def test_structure_transform(self):
# Test trivial case
trivial = self.fit_r4.structure_transform(self.structure,
self.structure.copy())
self.assertArrayAlmostEqual(trivial, self.fit_r4)
# Test simple rotation
rot_symm_op = SymmOp.from_axis_angle_and_translation([1, 1, 1], 55.5)
rot_struct = self.structure.copy()
rot_struct.apply_operation(rot_symm_op)
rot_tensor = self.fit_r4.rotate(rot_symm_op.rotation_matrix)
trans_tensor = self.fit_r4.structure_transform(self.structure, rot_struct)
self.assertArrayAlmostEqual(rot_tensor, trans_tensor)
# Test supercell
bigcell = self.structure.copy()
bigcell.make_supercell([2, 2, 3])
trans_tensor = self.fit_r4.structure_transform(self.structure, bigcell)
self.assertArrayAlmostEqual(self.fit_r4, trans_tensor)
# Test rotated primitive to conventional for fcc structure
sn = self.get_structure("Sn")
sn_prim = SpacegroupAnalyzer(sn).get_primitive_standard_structure()
sn_prim.apply_operation(rot_symm_op)
rotated = self.fit_r4.rotate(rot_symm_op.rotation_matrix)
transformed = self.fit_r4.structure_transform(sn, sn_prim)
self.assertArrayAlmostEqual(rotated, transformed)
def test_fit(self):
"""
Take two known matched structures
1) Ensure match
2) Ensure match after translation and rotations
3) Ensure no-match after large site translation
4) Ensure match after site shuffling
"""
sm = StructureMatcher()
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
# Test rotational/translational invariance
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
np.array([0.4, 0.7, 0.9]))
self.struct_list[1].apply_operation(op)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test failure under large atomic translation
self.struct_list[1].translate_sites([0], [.4, .4, .2],
frac_coords=True)
self.assertFalse(sm.fit(self.struct_list[0], self.struct_list[1]))
self.struct_list[1].translate_sites([0], [-.4, -.4, -.2],
frac_coords=True)
# random.shuffle(editor._sites)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test FrameworkComporator
sm2 = StructureMatcher(comparator=FrameworkComparator())
lfp = read_structure(os.path.join(test_dir, "LiFePO4.cif"))
nfp = read_structure(os.path.join(test_dir, "NaFePO4.cif"))
self.assertTrue(sm2.fit(lfp, nfp))
self.assertFalse(sm.fit(lfp, nfp))
#Test anonymous fit.
self.assertEqual(sm.fit_anonymous(lfp, nfp),
{Composition("Li"): Composition("Na")})
self.assertAlmostEqual(sm.get_minimax_rms_anonymous(lfp, nfp)[0],
0.096084154118549828)
#Test partial occupancies.
s1 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]],
[{"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
s2 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]],
[{"Fe": 0.25}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.75}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
self.assertFalse(sm.fit(s1, s2))
self.assertFalse(sm.fit(s2, s1))
s2 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]],
[{"Fe": 0.25}, {"Fe": 0.25}, {"Fe": 0.25},
{"Fe": 0.25}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
self.assertEqual(sm.fit_anonymous(s1, s2),
{Composition("Fe0.5"): Composition("Fe0.25")})
self.assertAlmostEqual(sm.get_minimax_rms_anonymous(s1, s2)[0], 0)
def test_init(self):
fitter = StructureFitter(self.b, self.a)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
#Now to try with rotated structure
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False, np.array([0, 0, 1]))
editor = StructureEditor(self.a)
editor.apply_operation(op)
fitter = StructureFitter(self.b, editor.modified_structure)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
#test with a supercell
mod = SupercellMaker(self.a, scaling_matrix=[[2, 0, 0], [0, 1, 0], [0, 0, 1]])
a_super = mod.modified_structure
fitter = StructureFitter(self.b, a_super)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
# Test with a structure with a translated point
editor = StructureEditor(self.a)
site = self.a[0]
editor.delete_site(0)
trans = np.random.randint(0, 1000, 3)
editor.insert_site(0, site.species_and_occu, site.frac_coords + trans, False, False)
fitter = StructureFitter(self.b, editor.modified_structure)
self.assertTrue(fitter.mapping_op != None, "No fit found for translation {}!".format(trans))
parser = CifParser(os.path.join(test_dir, "FePO4a.cif"))
a = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, "FePO4b.cif"))
b = parser.get_structures()[0]
fitter = StructureFitter(b, a)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.structure.apply_operation(op)
