return remainder
surf = Molecule.from_file('D:\\Users\\RyanTrottier\\Documents\\Scrap\\tmp.'+type)
center_i = 787
center = surf[center_i] # pymatgen.core.sites.Site
for radius in [3,4,5,6,8]:
dr = 4
stoich = get_stoichiometry(surf)
sites = [center] + [ x[0] for x in surf.get_neighbors(center, radius)]
mol = Molecule.from_sites(sites)
remainder = get_remainder(mol, stoich)
i = 0 # going to iterate over all sites, starting with the closest
add_sites = surf.get_neighbors_in_shell(center.coords, radius+dr, dr)
add_sites.sort(key=lambda a: a[1])
while max(remainder.values()) > 0: # while atoms still need to be added
(site, distance) = add_sites[i] # type: pymatgen.Site
if remainder[site.specie] > 0 : # if site should be added
mol.append(site.specie, site.coords, properties=site.properties) # Add site
remainder[site.specie] = remainder[site.specie] - 1
i = i + 1
type='gjf'
mol.to(type, 'D:\\Users\\RyanTrottier\\Documents\\Scrap\\feal2o4_{}.{}'.format(radius, type))
def site_layout(symmetrizer: StructureSymmetrizer):
columns = []
distance_cutoff = 2.0
angle_cutoff = 0.3
cnn = CrystalNN()
nn_info = cnn.get_all_nn_info(structure=symmetrizer.structure)
for name, site in symmetrizer.sites.items():
wyckoff_contents = []
data = dict()
data["Site Symmetry"] = site.site_symmetry
data["Wyckoff Letter"] = site.wyckoff_letter
wyckoff_contents.append(html.Label(f"{name}", className="mpc-label"))
site_data = []
repr_idx = site.equivalent_atoms[0]
for idx in site.equivalent_atoms:
coords = symmetrizer.structure[idx].frac_coords
site_data += [(pretty_frac_format(coords[0]),
pretty_frac_format(coords[1]),
pretty_frac_format(coords[2]))]
# lgf = LocalGeometryFinder()
# lgf.setup_structure(structure=symmetrizer.structure)
# se = lgf.compute_structure_environments(
# maximum_distance_factor=distance_cutoff + 0.01)
# strategy = SimplestChemenvStrategy(
# distance_cutoff=distance_cutoff, angle_cutoff=angle_cutoff
# )
# lse = LightStructureEnvironments.from_structure_environments(
# strategy=strategy, structure_environments=se)
# represent the local environment as a molecule
mol = Molecule.from_sites([symmetrizer.structure[repr_idx]] +
[i["site"] for i in nn_info[repr_idx]])
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
disable_callbacks=True,
id=
f"{symmetrizer.structure.composition.reduced_formula}_site_{repr_idx}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
)._sub_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
# env = lse.coordination_environments[repr_idx]
# all_ce = AllCoordinationGeometries()
# co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
# name = co.name
data.update({
# "Environment": name,
# "IUPAC Symbol": co.IUPAC_symbol_str,
"Structure": view,
})
wyckoff_contents.append(get_data_list(data))
wyckoff_contents.append(
Reveal(get_table(site_data),
title=f"Positions ({len(site_data)})",
id=f"{name}-positions"))
columns.append(Column(html.Div(wyckoff_contents)))
_layout = Columns(columns)
return Columns([Column([H4("Sites"), html.Div(_layout)])])
