def __init__(self,
name,
atoms=None,
vacuum=6.0,
h=0.17,
xc='PBE',
setups='paw',
mode='fd',
fragment_list=None):
self.name = name
if atoms:
self.system = atoms
else:
self.system = mol(name) #use the default g22
self.system.center(vacuum=vacuum)
cell = self.system.get_cell()
self.h = h
self.system.set_cell((cell / (4 * h)).round() * 4 * h)
self.system.center()
self.xc = xc
self.setups = setups
self.mode = mode
self.calc = None
if fragment_list:
self.fragment_list = fragment_list
else:
self.fragment_list = self.system.get_chemical_symbols()
def __init__(self,name, atoms = None, fragment_list=None, minimize = False):
self.name = name
if atoms:
self.system = atoms
else:
self.system = mol(name) #use the default g22
self.system.center(vacuum=10.0)
self.calc = None
if fragment_list:
self.fragment_list = fragment_list
else:
self.fragment_list = self.system.get_chemical_symbols()
self.minimize = minimize
def __init__(self,name, atoms = None, fragment_list=None,
minimize = False, ff_file_path=get_datafile('ffield.reax')):
self.name = name
if atoms:
self.system = atoms
else:
self.system = mol(name) #use the default g22
self.system.center(vacuum=10.0)
self.calc = None
if fragment_list:
self.fragment_list = fragment_list
else:
self.fragment_list = self.system.get_chemical_symbols()
self.minimize = minimize
self.ff_file_path = ff_file_path
def __init__(self,name, atoms = None,vacuum=6.0, h=0.17, xc='PBE',
setups='paw', mode='fd',fragment_list=None):
self.name = name
if atoms:
self.system = atoms
else:
self.system = mol(name) #use the default g22
self.system.center(vacuum=vacuum)
cell = self.system.get_cell()
self.h = h
self.system.set_cell((cell / (4 * h)).round() * 4 * h)
self.system.center()
self.xc = xc
self.setups = setups
self.mode = mode
self.calc = None
if fragment_list:
self.fragment_list = fragment_list
else:
self.fragment_list = self.system.get_chemical_symbols()
def __init__(self,
name,
atoms=None,
vacuum=6.0,
h=0.2,
fragment_list=None,
minimize=False):
self.name = name
if atoms:
self.system = atoms
else:
self.system = mol(name) #use the default g22
self.system.center(vacuum=vacuum)
self.h = h
cell = self.system.get_cell()
self.system.set_cell((cell / (4 * h)).round() * 4 * h)
self.system.center()
self.calc = None
if fragment_list:
self.fragment_list = fragment_list
else:
self.fragment_list = self.system.get_chemical_symbols()
self.minimize = minimize
