def analysis(struct, symprec=1e-5):
ensure_pyspg_is_imported()
atoms = structure_to_spglib_atoms(struct)
val = spglib.get_spacegroup(atoms)
print("Spacegroup is:", val)
val = spglib.refine_cell(atoms, symprec=symprec)
print("Primitive", val)
def primitive(struct, symprec=1e-5):
ensure_pyspg_is_imported()
atoms = structure_to_spglib_atoms(struct)
prim = spglib.refine_cell(atoms, symprec=symprec)
sg = spglib.get_spacegroup(atoms)
struct = httk.iface.spglib_if.spglib_out_to_struct(prim)
struct.comment = "Spacegroup: " + sg
return struct
def writeCIF (cell, prec, basename):
# Find spacegroup name and number
sg = spglib.get_spacegroup(cell, symprec=prec)
sg, sgid = sg.split(" (")
sgid = sgid.replace(")", "")
# Find detailed info about the refined cell
lattice, scaled_positions, numbers = spglib.refine_cell (cell, prec)
a, b, c, alpha, beta, gamma = cellParameters (lattice)
f = open((basename + " " + sg + ".cif").replace("/","|"), "w")
f.write ("# Symmetrized structure with precision = %g\n" % prec)
f.write (("data_" + basename + sg + "\n").replace(" ", "_"))
f.write ("_cell_length_a %.7g\n" % a)
f.write ("_cell_length_b %.7g\n" % b)
f.write ("_cell_length_c %.7g\n" % c)
f.write ("_cell_angle_alpha %.7g\n" % alpha)
f.write ("_cell_angle_beta %.7g\n" % beta)
f.write ("_cell_angle_gamma %.7g\n" % gamma)
f.write ("_symmetry_space_group_name_H-M '" + sg + "'\n")
f.write ("_symmetry_Int_Tables_number " + str(sgid) + "\n")
# Write out atomic positions
f.write ("""
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
""")
for pos, at in zip(scaled_positions, numbers):
sym = element_symbols[at]
f.write ("%s %s 1.0 %.7f %.7f %.7f\n" % (sym, sym, pos[0], pos[1], pos[2]))
f.close()
print " %d -> %d" % ( i+1, x+1 )
print
print "[get_symmetry_dataset] ['rotations'], ['translations']"
print " Symmetry operations of Rutile unitcell are:"
for i, (rot,trans) in enumerate( zip( dataset['rotations'], dataset['translations'] ) ):
print " --------------- %4d ---------------" % (i+1)
print " rotation:"
for x in rot:
print " [%2d %2d %2d]" % (x[0], x[1], x[2])
print " translation:"
print " (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2])
print
print "[refine_cell]"
print " Refine distorted rutile structure"
lattice, positions, numbers = spglib.refine_cell(rutile_dist, symprec=1e-1)
show_cell(lattice, positions, numbers)
print
print "[standardize_cell]"
print " Standardize distorted rutile structure:"
print " (to_primitive=0 and no_idealize=0)"
lattice, positions, numbers = spglib.standardize_cell(rutile_dist,
to_primitive=0,
no_idealize=0,
symprec=1e-1)
show_cell(lattice, positions, numbers)
print
print "[standardize_cell]"
print " Standardize distorted rutile structure:"
