def write(state, filename, filter=All(), mode='wb', log=None):
"""Write the given simulation state out to a GSD file.
Args:
state (State): Simulation state.
filename (str): File name to write.
filter (`hoomd.filter.ParticleFilter`): Select the particles to
write.
mode (str): The file open mode. Defaults to ``'wb'``.
log (`hoomd.logging.Logger`): Provide log quantities to write.
The valid file modes for `write` are ``'wb'`` and ``'xb'``.
"""
if mode != 'wb' and mode != 'xb':
raise ValueError(f"Invalid GSD.write file mode: {mode}")
writer = _hoomd.GSDDumpWriter(state._cpp_sys_def, filename,
state._get_group(filter), mode, False)
if state._simulation._system_communicator is not None:
writer.setCommunicator(state._simulation._system_communicator)
if log is not None:
writer.log_writer = _GSDLogWriter(log)
writer.analyze(state._simulation.timestep)
def __init__(self,
filename,
period,
group,
overwrite=False,
truncate=False,
phase=0,
time_step=None,
dynamic=None):
categories = ['attribute', 'property', 'momentum', 'topology']
dynamic_quantities = ['property']
if dynamic is not None:
for v in dynamic:
if v not in categories:
hoomd.context.current.device.cpp_msg.warning(
"dump.gsd: dynamic quantity " + v +
" is not recognized\n")
dynamic_quantities = ['property'] + dynamic
# initialize base class
hoomd.analyze._analyzer.__init__(self)
self.cpp_analyzer = _hoomd.GSDDumpWriter(
hoomd.context.current.system_definition, filename, group.cpp_group,
overwrite, truncate)
self.cpp_analyzer.setWriteAttribute('attribute' in dynamic_quantities)
self.cpp_analyzer.setWriteProperty('property' in dynamic_quantities)
self.cpp_analyzer.setWriteMomentum('momentum' in dynamic_quantities)
self.cpp_analyzer.setWriteTopology('topology' in dynamic_quantities)
if period is not None:
self.setupAnalyzer(period, phase)
else:
if time_step is None:
time_step = hoomd.context.current.system.getCurrentTimeStep()
self.cpp_analyzer.analyze(time_step)
# store metadata
self.filename = filename
self.period = period
self.group = group
self.phase = phase
self.metadata_fields = ['filename', 'period', 'group', 'phase']
def __init__(self,
filename,
period,
group,
overwrite=False,
truncate=False,
phase=0,
time_step=None,
static=['attribute', 'momentum', 'topology']):
hoomd.util.print_status_line()
for v in static:
if v not in ['attribute', 'property', 'momentum', 'topology']:
hoomd.context.msg.warning("dump.gsd: static quantity", v,
"is not recognized")
# initialize base class
hoomd.analyze._analyzer.__init__(self)
self.cpp_analyzer = _hoomd.GSDDumpWriter(
hoomd.context.current.system_definition, filename, group.cpp_group,
overwrite, truncate)
self.cpp_analyzer.setWriteAttribute('attribute' not in static)
self.cpp_analyzer.setWriteProperty('property' not in static)
self.cpp_analyzer.setWriteMomentum('momentum' not in static)
self.cpp_analyzer.setWriteTopology('topology' not in static)
if period is not None:
self.setupAnalyzer(period, phase)
else:
if time_step is None:
time_step = hoomd.context.current.system.getCurrentTimeStep()
self.cpp_analyzer.analyze(time_step)
# store metadata
self.filename = filename
self.period = period
self.group = group
self.phase = phase
self.metadata_fields = ['filename', 'period', 'group', 'phase']
def _attach(self):
# validate dynamic property
categories = ['attribute', 'property', 'momentum', 'topology']
dynamic_quantities = ['property']
if self.dynamic is not None:
for v in self.dynamic:
if v not in categories:
raise RuntimeError(
f"GSD: dynamic quantity {v} is not valid")
dynamic_quantities = ['property'] + self.dynamic
self._cpp_obj = _hoomd.GSDDumpWriter(
self._simulation.state._cpp_sys_def, self.filename,
self._simulation.state._get_group(self.filter), self.mode,
self.truncate)
self._cpp_obj.setWriteAttribute('attribute' in dynamic_quantities)
self._cpp_obj.setWriteProperty('property' in dynamic_quantities)
self._cpp_obj.setWriteMomentum('momentum' in dynamic_quantities)
self._cpp_obj.setWriteTopology('topology' in dynamic_quantities)
self._cpp_obj.log_writer = self.log
super()._attach()
def __init__(self,
filename,
period,
group,
overwrite=False,
truncate=False,
phase=0,
time_step=None,
static=None,
dynamic=None):
hoomd.util.print_status_line()
if static is not None and dynamic is not None:
raise ValueError(
"Cannot specify both static and dynamic arguments")
categories = ['attribute', 'property', 'momentum', 'topology']
dynamic_quantities = ['property']
# process inputs and build list of dynamic quantities
if static is not None:
hoomd.context.msg.warning(
"The static argument to hoomd.dump.gsd is deprecated, use dynamic instead.\n"
)
# notify they user of possible typos
for v in static:
if v not in categories:
hoomd.context.msg.warning("dump.gsd: static quantity " +
v + " is not recognized\n")
# invert the sense of the static arg
dynamic_quantities = []
for v in categories:
if v not in static:
dynamic_quantities.append(v)
if dynamic is not None:
for v in dynamic:
if v not in categories:
hoomd.context.msg.warning("dump.gsd: dynamic quantity " +
v + " is not recognized\n")
dynamic_quantities = ['property'] + dynamic
# initialize base class
hoomd.analyze._analyzer.__init__(self)
self.cpp_analyzer = _hoomd.GSDDumpWriter(
hoomd.context.current.system_definition, filename, group.cpp_group,
overwrite, truncate)
self.cpp_analyzer.setWriteAttribute('attribute' in dynamic_quantities)
self.cpp_analyzer.setWriteProperty('property' in dynamic_quantities)
self.cpp_analyzer.setWriteMomentum('momentum' in dynamic_quantities)
self.cpp_analyzer.setWriteTopology('topology' in dynamic_quantities)
if period is not None:
self.setupAnalyzer(period, phase)
else:
if time_step is None:
time_step = hoomd.context.current.system.getCurrentTimeStep()
self.cpp_analyzer.analyze(time_step)
# store metadata
self.filename = filename
self.period = period
self.group = group
self.phase = phase
self.metadata_fields = ['filename', 'period', 'group', 'phase']