self.assertArrayAlmostEqual(
self.structure.lattice.matrix,
[[0.000000, 3.840198, 0.000000],
[-3.325710, 1.920099, 0.000000],
[2.217138, -0.000000, 3.135509]], 5)
def test_fit(self):
"""
Take two known matched structures
1) Ensure match
2) Ensure match after translation and rotations
3) Ensure no-match after large site translation
4) Ensure match after site shuffling
"""
sm = StructureMatcher()
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
# Test rotational/translational invariance
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
np.array([0.4, 0.7, 0.9]))
self.struct_list[1].apply_operation(op)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test failure under large atomic translation
self.struct_list[1].translate_sites([0], [.4, .4, .2],
frac_coords=True)
self.assertFalse(sm.fit(self.struct_list[0], self.struct_list[1]))
self.struct_list[1].translate_sites([0], [-.4, -.4, -.2],
frac_coords=True)
# random.shuffle(editor._sites)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test FrameworkComporator
sm2 = StructureMatcher(comparator=FrameworkComparator())
lfp = self.get_structure("LiFePO4")
nfp = self.get_structure("NaFePO4")
self.assertTrue(sm2.fit(lfp, nfp))
self.assertFalse(sm.fit(lfp, nfp))
#Test anonymous fit.
self.assertEqual(sm.fit_anonymous(lfp, nfp), True)
self.assertAlmostEqual(sm.get_rms_anonymous(lfp, nfp)[0],
0.060895871160262717)
#Test partial occupancies.
s1 = Structure(Lattice.cubic(3),
[{"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
s2 = Structure(Lattice.cubic(3),
[{"Fe": 0.25}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.75}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
self.assertFalse(sm.fit(s1, s2))
self.assertFalse(sm.fit(s2, s1))
s2 = Structure(Lattice.cubic(3),
[{"Mn": 0.5}, {"Mn": 0.5}, {"Mn": 0.5},
{"Mn": 0.5}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
self.assertEqual(sm.fit_anonymous(s1, s2), True)
self.assertAlmostEqual(sm.get_rms_anonymous(s1, s2)[0], 0)
def __init__(self, axis, angle, angle_in_radians=False):
"""
"""
self._axis = axis
self._angle = angle
self._angle_in_radians = angle_in_radians
self._symmop = SymmOp.from_axis_angle_and_translation(
self._axis, self._angle, self._angle_in_radians)
def __init__(self, axis, angle, angle_in_radians=False):
"""
"""
self.axis = axis
self.angle = angle
self.angle_in_radians = angle_in_radians
self._symmop = SymmOp.from_axis_angle_and_translation(
self.axis, self.angle, self.angle_in_radians)
def test_list_based_functions(self):
# zeroed
tc = TensorCollection([1e-4 * Tensor(np.eye(3))] * 4)
for t in tc.zeroed():
self.assertArrayEqual(t, np.zeros((3, 3)))
for t in tc.zeroed(1e-5):
self.assertArrayEqual(t, 1e-4 * np.eye(3))
self.list_based_function_check("zeroed", tc)
self.list_based_function_check("zeroed", tc, tol=1e-5)
# transform
symm_op = SymmOp.from_axis_angle_and_translation(
[0, 0, 1], 30, False, [0, 0, 1]
)
self.list_based_function_check("transform", self.seq_tc, symm_op=symm_op)
# symmetrized
self.list_based_function_check("symmetrized", self.seq_tc)
# rotation
a = 3.14 * 42.5 / 180
rotation = SquareTensor(
[[math.cos(a), 0, math.sin(a)], [0, 1, 0], [-math.sin(a), 0, math.cos(a)]]
)
self.list_based_function_check("rotate", self.diff_rank, matrix=rotation)
# is_symmetric
self.assertFalse(self.seq_tc.is_symmetric())
self.assertTrue(self.diff_rank.is_symmetric())
# fit_to_structure
self.list_based_function_check("fit_to_structure", self.diff_rank, self.struct)
self.list_based_function_check("fit_to_structure", self.seq_tc, self.struct)
# fit_to_structure
self.list_based_function_check("fit_to_structure", self.diff_rank, self.struct)
self.list_based_function_check("fit_to_structure", self.seq_tc, self.struct)
# voigt
self.list_based_function_check("voigt", self.diff_rank)
# is_voigt_symmetric
self.assertTrue(self.diff_rank.is_voigt_symmetric())
self.assertFalse(self.seq_tc.is_voigt_symmetric())
# Convert to ieee
for entry in self.ieee_data[:2]:
xtal = entry["xtal"]
tc = TensorCollection([entry["original_tensor"]] * 3)
struct = entry["structure"]
self.list_based_function_check("convert_to_ieee", tc, struct)
# from_voigt
tc_input = [t for t in np.random.random((3, 6, 6))]
tc = TensorCollection.from_voigt(tc_input)
for t_input, t in zip(tc_input, tc):
self.assertArrayAlmostEqual(Tensor.from_voigt(t_input), t)
def _check_R2_axes_asym(self):
"""
Test for 2-fold rotation along the principal axes. Used to handle
asymetric top molecules.
