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Update python api examples
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‎example/python_api/example.py‎

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#!/usr/bin/env python
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"""Examples of python APIs."""
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import numpy as np
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import spglib
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def _show_symmetry(symmetry):
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for i in range(symmetry["rotations"].shape[0]):
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print(" --------------- %4d ---------------" % (i + 1))
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rot = symmetry["rotations"][i]
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trans = symmetry["translations"][i]
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print(" rotation:")
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for x in rot:
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print(" [%2d %2d %2d]" % (x[0], x[1], x[2]))
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print(" translation:")
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print(" (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2]))
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def _show_lattice(lattice):
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print("Basis vectors:")
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for vec, axis in zip(lattice, ("a", "b", "c")):
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print(
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"%s %10.5f %10.5f %10.5f"
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% (
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tuple(
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axis,
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)
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+ tuple(vec)
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)
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)
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def _show_cell(lattice, positions, numbers):
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_show_lattice(lattice)
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print("Atomic points:")
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for p, s in zip(positions, numbers):
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print("%2d %10.5f %10.5f %10.5f" % ((s,) + tuple(p)))
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def main():
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silicon = (
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[(4, 0, 0), (0, 4, 0), (0, 0, 4)],
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[
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(0, 0, 0),
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(0, 0.5, 0.5),
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(0.5, 0, 0.5),
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(0.5, 0.5, 0),
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(0.25, 0.25, 0.25),
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(0.25, 0.75, 0.75),
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(0.75, 0.25, 0.75),
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(0.75, 0.75, 0.25),
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],
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[
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14,
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]
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* 8,
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)
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silicon_dist = (
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[(4.01, 0, 0), (0, 4, 0), (0, 0, 3.99)],
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[
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(0.001, 0, 0),
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(0, 0.5, 0.5),
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(0.5, 0, 0.5),
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(0.5, 0.5, 0),
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(0.25, 0.25, 0.251),
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(0.25, 0.75, 0.75),
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(0.75, 0.25, 0.75),
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(0.75, 0.75, 0.25),
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],
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[
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14,
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]
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* 8,
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)
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silicon_prim = (
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[(0, 2, 2), (2, 0, 2), (2, 2, 0)],
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[(0, 0, 0), (0.25, 0.25, 0.25)],
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[14, 14],
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)
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rutile = (
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[(4, 0, 0), (0, 4, 0), (0, 0, 3)],
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[
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(0, 0, 0),
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(0.5, 0.5, 0.5),
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(0.3, 0.3, 0.0),
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(0.7, 0.7, 0.0),
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(0.2, 0.8, 0.5),
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(0.8, 0.2, 0.5),
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],
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[14, 14, 8, 8, 8, 8],
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)
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rutile_dist = (
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[(3.97, 0, 0), (0, 4.03, 0), (0, 0, 3.0)],
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[
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(0, 0, 0),
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(0.5001, 0.5, 0.5),
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(0.3, 0.3, 0.0),
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(0.7, 0.7, 0.002),
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(0.2, 0.8, 0.5),
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(0.8, 0.2, 0.5),
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],
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[14, 14, 8, 8, 8, 8],
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)
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a = 3.07
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c = 3.52
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MgB2 = (
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[(a, 0, 0), (-a / 2, a / 2 * np.sqrt(3), 0), (0, 0, c)],
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[(0, 0, 0), (1.0 / 3, 2.0 / 3, 0.5), (2.0 / 3, 1.0 / 3, 0.5)],
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[12, 5, 5],
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)
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a = [3.0, 0.0, 0.0]
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b = [-3.66666667, 3.68178701, 0.0]
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c = [-0.66666667, -1.3429469, 1.32364995]
