def __init__(self, molecule, **kwargs):
GenericQMInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
if 'basis_set' not in kwargs:
self.setting['basis_set'] = 'def2-tzvp'
def __init__(self, molecule, **kwargs):
GenericQMInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
if 'basis_set' not in kwargs:
self.setting['basis_set'] = 'def2-tzvp'
def __init__(self, molecule, **kwargs):
GenericQMInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
if self.setting['periodic']:
univ.getCelldm(self)
box = copy.deepcopy(self.setting['celldm'][:3])
self.setting['box'] = box
else:
self.setting['box'] = False
self.setting['celldm'] = False
def __init__(self, molecule, **kwargs):
GenericQMInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
if self.setting['periodic']:
univ.getCelldm(self)
box = copy.deepcopy(self.setting['celldm'][:3])
self.setting['box'] = box
else:
self.setting['box'] = False
self.setting['celldm'] = False
def write(self, name=None, **kwargs):
#if self.setting['periodic']:
self.celldm2lattice()
inp, molecule = \
GenericQMInput.write(self, name, **self.setting)
if 'isolated' in self.setting and self.setting['isolated']\
or 'periodic' in self.setting and not self.setting['periodic']:
if 'center_molecule' in self.setting and self.setting[
'center_molecule']:
cm = molecule.getCenterOfMass()
molecule.center(cm)
molecule.shift(self.setting['lattice'].sum(0) / 2)
if 'pp_list' in self.setting:
pp_list = self.setting['pp_list']
itr = 1
for pp_data in pp_list:
pp_inds = pp_data[0]
if type(pp_inds) is not list:
pp_inds = [pp_inds]
pp_name = pp_data[1]
pp = pp_data[2]
pp.setting['program'] = self.setting['program']
pp.write(pp_name, inplace=False)
molecule.setAtoms(pp_inds, string=pp_name)
Zn = molecule.type_list[pp_inds[0]]
molecule.setAtoms(pp_inds, element=Zn + str(itr))
itr += 1
return inp, molecule
def __init__(self, molecule, **kwargs):
GenericQMInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
if 'cutoff' not in kwargs:
self.setting['cutoff'] = 100
if not self.setting['periodic'] and 'isolation' not in kwargs:
self.setting['isolation'] = 'mt'
self.pp_files = []
if 'periodic' in self.setting and self.setting['periodic']:
self.celldm2lattice()
if 'pp_type' not in kwargs:
self.setting['pp_type'] = 'geodecker'
if 'full_kmesh' not in self.setting:
self.setting['full_kmesh'] = False
if 'theory' in self.setting and self.setting['theory'] == 'hse06':
if 'pp_theory' not in self.setting:
self.setting['pp_theory'] = 'pbe'
if 'fractional_coordinate' not in kwargs:
self.setting['fractional_coordinate'] = False
univ.getCelldm(self)
def __init__(self, molecule, **kwargs):
GenericQMInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
if 'cutoff' not in kwargs:
self.setting['cutoff'] = 100
if not self.setting['periodic'] and 'isolation' not in kwargs:
self.setting['isolation'] = 'mt'
self.pp_files = []
if 'periodic' in self.setting and self.setting['periodic']:
self.celldm2lattice()
if 'pp_type' not in kwargs:
self.setting['pp_type'] = 'geodecker'
if 'full_kmesh' not in self.setting:
self.setting['full_kmesh'] = False
if 'theory' in self.setting and self.setting['theory'] == 'hse06':
if 'pp_theory' not in self.setting:
self.setting['pp_theory'] = 'pbe'
if 'fractional_coordinate' not in kwargs:
self.setting['fractional_coordinate'] = False
univ.getCelldm(self)
def write(self, name=None, **kwargs):
if self.setting['periodic']:
self.celldm2lattice()
inp, molecule = \
GenericQMInput.write(self, name, **self.setting)
if 'pp_list' in self.setting:
pp_list = self.setting['pp_list']
itr = 1
for pp_data in pp_list:
pp_inds = pp_data[0]
if type(pp_inds) is not list:
pp_inds = [pp_inds]
pp_name = pp_data[1]
pp = pp_data[2]
pp.setting['program'] = self.setting['program']
pp.write(pp_name, inplace=False)
molecule.setAtoms(pp_inds, string=pp_name)
Zn = molecule.type_list[pp_inds[0]]
molecule.setAtoms(pp_inds, element=Zn + str(itr))
itr += 1
return inp, molecule