"""
for v in self.principal_axes:
op = SymmOp.from_axis_angle_and_translation(v, 180)
if self.is_valid_op(op):
self.symmops.append(op)
self.rot_sym.append((v, 2))
def _check_R2_axes_asym(self):
"""
Test for 2-fold rotation along the principal axes. Used to handle
asymetric top molecules.
"""
for v in self.principal_axes:
op = SymmOp.from_axis_angle_and_translation(v, 180)
if self.is_valid_op(op):
self.symmops.append(op)
self.rot_sym.append((v, 2))
def test_list_based_functions(self):
# zeroed
tc = TensorCollection([1e-4*Tensor(np.eye(3))]*4)
for t in tc.zeroed():
self.assertArrayEqual(t, np.zeros((3, 3)))
for t in tc.zeroed(1e-5):
self.assertArrayEqual(t, 1e-4*np.eye(3))
self.list_based_function_check("zeroed", tc)
self.list_based_function_check("zeroed", tc, tol=1e-5)
# transform
symm_op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30,
False, [0, 0, 1])
self.list_based_function_check("transform", self.seq_tc, symm_op=symm_op)
# symmetrized
self.list_based_function_check("symmetrized", self.seq_tc)
# rotation
a = 3.14 * 42.5 / 180
rotation = SquareTensor([[math.cos(a), 0, math.sin(a)], [0, 1, 0],
[-math.sin(a), 0, math.cos(a)]])
self.list_based_function_check("rotate", self.diff_rank, matrix=rotation)
# is_symmetric
self.assertFalse(self.seq_tc.is_symmetric())
self.assertTrue(self.diff_rank.is_symmetric())
# fit_to_structure
self.list_based_function_check("fit_to_structure", self.diff_rank, self.struct)
self.list_based_function_check("fit_to_structure", self.seq_tc, self.struct)
# fit_to_structure
self.list_based_function_check("fit_to_structure", self.diff_rank, self.struct)
self.list_based_function_check("fit_to_structure", self.seq_tc, self.struct)
# voigt
self.list_based_function_check("voigt", self.diff_rank)
# is_voigt_symmetric
self.assertTrue(self.diff_rank.is_voigt_symmetric())
self.assertFalse(self.seq_tc.is_voigt_symmetric())
# Convert to ieee
for entry in self.ieee_data[:2]:
xtal = entry['xtal']
tc = TensorCollection([entry['original_tensor']]*3)
struct = entry['structure']
self.list_based_function_check("convert_to_ieee", tc, struct)
# from_voigt
tc_input = [t for t in np.random.random((3, 6, 6))]
tc = TensorCollection.from_voigt(tc_input)
for t_input, t in zip(tc_input, tc):
self.assertArrayAlmostEqual(Tensor.from_voigt(t_input), t)
def __init__(self, axis, angle, angle_in_radians=False):
"""
Args:
axis (3x1 array): Axis of rotation, e.g., [1, 0, 0]
angle (float): Angle to rotate
angle_in_radians (bool): Set to True if angle is supplied in radians.
Else degrees are assumed.
