"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(), "init_lab": initializer.InputInitLabels(), "init_mass": initializer.InputInitMasses(), "init_vel": initializer.InputInitVelocities(), "init_cell": initializer.InputInitCell(), "init_therm": initializer.InputInitThermo(),
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)