def _create_supercell(self, unitcell, symprec):
mat = self._supercell_matrix
frame = self._get_surrounding_frame(mat)
sur_cell, u2sur_map = self._get_simple_supercell(frame, unitcell)
# Trim the simple supercell by the supercell matrix
trim_frame = np.array([
mat[0] / float(frame[0]), mat[1] / float(frame[1]),
mat[2] / float(frame[2])
])
supercell, sur2s_map, mapping_table = trim_cell(
trim_frame, sur_cell, symprec)
multi = supercell.get_number_of_atoms(
) // unitcell.get_number_of_atoms()
if multi != determinant(self._supercell_matrix):
print("Supercell creation failed.")
print("Probably some atoms are overwrapped. "
"The mapping table is give below.")
print(mapping_table)
Atoms.__init__(self)
else:
Atoms.__init__(
self,
numbers=supercell.get_atomic_numbers(),
masses=supercell.get_masses(),
#magmoms=supercell.get_magnetic_moments(),
scaled_positions=supercell.get_scaled_positions(),
cell=supercell.get_cell(),
#pbc=True)
)
self._u2s_map = np.arange(unitcell.get_number_of_atoms()) * multi
self._u2u_map = dict([(j, i) for i, j in enumerate(self._u2s_map)])
self._s2u_map = np.array(u2sur_map)[sur2s_map] * multi
def __init__(self, symbols=None,
positions=None, numbers=None,
tags=None, momenta=None, masses=None,
magmoms=None, charges=None,
scaled_positions=None,
cell=None, pbc=None,
constraint=None,
calculator=None,
container=None,
atoms=None):
"""
Modified atoms class for hotbit.
Input parameters as for ase.Atoms, except for keyword container.
@param container: either container type ('Bravais','Wedge','Chiral' or any other
container from hotbit/containers/*.py), or
dictionary describing the generalized unit cell, where
container['type'] selects the cell class; for other keywords,
look at the selected classes
"""
ase_Atoms.__init__(self,symbols=symbols,
positions=positions, numbers=numbers,
tags=tags, momenta=momenta, masses=masses,
magmoms=magmoms, charges=charges,
scaled_positions=scaled_positions,
cell=cell, pbc=pbc,
constraint=constraint,
calculator=calculator)
if type(atoms)!=type(None):
self += atoms
self.set_pbc( atoms.get_pbc() )
self.set_cell( atoms.get_cell() )
if container==None:
dict = {'type':container_magic(self)}
elif type(container)==type(''):
dict = {'type':container}
else:
dict = container.copy()
# create the container instance
assert 'type' in dict
exec( 'self.container_class = %s' %dict['type'] )
self.container = self.container_class(atoms=self,type=dict['type'])
container_magic(self,container=dict['type'])
dict.pop('type')
if dict!={}:
self.container.set(**dict)
# these are just for shorter references
self._transform = self.container.transform
self._rotation = self.container.rotation
def __init__(self, symbols=None,
positions=None, numbers=None,
tags=None, momenta=None, masses=None,
magmoms=None, charges=None,
scaled_positions=None,
cell=None, pbc=None,
constraint=None,
calculator=None,
container=None,
atoms=None):
"""
Modified atoms class for hotbit.
Input parameters as for ase.Atoms, except for keyword container.
@param container: either container type ('Bravais','Wedge','Chiral' or any other
container from hotbit/containers/*.py), or
dictionary describing the generalized unit cell, where
container['type'] selects the cell class; for other keywords,
look at the selected classes
"""
ase_Atoms.__init__(self,symbols=symbols,
positions=positions, numbers=numbers,
tags=tags, momenta=momenta, masses=masses,
magmoms=magmoms, charges=charges,
scaled_positions=scaled_positions,
cell=cell, pbc=pbc,
constraint=constraint,
calculator=calculator)
if type(atoms)!=type(None):
self += atoms
self.set_pbc( atoms.get_pbc() )
self.set_cell( atoms.get_cell() )
if container==None:
dict = {'type':container_magic(self)}
elif type(container)==type(''):
dict = {'type':container}
else:
dict = container.copy()
# create the container instance
assert 'type' in dict
exec( 'self.container_class = %s' %dict['type'] )
self.container = self.container_class(atoms=self,type=dict['type'])
container_magic(self,container=dict['type'])
dict.pop('type')
if dict!={}:
self.container.set(**dict)
# these are just for shorter references
self._transform = self.container.transform
self._rotation = self.container.rotation
def _primitive_cell(self, supercell):
trimed_cell, p2s_map, mapping_table = trim_cell(
self._primitive_matrix, supercell, self._symprec)
Atoms.__init__(
self,
numbers=trimed_cell.get_atomic_numbers(),
masses=trimed_cell.get_masses(),
#magmoms=trimed_cell.get_magnetic_moments(),
scaled_positions=trimed_cell.get_scaled_positions(),
cell=trimed_cell.get_cell(),
pbc=True)
self._p2s_map = np.array(p2s_map, dtype='intc')
def __init__(self, *args, **kwargs):
if kwargs.get('filename') is not None:
filename = kwargs.pop('filename')
ase_Atoms.__init__(self, *args, **kwargs)
#ase_Atoms.read(self,filename, kwargs.get('filetype'))
#elif isinstance(args[0],ase_Atoms):
#self=args[0]
#print 'dsdsdsdsdgsdgsdgsdg'
#assert False
else:
ase_Atoms.__init__(self, *args, **kwargs)
self.data = {}
self.set_data()
self.analyzed = []
def __init__(self, *args, **kwargs):
if kwargs.get('filename') is not None:
filename = kwargs.pop('filename')
ase_Atoms.__init__(self, *args, **kwargs)
#ase_Atoms.read(self,filename, kwargs.get('filetype'))
#elif isinstance(args[0],ase_Atoms):
#self=args[0]
#print 'dsdsdsdsdgsdgsdgsdg'
#assert False
else:
ase_Atoms.__init__(self, *args, **kwargs)
self.data={}
self.set_data()
self.analyzed=[]
def __init__(self, *args, **kwargs):
self.data = {}
if len(args) > 0:
filename = args[0]
if isinstance(filename, str):
self.read(filename, kwargs.get('filetype'))
return
else:
Atoms.__init__(self, [])
if kwargs.get('filename') is not None:
filename = kwargs.pop('filename')
Atoms.__init__(self, *args, **kwargs)
self.read(filename, kwargs.get('filetype'))
else:
Atoms.__init__(self, *args, **kwargs)
def __init__(self, *args, **kwargs):
self.mc_optim = np.zeros(101, np.intc)
Atoms.__init__(self, *args, **kwargs)