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niggli_lattice = np.array([a, b, c])
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print("[get_spacegroup]")
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print(" Spacegroup of Silicon is %s." % spglib.get_spacegroup(silicon))
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print("")
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print("[get_spacegroup]")
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print(" Spacegroup of Silicon is %s." % spglib.get_spacegroup(silicon))
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print("")
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print("[get_spacegroup]")
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print(" Spacegroup of Rutile is %s." % spglib.get_spacegroup(rutile))
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print("")
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print("[get_spacegroup]")
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print(" Spacegroup of MgB2 is %s." % spglib.get_spacegroup(MgB2))
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print("")
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print("[get_symmetry]")
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print(" Symmetry operations of Rutile unitcell are:")
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print("")
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symmetry = spglib.get_symmetry(rutile)
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_show_symmetry(symmetry)
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print("")
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print("[get_symmetry]")
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print(" Symmetry operations of MgB2 are:")
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print("")
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symmetry = spglib.get_symmetry(MgB2)
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_show_symmetry(symmetry)
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print("")
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print("[get_pointgroup]")
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print(" Pointgroup of Rutile is %s." % spglib.get_pointgroup(symmetry["rotations"])[0])
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print("")
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dataset = spglib.get_symmetry_dataset(rutile)
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print("[get_symmetry_dataset] ['international']")
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print(
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" Spacegroup of Rutile is %s (%d)." % (dataset["international"], dataset["number"])
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)
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print("")
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print("[get_symmetry_dataset] ['pointgroup']")
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print(" Pointgroup of Rutile is %s." % (dataset["pointgroup"]))
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print("")
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print("[get_symmetry_dataset] ['hall']")
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print(" Hall symbol of Rutile is %s (%d)." % (dataset["hall"], dataset["hall_number"]))
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print("")
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print("[get_symmetry_dataset] ['wyckoffs']")
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alphabet = "abcdefghijklmnopqrstuvwxyz"
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print(" Wyckoff letters of Rutile are: ", dataset["wyckoffs"])
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print("")
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print("[get_symmetry_dataset] ['equivalent_atoms']")
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print(" Mapping to equivalent atoms of Rutile are: ")
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for i, x in enumerate(dataset["equivalent_atoms"]):
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print(" %d -> %d" % (i + 1, x + 1))
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print("")
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print("[get_symmetry_dataset] ['rotations'], ['translations']")
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print(" Symmetry operations of Rutile unitcell are:")
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for i, (rot, trans) in enumerate(zip(dataset["rotations"], dataset["translations"])):
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print(" --------------- %4d ---------------" % (i + 1))
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print(" rotation:")
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for x in rot:
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print(" [%2d %2d %2d]" % (x[0], x[1], x[2]))
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print(" translation:")
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print(" (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2]))
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print("")
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print("[refine_cell]")
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print(" Refine distorted rutile structure")
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lattice, positions, numbers = spglib.refine_cell(rutile_dist, symprec=1e-1)
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_show_cell(lattice, positions, numbers)
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print("")
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print("[find_primitive]")
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print(" Fine primitive distorted silicon structure")
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lattice, positions, numbers = spglib.find_primitive(silicon_dist, symprec=1e-1)
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_show_cell(lattice, positions, numbers)
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print("")
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print("[standardize_cell]")
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print(" Standardize distorted rutile structure:")
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print(" (to_primitive=0 and no_idealize=0)")
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lattice, positions, numbers = spglib.standardize_cell(
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rutile_dist, to_primitive=0, no_idealize=0, symprec=1e-1
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)
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_show_cell(lattice, positions, numbers)
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print("")
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print("[standardize_cell]")
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print(" Standardize distorted rutile structure:")
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print(" (to_primitive=0 and no_idealize=1)")
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lattice, positions, numbers = spglib.standardize_cell(
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rutile_dist, to_primitive=0, no_idealize=1, symprec=1e-1
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)
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_show_cell(lattice, positions, numbers)
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print("")
