def _initialize(self,atoms):
""" Initialization of hotbit. """
if not self.init:
self.set_text(self.txt)
self.timer=Timer('Hotbit',txt=self.get_output())
self.start_timing('initialization')
self.el=Elements(self,atoms)
self.ia=Interactions(self)
self.st=States(self)
self.rep=Repulsion(self)
self.pp=PairPotential(self)
if self.get('vdw'):
if self.get('vdw_parameters') is not None:
self.el.update_vdw(self.get('vdw_parameters'))
setup_vdw(self)
self.env=Environment(self)
pbc=atoms.get_pbc()
# FIXME: gamma_cut -stuff
#if self.get('SCC') and np.any(pbc) and self.get('gamma_cut')==None:
# raise NotImplementedError('SCC not implemented for periodic systems yet (see parameter gamma_cut).')
if np.any(pbc) and abs(self.get('charge'))>0.0 and self.get('SCC'):
raise AssertionError('Charged system cannot be periodic.')
self.flush()
self.flags = {}
self.flags['Mulliken'] = False
self.flags['DOS'] = False
self.flags['bonds'] = False
self.flags['grid'] = False
self.stop_timing('initialization')
self.el.set_atoms(atoms)
if not self.init:
self.init=True
self.greetings()
def _initialize(self, atoms):
""" Initialization of hotbit. """
if not self.init:
self.set_text(self.txt)
self.timer = Timer("Hotbit", txt=self.get_output())
self.start_timing("initialization")
self.el = Elements(self, atoms)
self.ia = Interactions(self)
self.st = States(self)
self.rep = Repulsion(self)
self.pp = PairPotential(self)
if self.get("vdw"):
if self.get("vdw_parameters") is not None:
self.el.update_vdw(self.get("vdw_parameters"))
setup_vdw(self)
self.env = Environment(self)
pbc = atoms.get_pbc()
# FIXME: gamma_cut -stuff
# if self.get('SCC') and np.any(pbc) and self.get('gamma_cut')==None:
# raise NotImplementedError('SCC not implemented for periodic systems yet (see parameter gamma_cut).')
if np.any(pbc) and abs(self.get("charge")) > 0.0 and self.get("SCC"):
raise AssertionError("Charged system cannot be periodic.")
self.flush()
self.flags = {}
self.flags["Mulliken"] = False
self.flags["DOS"] = False
self.flags["bonds"] = False
self.flags["grid"] = False
self.stop_timing("initialization")
self.el.set_atoms(atoms)
if not self.init:
self.init = True
self.greetings()