def get_string(self):
"""
Returns a string representation of atomic shell coordinates.
Returns:
String representation of Atomic Coordinate Shells.
"""
center_index = self.struct.indices_from_symbol(self.central_atom)[0]
center = self.struct[center_index].coords
sphere = Structure.get_sites_in_sphere(self.struct, center, self.radius)
row = []
for i, site_dist in enumerate(sphere):
site_symbol = re.sub(r"[^aA-zZ]+", "", site_dist[0].species_string)
ipot = self.pot_dict[site_symbol]
coords = site_dist[0].coords - center
row.append(["{:f}".format(coords[0]), "{:f}".format(coords[1]),
"{:f}".format(coords[2]), ipot, site_symbol,
"{:f}".format(site_dist[1]), i])
row_sorted = str(tabulate(sorted(row, key=itemgetter(5)),
headers=["* x", "y", "z", "ipot",
"Atom", "Distance", "Number"]))
atom_list = row_sorted.replace("--", "**")
return ''.join(["ATOMS\n", atom_list, "\nEND\n"])
def get_supercell_site(unit: Structure, supercell: Structure, site_i: int, image: tuple):
coords = unit[site_i].frac_coords # get coords from unit_cell
scale = np.array(unit.lattice.abc) / supercell.lattice.abc
coords = coords * scale # Scale coords from supercell
coords = coords + (scale * image) # scale coords to image
sites = supercell.get_sites_in_sphere(supercell.lattice.get_cartesian_coords(coords), 0.001, include_index=True)
if len(sites) != 1:
raise Exception('Wrong number of sites at supercell destination {}'.format(sites))
new_site = sites[0][2]
return new_site
def get_center_i(structure : Structure, element : Element, skew_positive=True, delta=0.05):
center_coords = structure.lattice.get_cartesian_coords([0.5, 0.5, 0.5])
sites = structure.get_sites_in_sphere(center_coords, 4, include_index=True)
sites.sort(key=lambda x : x[1])
best_i = None
best_dist = 999999
best_location = 3
for (site, dist, i) in sites: #type: PeriodicSite
if site.specie == element:
if dist < best_dist+delta:
if sum(1 - (site.frac_coords % 1)) < best_location:
best_i = i
best_dist = best_dist
best_location = sum(1 - site.frac_coords)
if best_i:
return best_i
raise Exception('Could not find specified {}'.format(element))
def remove_unstable_interstitials(structure: Structure, relaxed_interstitials: list, dist=0.2, site_indices=None):
"""
:param structure: Structure decorated with all interstitials
:param relaxed_interstitials: list of structures with interstitial as last index
:param dist: tolerance for determining if site belongs to another site
:return:
"""
to_keep = list(range(len(relaxed_interstitials[0])-1))
try:
sga = SpacegroupAnalyzer(structure, symprec=0.1)
structure = sga.get_symmetrized_structure()
except TypeError:
sga = SpacegroupAnalyzer(structure, symprec=0.01)
structure = sga.get_symmetrized_structure()
for ri in relaxed_interstitials: #type: Structure
sites=structure.get_sites_in_sphere(ri.cart_coords[-1], dist, include_index=True)
for indices in structure.equivalent_indices: #look at all sets of equivalent indices
index = sites[0][2]
if index in to_keep: # Already keeping this index
continue
if index in indices:
to_keep = to_keep + indices #keep equivalent indices
break
if len(sites) != 1: # make sure only one site is found
okay = False
if len(sites) > 1:
if all([ x[2] in indices for x in sites]):
okay = True
if not okay:
if site_indices:
raise Exception('Found {} sites for {}'.format(len(sites), site_indices[relaxed_interstitials.index(ri)]))
raise Exception('Found {} sites'.format(len(sites)))
to_remove = [i for i in range(len(structure)) if i not in to_keep]
structure.remove_sites(to_remove)
return structure
def perturb_structure(structure: Structure, center: List[float],
cutoff: float) -> Structure:
""" structure perturbation
Args:
structure: pmg Structure class object
center: Fractional coordinates of a central position.
cutoff: Radius of a sphere in which atoms are perturbed.
"""
result = structure.copy()
cartesian_coords = structure.lattice.get_cartesian_coords(center)
neighboring_atoms = structure.get_sites_in_sphere(pt=cartesian_coords,
r=cutoff,
include_index=True)
# assert cutoff < min(structure.lattice.lengths) / 2.0
# neighboring_atom is composed of (PeriodicSite, distance, index)
for _, _, site_index in neighboring_atoms:
vector = random_3d_vector(defaults.displace_distance)
result.translate_sites(site_index, vector, frac_coords=False)
return result
