def make_supercell(self, disord, replace_dict, dim=(2, 2, 2)):
"""
supercell を作成する
サイトを埋める元素種は置き換える対象を replace dict で指定
"""
latt_dis = np.dot(SymOp.trans(disord.brav), disord.lattice.array)
latt = self.lattice.array
trans = np.linalg.solve(np.array(latt_dis).T, np.array(latt).T).T
int_trans = np.round(trans).astype(np.int)
if (np.abs(trans - int_trans) > 0.01).any():
print(" transration vect seems to be wrong !!!")
exit()
else:
trans = int_trans
trans = np.dot(trans, SymOp.trans(disord.brav))
new_sites = copy.deepcopy(self.sites.sites)
for num, t in zip(dim, trans):
add_site = []
for i in range(1, num):
add_trans = i * t
for site in new_sites:
try:
atom = replace_dict[site.atom[0]]
except KeyError:
replace_dict.update({site.atom[0]: site.atom[0]})
atom = site.atom[0]
add_site.append(CVMSite(atom, site.coord+add_trans))
new_sites += add_site
new_sites = CVMSites(new_sites)
new_label = 'SC' + self.label.label
elems = f_chain(
self.label.elements + new_sites.elements_counter.keys(),
lambda x: [x0[0] for x0 in x],
set, sorted)
new_label = CVMLabel.from_sites(new_sites, new_label, elems)
new_latt = f_chain(latt*(np.array(dim).reshape(3, 1)),
CVMLattice.from_array)
return CVMStructure(new_label, self.brav, self.disord, self.nph,
new_latt, new_sites) # | fnc.echo
def from_sites(cls, sites, label, elements=None):
""" sites obj から生成 """
if not elements:
elements = f_chain(sites.elements_counter.keys(), set, sorted)
num_atoms = [sites.elements_counter[elem] for elem in elements]
return cls(label, elements, num_atoms)