"""
self.axis = axis
self.angle = angle
self.angle_in_radians = angle_in_radians
self._symmop = SymmOp.from_axis_angle_and_translation(self.axis, self.angle, self.angle_in_radians)
def test_transform(self):
# Rank 3
tensor = Tensor(np.arange(0, 27).reshape(3, 3, 3))
symm_op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
[0, 0, 1])
new_tensor = tensor.transform(symm_op)
self.assertArrayAlmostEqual(
new_tensor, [[[-0.871, -2.884, -1.928], [-2.152, -6.665, -4.196],
[-1.026, -2.830, -1.572]],
[[0.044, 1.531, 1.804], [4.263, 21.008, 17.928],
[5.170, 23.026, 18.722]],
[[1.679, 7.268, 5.821], [9.268, 38.321, 29.919],
[8.285, 33.651, 26.000]]], 3)
def _find_spherical_axes(self):
"""
Looks for R5, R4, R3 and R2 axes in speherical top molecules. Point
group T molecules have only one unique 3-fold and one unique 2-fold
axis. O molecules have one unique 4, 3 and 2-fold axes. I molecules
have a unique 5-fold axis.
"""
rot_present = defaultdict(bool)
origin_site, dist_el_sites = cluster_sites(self.centered_mol, self.tol)
test_set = min(dist_el_sites.values(), key=lambda s: len(s))
coords = [s.coords for s in test_set]
for c1, c2, c3 in itertools.combinations(coords, 3):
for cc1, cc2 in itertools.combinations([c1, c2, c3], 2):
if not rot_present[2]:
test_axis = cc1 + cc2
if np.linalg.norm(test_axis) > self.tol:
op = SymmOp.from_axis_angle_and_translation(test_axis,
180)
rot_present[2] = self.is_valid_op(op)
if rot_present[2]:
self.symmops.append(op)
self.rot_sym.append((test_axis, 2))
test_axis = np.cross(c2 - c1, c3 - c1)
if np.linalg.norm(test_axis) > self.tol:
for r in (3, 4, 5):
if not rot_present[r]:
op = SymmOp.from_axis_angle_and_translation(
test_axis, 360 / r)
rot_present[r] = self.is_valid_op(op)
if rot_present[r]:
self.symmops.append(op)
self.rot_sym.append((test_axis, r))
break
if rot_present[2] and rot_present[3] and (
rot_present[4] or rot_present[5]):
break
def _find_spherical_axes(self):
"""
Looks for R5, R4, R3 and R2 axes in speherical top molecules. Point
group T molecules have only one unique 3-fold and one unique 2-fold
axis. O molecules have one unique 4, 3 and 2-fold axes. I molecules
have a unique 5-fold axis.
"""
rot_present = defaultdict(bool)
origin_site, dist_el_sites = cluster_sites(self.centered_mol, self.tol)
test_set = min(dist_el_sites.values(), key=lambda s: len(s))
coords = [s.coords for s in test_set]
for c1, c2, c3 in itertools.combinations(coords, 3):
for cc1, cc2 in itertools.combinations([c1, c2, c3], 2):
if not rot_present[2]:
test_axis = cc1 + cc2
if np.linalg.norm(test_axis) > self.tol:
op = SymmOp.from_axis_angle_and_translation(
test_axis, 180)
rot_present[2] = self.is_valid_op(op)
if rot_present[2]:
self.symmops.append(op)
self.rot_sym.append((test_axis, 2))
test_axis = np.cross(c2 - c1, c3 - c1)
if np.linalg.norm(test_axis) > self.tol:
for r in (3, 4, 5):
if not rot_present[r]:
op = SymmOp.from_axis_angle_and_translation(
test_axis, 360 / r)
rot_present[r] = self.is_valid_op(op)
if rot_present[r]:
self.symmops.append(op)
self.rot_sym.append((test_axis, r))
break
if rot_present[2] and rot_present[3] and (rot_present[4]
or rot_present[5]):
break
def _check_perpendicular_r2_axis(self, axis):
"""
Checks for R2 axes perpendicular to unique axis. For handling
symmetric top molecules.
"""
min_set = self._get_smallest_set_not_on_axis(axis)
for s1, s2 in itertools.combinations(min_set, 2):
test_axis = np.cross(s1.coords - s2.coords, axis)
if np.linalg.norm(test_axis) > self.tol:
op = SymmOp.from_axis_angle_and_translation(test_axis, 180)
r2present = self.is_valid_op(op)
if r2present:
self.symmops.append(op)
self.rot_sym.append((test_axis, 2))
return True
def __init__(self, axis, angle, angle_in_radians=False):
"""
Args:
axis:
Axis of rotation, e.g., [1, 0, 0]
angle:
Angle to rotate
angle_in_radians:
Set to True if angle is supplied in radians. Else degrees are
assumed.
