mirror of https://github.com/phonopy/phonopy.git
A test for Symmetry class is added.
This commit is contained in:
Atsushi Togo
parent
9bd28af1ef
commit
9dc26f7546
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@ -69,13 +69,17 @@ class PhonopyYaml:
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self._supercell_matrix = None
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self._primitive_matrix = None
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self._force_constants = None
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self._p2s_map = None
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self._s2p_map = None
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self._p2p_map = None
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self._u2p_map = None
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self._nac_params = None
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self._version = None
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def get_unitcell(self):
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return self._unitcell
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def set_unitcell(self, cell):
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self._unitcell = cell
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def get_primitive(self):
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return self._primitive
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@ -113,8 +117,9 @@ class PhonopyYaml:
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nac_factor = self._nac_params['factor']
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dielectric = self._nac_params['dielectric']
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lines.append("phonopy:")
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lines.append(" version: %s" % self._version)
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if self._version:
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lines.append("phonopy:")
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lines.append(" version: %s" % self._version)
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if self._calculator:
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lines.append(" calculator: %s" % self._calculator)
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if self._nac_params:
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@ -212,7 +212,8 @@ class Symmetry:
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zip(ops['rotations'], ops['translations'])):
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diff = np.dot(pos[i], r.T) + t - pos[eq_atom]
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if (abs(diff - np.rint(diff)) < self._symprec).all():
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diff -= np.rint(diff)
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if np.linalg.norm(diff) < self._symprec:
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map_operations[i] = j
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break
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@ -289,42 +290,4 @@ def get_lattice_vector_equivalence(point_symmetry):
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equivalence[0] = True
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return equivalence
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if __name__ == '__main__':
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from phonopy.structure.symmetry import Symmetry
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from phonopy.interface.vasp import read_vasp
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def get_magmom(text):
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magmom = []
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for numxmag in text.split():
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if '*' in numxmag:
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num, mag = numxmag.split('*')
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magmom += [float(mag)] * int(num)
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else:
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magmom.append(float(numxmag))
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return magmom
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def parse_incar(filename):
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for line in open(filename):
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for conf in line.split(';'):
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if 'MAGMOM' in conf:
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return get_magmom(conf.split('=')[1])
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cell = read_vasp("POSCAR")
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symmetry = Symmetry(cell, symprec=1e-3)
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map_nonspin = symmetry.get_map_atoms()
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print("Number of operations w/o spin %d" %
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len(symmetry.get_symmetry_operations()['rotations']))
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magmoms = parse_incar("INCAR")
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cell.set_magnetic_moments(magmoms)
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symmetry = Symmetry(cell, symprec=1e-3)
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print("Number of operations w spin %d" %
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len(symmetry.get_symmetry_operations()['rotations']))
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map_withspin = symmetry.get_map_atoms()
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if ((map_nonspin - map_withspin) == 0).all():
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print(True)
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else:
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print(False)
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print(map_nonspin)
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print(map_withspin)
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@ -7,7 +7,7 @@ from phonopy.structure.cells import get_supercell, get_primitive
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class TestDynmatToFc(unittest.TestCase):
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def setUp(self):
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filename = "POSCAR.yaml"
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filename = "../NaCl.yaml"
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self._cell = get_unitcell_from_phonopy_yaml(filename)
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def tearDown(self):
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@ -35,7 +35,7 @@ class TestPhonopyYaml(unittest.TestCase):
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# print(unitcell)
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def _get_phonon(self):
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cell = read_vasp("POSCAR_NaCl")
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cell = read_vasp("../POSCAR_NaCl")
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phonon = Phonopy(cell,
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np.diag([2, 2, 2]),
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primitive_matrix=[[0, 0.5, 0.5],
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@ -0,0 +1,11 @@
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lattice:
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- [ 2.812696943681890, 0.000000000000000, 0.000000000000000 ] # a
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- [ 0.000000000000000, 2.812696943681890, 0.000000000000000 ] # b
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- [ 0.000000000000000, 0.000000000000000, 2.812696943681890 ] # c
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points:
