def store(self, simul):
"""Takes a simulation instance and stores a minimal representation of it.
Args:
simul: A simulation object.
"""
super(InputSimulation, self).store()
self.output.store(simul.outtemplate)
self.prng.store(simul.prng)
self.step.store(simul.step)
self.total_steps.store(simul.tsteps)
self.total_time.store(simul.ttime)
self.paratemp.store(simul.paratemp)
# this we pick from the messages class. kind of a "global" but it seems to
# be the best way to pass around the (global) information on the level of output.
if verbosity.debug:
self.verbosity.store("debug")
elif verbosity.high:
self.verbosity.store("high")
elif verbosity.medium:
self.verbosity.store("medium")
elif verbosity.low:
self.verbosity.store("low")
elif verbosity.quiet:
self.verbosity.store("quiet")
else:
raise ValueError("Invalid verbosity level")
self.mode.store(simul.mode)
self.extra = []
for fname in simul.fflist:
ff = simul.fflist[fname]
if type(ff) is eforcefields.FFSocket:
iff = iforcefields.InputFFSocket()
iff.store(ff)
self.extra.append(("ffsocket", iff))
elif type(ff) is eforcefields.FFLennardJones:
iff = iforcefields.InputFFLennardJones()
iff.store(ff)
self.extra.append(("fflj", iff))
elif type(ff) is eforcefields.FFDebye:
iff = iforcefields.InputFFDebye()
iff.store(ff)
self.extra.append(("ffdebye", iff))
elif type(ff) is eforcefields.FFYaff:
iff = iforcefields.InputFFYaff()
iff.store(ff)
self.extra.append(("ffyaff", iff))
for s in simul.syslist:
isys = InputSystem()
isys.store(s)
self.extra.append(("system", isys))
'simulation': simulation.InputSimulation(), 'smotion': smotion.smotion.InputSmotion(), 'remd': smotion.remd.InputReplicaExchange(), 'meta': smotion.metad.InputMetaDyn(), 'system': system.InputSystem(), 'ensembles': ensembles.InputEnsemble(), 'motion': motion.motion.InputMotion(), 'dynamics': motion.dynamics.InputDynamics(), 'alchemy': motion.alchemy.InputAlchemy(), 'instanton': motion.instanton.InputInst(), 'phonons': motion.phonons.InputDynMatrix(), 'geop': motion.geop.InputGeop(), 'neb': motion.neb.InputNEB(), 'thermostats': thermostats.InputThermo(), 'forcefield': forcefields.InputForceField(), 'ffsocket': forcefields.InputFFSocket(), 'fflj': forcefields.InputFFLennardJones(), 'ffdebye': forcefields.InputFFDebye(), 'ffplumed': forcefields.InputFFPlumed(), 'ffyaff': forcefields.InputFFYaff(), 'forcecomponent': forces.InputForceComponent(), 'forces': forces.InputForces(), 'atoms': atoms.InputAtoms(), 'beads': beads.InputBeads(), 'prng': prng.InputRandom(), 'normalmodes': normalmodes.InputNormalModes(), 'nmfrequencies': normalmodes.InputNMFrequencies(), 'init_file': initializer.InputInitFile(), 'init_pos': initializer.InputInitPositions(), 'init_mom': initializer.InputInitMomenta(), 'init_lab': initializer.InputInitLabels(),
"system": system.InputSystem(), "ensembles": ensembles.InputEnsemble(), "motion": motion.motion.InputMotion(), "dynamics": motion.dynamics.InputDynamics(), "t_ramp": motion.ramp.InputTemperatureRamp(), "p_ramp": motion.ramp.InputPressureRamp(), "alchemy": motion.alchemy.InputAlchemy(), "planetary": motion.planetary.InputPlanetary(), "atomswap": motion.atomswap.InputAtomSwap(), "instanton": motion.instanton.InputInst(), "phonons": motion.phonons.InputDynMatrix(), "geop": motion.geop.InputGeop(), "neb": motion.neb.InputNEB(), "thermostats": thermostats.InputThermo(), "forcefield": forcefields.InputForceField(), "ffsocket": forcefields.InputFFSocket(), "fflj": forcefields.InputFFLennardJones(), "ffdebye": forcefields.InputFFDebye(), "ffplumed": forcefields.InputFFPlumed(), "ffyaff": forcefields.InputFFYaff(), "ffsgdml": forcefields.InputFFsGDML(), "forcecomponent": forces.InputForceComponent(), "forces": forces.InputForces(), "atoms": atoms.InputAtoms(), "beads": beads.InputBeads(), "prng": prng.InputRandom(), "normalmodes": normalmodes.InputNormalModes(), "nmfrequencies": normalmodes.InputNMFrequencies(), "init_file": initializer.InputInitFile(), "init_pos": initializer.InputInitPositions(), "init_mom": initializer.InputInitMomenta(),
def store(self, simul):
"""Takes a simulation instance and stores a minimal representation of it.
Args:
simul: A simulation object.
"""
super(InputSimulation, self).store()
self.output.store(simul.outtemplate)
self.prng.store(simul.prng)
self.step.store(simul.step)
self.total_steps.store(simul.tsteps)
self.total_time.store(simul.ttime)
self.smotion.store(simul.smotion)
self.threading.store(simul.threading)
# this we pick from the messages class. kind of a "global" but it seems to
# be the best way to pass around the (global) information on the level of output.
if verbosity.debug:
self.verbosity.store("debug")
elif verbosity.high:
self.verbosity.store("high")
elif verbosity.medium:
self.verbosity.store("medium")
elif verbosity.low:
self.verbosity.store("low")
elif verbosity.quiet:
self.verbosity.store("quiet")
else:
raise ValueError("Invalid verbosity level")
self.mode.store(simul.mode)
_fflist = [v for k, v in sorted(simul.fflist.items())]
if len(self.extra) != len(_fflist) + len(simul.syslist):
self.extra = [0] * (len(_fflist) + len(simul.syslist))
for _ii, _obj, in enumerate(_fflist + simul.syslist):
if self.extra[_ii] == 0:
if isinstance(_obj, eforcefields.FFSocket):
_iobj = iforcefields.InputFFSocket()
_iobj.store(_obj)
self.extra[_ii] = ("ffsocket", _iobj)
elif isinstance(_obj, eforcefields.FFLennardJones):
_iobj = iforcefields.InputFFLennardJones()
_iobj.store(_obj)
self.extra[_ii] = ("fflj", _iobj)
elif isinstance(_obj, eforcefields.FFDebye):
_iobj = iforcefields.InputFFDebye()
_iobj.store(_obj)
self.extra[_ii] = ("ffdebye", _iobj)
elif isinstance(_obj, eforcefields.FFPlumed):
_iobj = iforcefields.InputFFPlumed()
_iobj.store(_obj)
self.extra[_ii] = ("ffplumed", _iobj)
elif isinstance(_obj, eforcefields.FFYaff):
_iobj = iforcefields.InputFFYaff()
_iobj.store(_obj)
self.extra[_ii] = ("ffyaff", _iobj)
elif isinstance(_obj, eforcefields.FFsGDML):
_iobj = iforcefields.InputFFsGDML()
_iobj.store(_obj)
self.extra[_ii] = ("ffsgdml", _iobj)
elif isinstance(_obj, System):
_iobj = InputSystem()
_iobj.store(_obj)
self.extra[_ii] = ("system", _iobj)
else:
self.extra[_ii][1].store(_obj)
