def __init__(self, atoms, timestep=None, temperature=None, friction=None, trajectory=None, **kwargs): Langevin.__init__(self, atoms, timestep, temperature, friction) OTF.__init__(self, **kwargs) self.md_engine = 'Langevin'
def __init__(self, atoms, timestep, temperature, friction, fixcm=True, trajectory=None, logfile=None, loginterval=1): assert(getattr(Langevin_ASE, "_lgv_version", 1) >= 2) ParallelMolDynMixin.__init__(self, "Langevin", atoms) self._uselocaldata = False # Need to store on atoms for serial simul too. self.calculator = atoms.get_calculator() self.asap_md = asap3._asap.Langevin(atoms, self.calculator, timestep, self.prefix+"sdpos", self.prefix+"sdmom", self.prefix+"c1", self.prefix+"c2", fixcm, randint(1 << 30)) if not atoms.has('momenta'): atoms.set_momenta(np.zeros((len(atoms), 3), float)) if atoms.constraints: assert len(atoms.constraints) == 1 constraint = atoms.constraints[0] assert isinstance(constraint, asap3.constraints.FixAtoms) constraint.prepare_for_asap(atoms) # Make all constants arrays by making friction an array friction = friction * np.zeros(len(atoms)) Langevin_ASE.__init__(self, atoms, timestep, temperature, friction, fixcm, trajectory, logfile, loginterval, communicator=None)
def __init__(self, atoms, timestep, temperature, friction, fixcm=True, trajectory=None, logfile=None, loginterval=1): assert(getattr(Langevin_ASE, "_lgv_version", 1) >= 2) ParallelMolDynMixin.__init__(self, "Langevin", atoms) Langevin_ASE.__init__(self, atoms, timestep, temperature, friction, fixcm, trajectory, logfile, loginterval, communicator=None)