"""
self._axis = axis
self._angle = angle
self._angle_in_radians = angle_in_radians
self._symmop = SymmOp.from_axis_angle_and_translation(self._axis, self._angle, self._angle_in_radians)
def _check_perpendicular_r2_axis(self, axis):
"""
Checks for R2 axes perpendicular to unique axis. For handling
symmetric top molecules.
"""
min_set = self._get_smallest_set_not_on_axis(axis)
for s1, s2 in itertools.combinations(min_set, 2):
test_axis = np.cross(s1.coords - s2.coords, axis)
if np.linalg.norm(test_axis) > self.tol:
op = SymmOp.from_axis_angle_and_translation(test_axis, 180)
r2present = self.is_valid_op(op)
if r2present:
self.symmops.append(op)
self.rot_sym.append((test_axis, 2))
return True
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
s = self.structure.copy()
s.apply_operation(op)
self.assertArrayAlmostEqual(
s.lattice.matrix,
[[0.000000, 3.840198, 0.000000], [-3.325710, 1.920099, 0.000000],
[2.217138, -0.000000, 3.135509]], 5)
op = SymmOp([[1, 1, 0, 0.5], [1, 0, 0, 0.5], [0, 0, 1, 0.5],
[0, 0, 0, 1]])
s = self.structure.copy()
s.apply_operation(op, fractional=True)
self.assertArrayAlmostEqual(
s.lattice.matrix,
[[5.760297, 3.325710, 0.000000], [3.840198, 0.000000, 0.000000],
[0.000000, -2.217138, 3.135509]], 5)
def test_transform(self):
# Rank 3
tensor = TensorBase(np.arange(0, 27).reshape(3, 3, 3))
symm_op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30,
False, [0, 0, 1])
new_tensor = tensor.transform(symm_op)
self.assertArrayAlmostEqual(new_tensor,
[[[-0.871, -2.884, -1.928],
[-2.152, -6.665, -4.196],
[-1.026, -2.830, -1.572]],
[[0.044, 1.531, 1.804],
[4.263, 21.008, 17.928],
[5.170, 23.026, 18.722]],
[[1.679, 7.268, 5.821],
[9.268, 38.321, 29.919],
[8.285, 33.651, 26.000]]], 3)
def _check_rot_sym(self, axis):
"""
Determines the rotational symmetry about supplied axis. Used only for
symmetric top molecules which has possible rotational symmetry
operations > 2.
"""
min_set = self._get_smallest_set_not_on_axis(axis)
max_sym = len(min_set)
for i in range(max_sym, 0, -1):
if max_sym % i != 0:
continue
op = SymmOp.from_axis_angle_and_translation(axis, 360 / i)
rotvalid = self.is_valid_op(op)
if rotvalid:
self.symmops.append(op)
self.rot_sym.append((axis, i))
return i
return 1
def _check_rot_sym(self, axis):
"""
Determines the rotational symmetry about supplied axis. Used only for
symmetric top molecules which has possible rotational symmetry
operations > 2.
"""
min_set = self._get_smallest_set_not_on_axis(axis)
max_sym = len(min_set)
for i in range(max_sym, 0, -1):
if max_sym % i != 0:
continue
op = SymmOp.from_axis_angle_and_translation(axis, 360 / i)
rotvalid = self.is_valid_op(op)
if rotvalid:
self.symmops.append(op)
self.rot_sym.append((axis, i))
return i
return 1
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
s = self.structure.copy()
s.apply_operation(op)
self.assertArrayAlmostEqual(
s.lattice.matrix,
[[0.000000, 3.840198, 0.000000],
[-3.325710, 1.920099, 0.000000],
[2.217138, -0.000000, 3.135509]], 5)
op = SymmOp([[1, 1, 0, 0.5], [1, 0, 0, 0.5], [0, 0, 1, 0.5],
[0, 0, 0, 1]])
s = self.structure.copy()
s.apply_operation(op, fractional=True)
self.assertArrayAlmostEqual(
s.lattice.matrix,
[[5.760297, 3.325710, 0.000000],
[3.840198, 0.000000, 0.000000],
[0.000000, -2.217138, 3.135509]], 5)
def cover_surface(self, site_indices):
"""
puts the ligand molecule on the given list of site indices
"""
num_atoms = len(self.ligand)
normal = self.normal
# get a vector that points from one atom in the botton plane
# to one atom on the top plane. This is required to make sure
# that the surface normal points outwards from the surface on
# to which we want to adsorb the ligand
vec_vac = self.cart_coords[self.top_atoms[0]] - \
self.cart_coords[self.bottom_atoms[0]]
# mov_vec = the vector along which the ligand will be displaced
mov_vec = normal * self.displacement
angle = get_angle(vec_vac, self.normal)
