def test_apply_transformation(self):
t = TranslateSitesTransformation([0], [0.1, 0.2, 0.3])
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
inv_t = t.inverse
s = inv_t.apply_transformation(s)
self.assertTrue(np.allclose(s[0].frac_coords, [0, 0, 0]))
def test_apply_transformation(self):
t = TranslateSitesTransformation([0], [0.1, 0.2, 0.3])
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
inv_t = t.inverse
s = inv_t.apply_transformation(s)
self.assertTrue(np.allclose(s[0].frac_coords, [0, 0, 0]))
str(t)
def translate_sites(self, lattice):
s = Structure(lattice, [self.central_subsite.specie] + [site.specie for site in self.peripheral_subsites], [self.central_subsite.site.coords] + [site.site.coords for site in self.peripheral_subsites], coords_are_cartesian=True)
trans = TranslateSitesTransformation(range(len(s)), -(lattice.get_fractional_coords(s[0].coords)))
new_s = trans.apply_transformation(s)
trans2 = TranslateSitesTransformation(range(len(s)), (-0.5, -0.5, -0.5))
new_s = trans2.apply_transformation(Structure.from_sites(new_s.sites, to_unit_cell=True))
self.peripheral_subsites = [SubStructureSite.from_coords_and_specie(site.coords, site.specie) for site in new_s.sites[1:]]
self.central_subsite = SubStructureSite.from_coords_and_specie(new_s[0].coords, new_s[0].specie)
def test_apply_transformation_site_by_site(self):
t = TranslateSitesTransformation([0, 1], [[0.1, 0.2, 0.3], [-0.075, -0.075, -0.075]])
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s[1].frac_coords, [0.3, 0.3, 0.3]))
inv_t = t.inverse
s = inv_t.apply_transformation(s)
self.assertAlmostEqual(s[0].distance_and_image_from_frac_coords([0, 0, 0])[0], 0)
self.assertArrayAlmostEqual(s[1].frac_coords, [0.375, 0.375, 0.375])
def test_apply_transformation(self):
t = TranslateSitesTransformation([0, 1], [0.1, 0.2, 0.3])
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s[1].frac_coords, [0.475, 0.575, 0.675]))
inv_t = t.inverse
s = inv_t.apply_transformation(s)
self.assertAlmostEqual(s[0].distance_and_image_from_frac_coords([0, 0, 0])[0], 0)
self.assertTrue(np.allclose(s[1].frac_coords, [0.375, 0.375, 0.375]))
def test_apply_transformation_site_by_site(self):
t = TranslateSitesTransformation(
[0, 1], [[0.1, 0.2, 0.3], [-0.075, -0.075, -0.075]])
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s[1].frac_coords, [0.3, 0.3, 0.3]))
inv_t = t.inverse
s = inv_t.apply_transformation(s)
self.assertTrue(np.allclose(s[0].frac_coords, [0, 0, 0]))
self.assertTrue(np.allclose(s[1].frac_coords, [0.375, 0.375, 0.375]))
str(t)
def test_apply_transformation_site_by_site(self):
t = TranslateSitesTransformation([0, 1], [[0.1, 0.2, 0.3],
[-0.075, -0.075, -0.075]])
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s[1].frac_coords, [0.3, 0.3, 0.3]))
inv_t = t.inverse
s = inv_t.apply_transformation(s)
self.assertTrue(np.allclose(s[0].frac_coords, [0, 0, 0]))
self.assertTrue(np.allclose(s[1].frac_coords, [0.375, 0.375, 0.375]))
str(t)
def test_to_from_dict(self):
d1 = TranslateSitesTransformation([0], [0.1, 0.2, 0.3]).as_dict()
d2 = TranslateSitesTransformation([0, 1], [[0.1, 0.2, 0.3], [-0.075, -0.075, -0.075]]).as_dict()
t1 = TranslateSitesTransformation.from_dict(d1)
t2 = TranslateSitesTransformation.from_dict(d2)
s1 = t1.apply_transformation(self.struct)
s2 = t2.apply_transformation(self.struct)
self.assertTrue(np.allclose(s1[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s2[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s2[1].frac_coords, [0.3, 0.3, 0.3]))
str(t1)
str(t2)
def test_to_from_dict(self):
d1 = TranslateSitesTransformation([0], [0.1, 0.2, 0.3]).as_dict()
d2 = TranslateSitesTransformation([0, 1], [[0.1, 0.2, 0.3],
[-0.075, -0.075, -0.075]]).as_dict()
t1 = TranslateSitesTransformation.from_dict(d1)
t2 = TranslateSitesTransformation.from_dict(d2)
s1 = t1.apply_transformation(self.struct)
s2 = t2.apply_transformation(self.struct)
self.assertTrue(np.allclose(s1[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s2[0].frac_coords, [0.1, 0.2, 0.3]))
self.assertTrue(np.allclose(s2[1].frac_coords, [0.3, 0.3, 0.3]))
str(t1)
str(t2)
def move_all_atoms(structure, disp_ion):
"""
Create structures with displaced ions
"""
yield 'calc_00_0', structure
atoms = [i for i in range(len(structure))]
for atom in atoms:
for direction in range(3):
displacement = [0.] * 3
displacement[direction] = disp_ion
for orientation in ['+', '-']:
transform = TranslateSitesTransformation(
[atom], displacement, vector_in_frac_coords=True)
structure_displaced = transform.apply_transformation(structure)
yield 'calc_%02d_%s%d' % (atom + 1, orientation,
direction + 1), structure_displaced
displacement[direction] = -displacement[direction]
def planar_structure_normalization(structure):
'''
This function does the following:
1. check whether the structure is planar using coordniates standard deviation
2. move the planar layer to the center of c-direction
Args:
structure: pymatgen structure
Return:
a boolean whether the structure is planar
tranformed pymatgen structure
'''
tol = 1E-3 # tolerance to check whether the structure is planar
is_planar = True
coords = structure.frac_coords
ts = TransformedStructure(structure, [])
if np.std(coords[:,2]) < tol :
center_translate = 0.5 - coords[:,2].mean()
elif np.std(coords[:,0]) < tol :
ts.append_transformation(SupercellTransformation([[0,0,1],[0,1,0],[1,0,0]]))
ts.append_transformation(RotationTransformation([0,1,0], 90))
center_translate = 0.5 - coords[:,0].mean()
elif np.std(coords[:,1]) < tol :
ts.append_transformation(SupercellTransformation([[1,0,0],[0,0,1],[0,1,0]]))
ts.append_transformation(RotationTransformation([1,0,0], 90))
center_translate = 0.5 - coords[:,1].mean()
else :
is_planar = False
transformed_structure = None
if is_planar:
ts.append_transformation(TranslateSitesTransformation(
list(range(len(structure))), [0,0,center_translate]))
# Use pymatgen 2019.7.2, ts.structures[-1] may change in a newer version
transformed_structure = ts.structures[-1]
return is_planar, transformed_structure
def test_to_from_dict(self):
d = TranslateSitesTransformation([0], [0.1, 0.2, 0.3]).to_dict
t = TranslateSitesTransformation.from_dict(d)
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
str(t)
def test_to_from_dict(self):
d = TranslateSitesTransformation([0], [0.1, 0.2, 0.3]).as_dict()
t = TranslateSitesTransformation.from_dict(d)
s = t.apply_transformation(self.struct)
self.assertTrue(np.allclose(s[0].frac_coords, [0.1, 0.2, 0.3]))
str(t)