, filename,
abs(frame), frame < 0)
snapshot = Snapshot._from_cpp_snapshot(reader.getSnapshot(),
self.device.communicator)
step = reader.getTimeStep() if self.timestep is None else self.timestep
self._state = State(self, snapshot, domain_decomposition)
reader.clearSnapshot()
self._init_system(step)