# flip the orientation of normal if it is not pointing in
# the right direction.
if (angle > 90):
normal_frac = self.lattice.get_fractional_coords(normal)
normal_frac[2] = -normal_frac[2]
normal = self.lattice.get_cartesian_coords(normal_frac)
mov_vec = normal * self.displacement
# get the index corresponding to the given atomic species in
# the ligand that will bond with the surface on which the
# ligand will be adsorbed
adatom_index = self.get_index(self.adatom_on_lig)
adsorbed_ligands_coords = []
# set the ligand coordinates for each adsorption site on
# the surface
for sindex in site_indices:
# align the ligand wrt the site on the surface to which
# it will be adsorbed
origin = self.cart_coords[sindex]
self.ligand.translate_sites(list(range(num_atoms)),
origin - self.ligand[
adatom_index].coords)
# displace the ligand by the given amount in the direction
# normal to surface
self.ligand.translate_sites(list(range(num_atoms)), mov_vec)
# vector pointing from the adatom_on_lig to the
# ligand center of mass
vec_adatom_cm = self.ligand.center_of_mass - \
self.ligand[adatom_index].coords
# rotate the ligand with respect to a vector that is
# normal to the vec_adatom_cm and the normal to the surface
# so that the ligand center of mass is aligned along the
# outward normal to the surface
origin = self.ligand[adatom_index].coords
angle = get_angle(vec_adatom_cm, normal)
if 1 < abs(angle % 180) < 179:
# For angles which are not 0 or 180,
# perform a rotation about the origin along an axis
# perpendicular to both bonds to align bonds.
axis = np.cross(vec_adatom_cm, normal)
op = SymmOp.from_origin_axis_angle(origin, axis, angle)
self.ligand.apply_operation(op)
elif abs(abs(angle) - 180) < 1:
# We have a 180 degree angle.
# Simply do an inversion about the origin
for i in range(len(self.ligand)):
self.ligand[i] = (self.ligand[i].species_and_occu,
origin - (
self.ligand[i].coords - origin))
# x - y - shifts
x = self.x_shift
y = self.y_shift
rot = self.rot
if x:
self.ligand.translate_sites(list(range(num_atoms)),
np.array([x, 0, 0]))
if y:
self.ligand.translate_sites(list(range(num_atoms)),
np.array([0, y, 0]))
if rot:
self.ligand.apply_operation(
SymmOp.from_axis_angle_and_translation(
(1, 0, 0), rot[0], angle_in_radians=False,
translation_vec=(0, 0, 0)))
self.ligand.apply_operation(
SymmOp.from_axis_angle_and_translation(
(0, 1, 0), rot[1], angle_in_radians=False,
translation_vec=(0, 0, 0)))
self.ligand.apply_operation(
SymmOp.from_axis_angle_and_translation(
(0, 0, 1), rot[2], angle_in_radians=False,
translation_vec=(0, 0, 0)))
# 3d numpy array
adsorbed_ligands_coords.append(self.ligand.cart_coords)
# extend the slab structure with the adsorbant atoms
adsorbed_ligands_coords = np.array(adsorbed_ligands_coords)
for j in range(len(site_indices)):
[self.append(self.ligand.species_and_occu[i],
adsorbed_ligands_coords[j, i, :],
coords_are_cartesian=True)
for i in range(num_atoms)]
def test_fit(self):
"""
Take two known matched structures
1) Ensure match
2) Ensure match after translation and rotations
3) Ensure no-match after large site translation
4) Ensure match after site shuffling
"""
sm = StructureMatcher()
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
# Test rotational/translational invariance
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
np.array([0.4, 0.7, 0.9]))
self.struct_list[1].apply_operation(op)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test failure under large atomic translation
self.struct_list[1].translate_sites([0], [.4, .4, .2],
frac_coords=True)
self.assertFalse(sm.fit(self.struct_list[0], self.struct_list[1]))
self.struct_list[1].translate_sites([0], [-.4, -.4, -.2],
frac_coords=True)
# random.shuffle(editor._sites)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test FrameworkComporator
sm2 = StructureMatcher(comparator=FrameworkComparator())
lfp = self.get_structure("LiFePO4")
nfp = self.get_structure("NaFePO4")
self.assertTrue(sm2.fit(lfp, nfp))
self.assertFalse(sm.fit(lfp, nfp))
#Test anonymous fit.
