def __init__(self,
structure,
rmax=15,
hkl_family=[(1, 0, 0), (1, 1, 1)],
surface_energies=[28, 25],
scell=None):
self.structure = structure
self.rmax = rmax
self.hkl_family = hkl_family
self.surface_energies = surface_energies
if scell is None:
ncella = int(np.ceil(2 * rmax / structure.lattice.a))
ncellb = int(np.ceil(2 * rmax / structure.lattice.b))
ncellc = int(np.ceil(2 * rmax / structure.lattice.c))
self.scell = [ncella, ncellb, ncellc]
else:
self.scell = scell
self.structure.make_supercell(self.scell)
recp_lattice = self.structure.lattice.reciprocal_lattice_crystallographic
self.recp_lattice = recp_lattice.scale(1)
self.set_miller_family()
Molecule.__init__(
self, [site.species_and_occu for site in self.structure.sites],
self.structure.cart_coords,
charge=0)
def __init__(self, structure, rmax=15,
hkl_family=[(1, 0, 0), (1, 1, 1)],
surface_energies=[28, 25] ):
self.structure = structure
self.rmax = rmax
self.hkl_family = hkl_family
self.surface_energies = surface_energies
spherical_neighbors = self.structure.get_sites_in_sphere([0.0,0.0,0.0], self.rmax)
recp_lattice = self.structure.lattice.reciprocal_lattice_crystallographic
self.recp_lattice = recp_lattice.scale(1)
self.set_miller_family()
Molecule.__init__(self, [sn[0].species_and_occu for sn in spherical_neighbors],
[sn[0].coords for sn in spherical_neighbors], charge=0)
def __init__(self, structure, rmax=15, hkl_family=((1, 0, 0), (1, 1, 1)),
surface_energies=(28, 25)):
self.structure = structure
self.rmax = rmax
self.hkl_family = list(hkl_family)
self.surface_energies = list(surface_energies)
spherical_neighbors = self.structure.get_sites_in_sphere(
[0.0, 0.0, 0.0], self.rmax)
recp_lattice = self.structure.lattice.reciprocal_lattice_crystallographic
self.recp_lattice = recp_lattice.scale(1)
self.set_miller_family()
Molecule.__init__(self, [sn[0].species_and_occu
for sn in spherical_neighbors],
[sn[0].coords for sn in spherical_neighbors],
charge=0)
def __init__(self, mols, cm_dist=[],
angle={}, link={}, remove=[],
charge=0, spin_multiplicity=None,
validate_proximity=False):
Molecule.__init__(self, mols[0].species_and_occu,
mols[0].cart_coords,
charge=charge,
spin_multiplicity=spin_multiplicity,
validate_proximity=validate_proximity,
site_properties=mols[0].site_properties)
self._sites = list(self._sites)
self.mols = mols
self.cm_dist = cm_dist
self.angle = angle
self.link = link
self.remove = remove
if len(self.mols) == 1:
self.set_distance_matrix(self.mols[0])
def __init__(self, mols, cm_dist=[],
angle={}, link={}, remove=[],
charge=0, spin_multiplicity=None,
validate_proximity=False):
Molecule.__init__(self, mols[0].species_and_occu,
mols[0].cart_coords,
charge=charge,
spin_multiplicity=spin_multiplicity,
validate_proximity=validate_proximity,
site_properties=mols[0].site_properties)
self._sites = list(self._sites)
self.mols = mols
self.cm_dist = cm_dist
self.angle = angle
self.link = link
self.remove = remove
if len(self.mols) == 1:
self.set_distance_matrix(self.mols[0])
def __init__(self, structure, rmax=15, hkl_family=[(1,0,0), (1,1,1)],
surface_energies=[28,25], scell=None):
self.structure = structure
self.rmax = rmax
self.hkl_family = hkl_family
self.surface_energies = surface_energies
if scell is None:
ncella = int(np.ceil(2*rmax/structure.lattice.a))
ncellb = int(np.ceil(2*rmax/structure.lattice.b))
ncellc = int(np.ceil(2*rmax/structure.lattice.c))
self.scell = [ncella, ncellb, ncellc]
else:
self.scell = scell
self.structure.make_supercell(self.scell)
recp_lattice = self.structure.lattice.reciprocal_lattice_crystallographic
self.recp_lattice = recp_lattice.scale(1)
self.set_miller_family()
Molecule.__init__(self, [site.species_and_occu
for site in self.structure.sites],
self.structure.cart_coords, charge=0 )