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- symbol: Cr # 1
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coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
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mass: 51.996100
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- symbol: Cr # 2
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coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
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mass: 51.996100
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@ -0,0 +1,71 @@
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import unittest
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import numpy as np
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import time
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from phonopy.structure.symmetry import Symmetry
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from phonopy.structure.cells import get_supercell
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from phonopy.interface.phonopy_yaml import get_unitcell_from_phonopy_yaml
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class TestSymmetry(unittest.TestCase):
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def setUp(self):
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pass
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def tearDown(self):
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pass
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def test_get_map_operations(self):
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symprec = 1e-5
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cell = get_unitcell_from_phonopy_yaml("../NaCl.yaml")
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scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
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symmetry = Symmetry(scell, symprec=symprec)
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map_ops_cmp = [ 0, 2, 51, 53, 8, 1, 65, 98, 3, 14,
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34, 24, 76, 69, 54, 110, 576, 198, 229, 208,
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201, 192, 210, 294, 5, 67, 36, 57, 18, 90,
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23, 114, 0, 9, 1, 96, 6, 323, 98, 326,
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3, 42, 17, 293, 16, 130, 99, 337, 192, 194,
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202, 199, 205, 196, 200, 193, 12, 5, 30, 108,
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37, 128, 291, 302]
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start = time.time()
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symmetry._set_map_operations()
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end = time.time()
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# print(end - start)
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map_ops = symmetry.get_map_operations()
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self.assertTrue((map_ops_cmp == map_ops).all())
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def test_magmom(self):
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symprec = 1e-5
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cell = get_unitcell_from_phonopy_yaml("Cr.yaml")
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symmetry_nonspin = Symmetry(cell, symprec=symprec)
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atom_map_nonspin = symmetry_nonspin.get_map_atoms()
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len_sym_nonspin = len(
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symmetry_nonspin.get_symmetry_operations()['rotations'])
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spin = [1, -1]
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cell_withspin = cell.copy()
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cell_withspin.set_magnetic_moments(spin)
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symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
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atom_map_withspin = symmetry_withspin.get_map_atoms()
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len_sym_withspin = len(
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symmetry_withspin.get_symmetry_operations()['rotations'])
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broken_spin = [1, -2]
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cell_brokenspin = cell.copy()
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cell_brokenspin = cell.copy()
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cell_brokenspin.set_magnetic_moments(broken_spin)
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symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
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atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
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len_sym_brokenspin = len(
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symmetry_brokenspin.get_symmetry_operations()['rotations'])
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self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
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self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
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self.assertTrue(len_sym_nonspin == len_sym_withspin)
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self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
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if __name__ == '__main__':
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suite = unittest.TestLoader().loadTestsFromTestCase(TestSymmetry)
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unittest.TextTestRunner(verbosity=2).run(suite)
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# unittest.main()
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@ -1,15 +0,0 @@
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Na Cl
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1.00000000000000
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5.6903014761756712 0.0000000000000000 0.0000000000000000
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0.0000000000000000 5.6903014761756712 0.0000000000000000
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0.0000000000000000 0.0000000000000000 5.6903014761756712
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4 4
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Direct
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0.0000000000000000 0.0000000000000000 0.0000000000000000
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0.0000000000000000 0.5000000000000000 0.5000000000000000
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0.5000000000000000 0.0000000000000000 0.5000000000000000
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0.5000000000000000 0.5000000000000000 0.0000000000000000
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0.5000000000000000 0.5000000000000000 0.5000000000000000
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0.5000000000000000 0.0000000000000000 0.0000000000000000
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0.0000000000000000 0.5000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 0.5000000000000000
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@ -12,7 +12,7 @@ from phonopy.structure.atoms import PhonopyAtoms as Atoms
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class TestUnfolding(unittest.TestCase):
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def setUp(self):
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self._cell = read_vasp("POSCAR")
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self._cell = read_vasp("../POSCAR_NaCl")
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# print(self._cell)
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self._unfolding = None
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