self.assertEqual(sm.fit_anonymous(lfp, nfp), True)
self.assertAlmostEqual(
sm.get_rms_anonymous(lfp, nfp)[0], 0.060895871160262717)
#Test partial occupancies.
s1 = Structure(Lattice.cubic(3), [{
"Fe": 0.5
}, {
"Fe": 0.5
}, {
"Fe": 0.5
}, {
"Fe": 0.5
}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5],
[0.75, 0.75, 0.75]])
s2 = Structure(Lattice.cubic(3), [{
"Fe": 0.25
}, {
"Fe": 0.5
}, {
"Fe": 0.5
}, {
"Fe": 0.75
}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5],
[0.75, 0.75, 0.75]])
self.assertFalse(sm.fit(s1, s2))
self.assertFalse(sm.fit(s2, s1))
s2 = Structure(Lattice.cubic(3), [{
"Mn": 0.5
}, {
"Mn": 0.5
}, {
"Mn": 0.5
}, {
"Mn": 0.5
}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5],
[0.75, 0.75, 0.75]])
self.assertEqual(sm.fit_anonymous(s1, s2), True)
self.assertAlmostEqual(sm.get_rms_anonymous(s1, s2)[0], 0)
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.mol.apply_operation(op)
self.assertArrayAlmostEqual(self.mol[2].coords,
[0.000000, 1.026719, -0.363000])
def setUp(self):
self.op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
[0, 0, 1])
def setUp(self):
self.op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
[0, 0, 1])
def coloumb_configured_interface(iface, random=True,
translations= None,
rotations=None,
samples=10, lowest=5, ecut=None):
"""
Creates Ligand Slab interfaces of user specified translations
and rotations away from the initial guess of binding site
configuration, returns lowest energy structure according to
Coulomb model
Args:
Interface: Interface object: initial interface object
random: True for using Gaussian sampled random numbers for
rotations and translations
translations: list of [x,y,z] translations to be performed
rotation: list of [a,b,c] rotations to be performed w.r.t
Ligand axis
samples: number of interfaces to create
lowest: number of structures to return according to order of
minimum energies
Returns:
list of lowest energy interface objects
"""
ifaces= []
transform= []
for i in range(samples):
if random:
x = np.random.normal() # shift along x direction
y = np.random.normal() # shift along y direction
z = np.random.normal() # shift aling z direction
a= SymmOp.from_axis_angle_and_translation(axis=[1,0,0],\
angle=np.random.normal(0,180))
b= SymmOp.from_axis_angle_and_translation(axis=[0,1,0],\
angle=np.random.normal(0,180))
c= SymmOp.from_axis_angle_and_translation(axis=[0,0,1],\
angle=np.random.normal(0,180))
ligand=iface.ligand
ligand.apply_operation(a)
ligand.apply_operation(b)
ligand.apply_operation(c)
# check if created interface maintains the ligand adsorbed
# over the surface
for j in iface.top_atoms:
if not iface.cart_coords[j][2] + iface.displacement > \
min(ligand.cart_coords[:,2]):
transform.append(True)
if all(transform):
iface= Interface(iface.strt, hkl=iface.hkl,
min_thick=iface.min_thick,
min_vac=iface.min_vac,
supercell=iface.supercell,
surface_coverage=iface.surface_coverage,
ligand=iface.ligand, displacement=z,
adatom_on_lig=iface.adatom_on_lig,
adsorb_on_species=iface.adsorb_on_species,
primitive= False, from_ase=True,
x_shift=x, y_shift=y)
iface.create_interface()
energy= iface.calc_energy()
iface.sort()
if energy<ecut:
ifaces.append((energy,iface))
# ifaces.zip(energy, iface)
return ifaces
def get_grain_boundary_interface(structure=None, hkl_pair= {'hkl': [[1,0,0],[1,1,0]],\
'thickness':[10,10]}, twist = 0, tilt = 0, separation=0):
"""
Args:
structure: pymatgen structure to create grain boundary in
hkl_pair: dict of {'hkl':thickness}
twist: twist in degrees
tilt: tilt in degrees
"""
structure = get_struct_from_mp(structure, MAPI_KEY="")
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
structure = structure_conventional.copy()
structure.sort()
#creation of lower part of grain boundary
lower= Interface(structure,\
hkl = hkl_pair['hkl'][0],
min_thick = hkl_pair['thickness'][0],
