def __init__(self,
atoms=None,
command=None,
xc='LDA',
spin='non-polarized',
ghosts=[],
**kwargs):
if atoms is not None:
finder = DojoFinder()
elems = list(dict.fromkeys(atoms.get_chemical_symbols()).keys())
elem_dict = dict(zip(elems, range(1, len(elems) + 1)))
symbols = atoms.get_chemical_symbols()
# ghosts
ghost_symbols = [symbols[i] for i in ghosts]
ghost_elems = list(dict.fromkeys(ghost_symbols).keys())
tags = [1 if i in ghosts else 0 for i in range(len(atoms))]
atoms.set_tags(tags)
pseudo_path = finder.get_pp_path(xc=xc)
if spin == 'spin-orbit':
rel = 'fr'
else:
rel = 'sr'
species = [
Species(symbol=elem,
pseudopotential=finder.get_pp_fname(elem,
xc=xc,
rel=rel),
ghost=False) for elem in elem_dict.keys()
]
for elem in ghost_elems:
species.append(
Species(symbol=elem,
pseudopotential=finder.get_pp_fname(elem,
xc=xc,
rel=rel),
tag=1,
ghost=True))
Siesta.__init__(self,
xc=xc,
spin=spin,
atoms=atoms,
pseudo_path=pseudo_path,
species=species,
**kwargs)
def __init__(self, nodes=1, ppn=8, **kwargs):
Siesta.__init__(self, **kwargs)
self.nodes=nodes
self.ppn=ppn
def __init__(self, nodes=1, ppn=8, **kwargs):
Siesta.__init__(self, **kwargs)
self.nodes = nodes
self.ppn = ppn
def __init__(self,
atoms=None,
command=None,
xc='LDA',
spin='non-polarized',
basis_set='DZP',
ghosts=[],
input_basis_set={},
pseudo_path=None,
input_pp={},
pp_accuracy='standard',
**kwargs):
# non-perturnbative polarized orbital.
self.npt_elems = set()
if atoms is not None:
finder = DojoFinder()
elems = list(dict.fromkeys(atoms.get_chemical_symbols()).keys())
self.elem_dict = dict(zip(elems, range(1, len(elems) + 1)))
symbols = atoms.get_chemical_symbols()
# ghosts
ghost_symbols = [symbols[i] for i in ghosts]
ghost_elems = list(dict.fromkeys(ghost_symbols).keys())
tags = [1 if i in ghosts else 0 for i in range(len(atoms))]
atoms.set_tags(tags)
if pseudo_path is None:
pseudo_path = finder.get_pp_path(xc=xc, accuracy=pp_accuracy)
if spin == 'spin-orbit':
rel = 'fr'
else:
rel = 'sr'
species = []
for elem, index in self.elem_dict.items():
if elem not in input_basis_set:
bselem = basis_set
if elem in ['Li', 'Be', 'Na', 'Mg']:
self.npt_elems.add(f"{elem}.{index}")
else:
bselem = PAOBasisBlock(input_basis_set[elem])
if elem not in input_pp:
pseudopotential = finder.get_pp_fname(
elem, xc=xc, rel=rel, accuracy=pp_accuracy)
else:
pseudopotential = os.path.join(
pseudo_path, input_pp[elem])
species.append(Species(symbol=elem,
pseudopotential=pseudopotential,
basis_set=bselem,
ghost=False))
for elem in ghost_elems:
species.append(
Species(symbol=elem,
pseudopotential=finder.get_pp_fname(
elem, xc=xc, rel=rel, accuracy=pp_accuracy),
tag=1,
ghost=True))
Siesta.__init__(self,
xc=xc,
spin=spin,
atoms=atoms,
pseudo_path=pseudo_path,
species=species,
**kwargs)
self.set_npt_elements()