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print("[standardize_cell]")
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print(" Standardize distorted silicon structure:")
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print(" (to_primitive=1 and no_idealize=0)")
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lattice, positions, numbers = spglib.standardize_cell(
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silicon_dist, to_primitive=1, no_idealize=0, symprec=1e-1
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)
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_show_cell(lattice, positions, numbers)
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print("")
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print("[standardize_cell]")
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print(" Standardize distorted silicon structure:")
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print(" (to_primitive=1 and no_idealize=1)")
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lattice, positions, numbers = spglib.standardize_cell(
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silicon_dist, to_primitive=1, no_idealize=1, symprec=1e-1
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)
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_show_cell(lattice, positions, numbers)
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print("")
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symmetry = spglib.get_symmetry(silicon)
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print("[get_symmetry]")
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print(" Number of symmetry operations of silicon conventional")
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print(" unit cell is %d (192)." % len(symmetry["rotations"]))
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_show_symmetry(symmetry)
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print("")
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symmetry = spglib.get_symmetry_from_database(525)
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print("[get_symmetry_from_database]")
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print(" Number of symmetry operations of silicon conventional")
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print(" unit cell is %d (192)." % len(symmetry["rotations"]))
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_show_symmetry(symmetry)
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print("")
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reduced_lattice = spglib.niggli_reduce(niggli_lattice)
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print("[niggli_reduce]")
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print(" Original lattice")
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_show_lattice(niggli_lattice)
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print(" Reduced lattice")
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_show_lattice(reduced_lattice)
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print("")
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mapping, grid = spglib.get_ir_reciprocal_mesh(
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[11, 11, 11], silicon_prim, is_shift=[0, 0, 0]
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)
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num_ir_kpt = len(np.unique(mapping))
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print("[get_ir_reciprocal_mesh]")
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print(" Number of irreducible k-points of primitive silicon with")
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print(" 11x11x11 Monkhorst-Pack mesh is %d (56)." % num_ir_kpt)
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print("")
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mapping, grid = spglib.get_ir_reciprocal_mesh([8, 8, 8], rutile, is_shift=[1, 1, 1])
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num_ir_kpt = len(np.unique(mapping))
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print("[get_ir_reciprocal_mesh]")
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print(" Number of irreducible k-points of Rutile with")
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print(" 8x8x8 Monkhorst-Pack mesh is %d (40)." % num_ir_kpt)
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print("")
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mapping, grid = spglib.get_ir_reciprocal_mesh([9, 9, 8], MgB2, is_shift=[0, 0, 1])
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num_ir_kpt = len(np.unique(mapping))
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print("[get_ir_reciprocal_mesh]")
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print(" Number of irreducible k-points of MgB2 with")
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print(" 9x9x8 Monkhorst-Pack mesh is %s (48)." % num_ir_kpt)
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print("")
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if __name__ == '__main__':
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main()
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"""Example to use get_symmetry_dataset with Wurtzite structure input (P6_3mc)."""
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from spglib import get_symmetry_dataset
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lattice = [[3.111, 0, 0], [-1.5555, 2.6942050311733885, 0], [0, 0, 4.988]]
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position = [
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[1.0 / 3, 2.0 / 3, 0.0],
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[2.0 / 3, 1.0 / 3, 0.5],
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[1.0 / 3, 2.0 / 3, 0.6181],
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[2.0 / 3, 1.0 / 3, 0.1181],
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]
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types = [1, 1, 2, 2]
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symprec = 1e-5
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cell = (lattice, position, types)
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dataset = get_symmetry_dataset(cell, symprec=symprec)
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print(f'International symbol: {dataset["international"]} ({dataset["number"]})')
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print(f'Hall symbol: {dataset["hall"]}')
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print("Wyckoff letters: ", end="")
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print(" ".join([f"{w}" for w in dataset["wyckoffs"]]))
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print("Equivalent atoms:")
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for i, equiv_atom in enumerate(dataset["equivalent_atoms"]):
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print(f"{i} -> {equiv_atom}")
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print("Space group operations:")
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for i, (r, t) in enumerate(zip(dataset["rotations"], dataset["translations"])):
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print(f"--- {i + 1} ---")
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for vec in r:
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print(f"{vec[0]:2d} {vec[1]:2d} {vec[2]:2d}")
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print(f"{t[0]:.5f} {t[1]:.5f} {t[2]:.5f}")

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