def make_o_si_o_sym_table(si_o_structure, si_o_bond_sym_table):
scatterers = si_o_structure.scatterers()
si_o_full_sym_table = si_o_bond_sym_table.full_connectivity(
site_symmetry_table=si_o_structure.site_symmetry_table())
o_si_o_sym_table = crystal.pair_sym_table(si_o_full_sym_table.size())
for i_seq,pair_sym_dict in enumerate(si_o_full_sym_table):
if (scatterers[i_seq].scattering_type != "Si"): continue
jr_list = []
for j_seq,sym_ops in pair_sym_dict.items():
if (scatterers[j_seq].scattering_type != "O"): continue
for rt_mx_ji in sym_ops:
jr_list.append((j_seq,rt_mx_ji))
for i_jj1 in xrange(0,len(jr_list)-1):
jr1 = jr_list[i_jj1]
i_seq = jr1[0]
rt_mx_jr1_inv = jr1[1].inverse()
for i_jj2 in xrange(i_jj1+1,len(jr_list)):
jr2 = jr_list[i_jj2]
j_seq = jr2[0]
rt_mx_jr21 = rt_mx_jr1_inv.multiply(jr2[1])
if (i_seq <= j_seq):
o_si_o_sym_table[i_seq].setdefault(j_seq).append(rt_mx_jr21)
else:
o_si_o_sym_table[j_seq].setdefault(i_seq).append(rt_mx_jr21.inverse())
return o_si_o_sym_table.tidy(
site_symmetry_table=si_o_structure.site_symmetry_table())
def __init__(self, si_structure, si_si_sym_table):
self.structure = si_structure.deep_copy_scatterers()
bond_sym_table = crystal.pair_sym_table(si_si_sym_table.size())
sites_frac = si_structure.sites_frac()
i_oxygen = count(1)
for i_seq,pair_sym_dict in enumerate(si_si_sym_table):
site_frac_i = mx.col(sites_frac[i_seq])
for j_seq,sym_ops in pair_sym_dict.items():
assert j_seq >= i_seq
for rt_mx_ji in sym_ops:
site_frac_ji = mx.col(rt_mx_ji * sites_frac[j_seq])
bond_center = (site_frac_i + site_frac_ji) / 2
i_seq_o = self.structure.scatterers().size()
self.structure.add_scatterer(xray.scatterer(
label="O%d"%i_oxygen.next(),
site=bond_center))
bond_sym_table[i_seq].setdefault(i_seq_o).append(
sgtbx.rt_mx(1,1))
bond_sym_table[j_seq].setdefault(i_seq_o).append(
rt_mx_ji.inverse_cancel())
bond_sym_table.append(crystal.pair_sym_dict())
self.bond_sym_table = bond_sym_table.tidy(
site_symmetry_table=self.structure.site_symmetry_table())