min_vac = separation+hkl_pair['thickness'][1],
primitive = False, from_ase = True, center_slab=False)
lower.to(fmt="poscar", filename="POSCAR_lower.vasp")
#creation of upper part of grain boundary
upper= Interface(structure,\
hkl = hkl_pair['hkl'][1],
min_thick = hkl_pair['thickness'][1],
min_vac = 0,
primitive = False, from_ase = True)
#find top atoms reference of lower part of gb
substrate_top_z = np.max(np.array([site.coords for site in lower])[:, 2])
# define twist and tilt vectors
twist_shift_normal = lower.lattice.matrix[2,:]/\
np.linalg.norm(lower.lattice.matrix[2,:])
tilt_normal = upper.lattice.matrix[1,:]/\
np.linalg.norm(upper.lattice.matrix[2,:])
#define twist operation SymmOp object
twist_op = SymmOp.from_axis_angle_and_translation(axis= twist_shift_normal,\
angle=twist, angle_in_radians=False,translation_vec=(0, 0, 0))
#define tilt operation SymmOp object
tilt_op = SymmOp.from_axis_angle_and_translation(axis= tilt_normal,\
angle=tilt, angle_in_radians=False,translation_vec=(0, 0, 0))
upper.apply_operation(twist_op)
upper.to(fmt="poscar", filename="POSCAR_upper.vasp")
upper.apply_operation(tilt_op)
#define shift separation along twist vector normal to upper plane
shift = -1 * twist_shift_normal / np.linalg.norm(
twist_shift_normal) * separation
#define origin to shift w.r.t top of the lower grain
origin = np.array([0, 0, substrate_top_z])
#shift sites in upper
for site in upper:
new_coords = site.coords - origin + shift
lower.append(site.specie, new_coords, coords_are_cartesian=True)
return lower
def cover_surface(self, site_indices):
"""
puts the ligand molecule on the given list of site indices
"""
num_atoms = len(self.ligand)
normal = self.normal
# get a vector that points from one atom in the botton plane
# to one atom on the top plane. This is required to make sure
# that the surface normal points outwards from the surface on
# to which we want to adsorb the ligand
vec_vac = self.cart_coords[self.top_atoms[0]] - \
self.cart_coords[self.bottom_atoms[0]]
# mov_vec = the vector along which the ligand will be displaced
mov_vec = normal * self.displacement
angle = get_angle(vec_vac, self.normal)
# flip the orientation of normal if it is not pointing in
# the right direction.
if (angle > 90):
normal_frac = self.lattice.get_fractional_coords(normal)
normal_frac[2] = -normal_frac[2]
normal = self.lattice.get_cartesian_coords(normal_frac)
mov_vec = normal * self.displacement
# get the index corresponding to the given atomic species in
# the ligand that will bond with the surface on which the
# ligand will be adsorbed
adatom_index = self.get_index(self.adatom_on_lig)
adsorbed_ligands_coords = []
# set the ligand coordinates for each adsorption site on
# the surface
for sindex in site_indices:
# align the ligand wrt the site on the surface to which
# it will be adsorbed
origin = self.cart_coords[sindex]
self.ligand.translate_sites(
list(range(num_atoms)),
origin - self.ligand[adatom_index].coords)
# displace the ligand by the given amount in the direction
# normal to surface
self.ligand.translate_sites(list(range(num_atoms)), mov_vec)
# vector pointing from the adatom_on_lig to the
# ligand center of mass
vec_adatom_cm = self.ligand.center_of_mass - \
self.ligand[adatom_index].coords
# rotate the ligand with respect to a vector that is
# normal to the vec_adatom_cm and the normal to the surface
# so that the ligand center of mass is aligned along the
# outward normal to the surface
origin = self.ligand[adatom_index].coords
angle = get_angle(vec_adatom_cm, normal)
if 1 < abs(angle % 180) < 179:
# For angles which are not 0 or 180,
# perform a rotation about the origin along an axis
# perpendicular to both bonds to align bonds.
axis = np.cross(vec_adatom_cm, normal)
op = SymmOp.from_origin_axis_angle(origin, axis, angle)
self.ligand.apply_operation(op)
elif abs(abs(angle) - 180) < 1:
# We have a 180 degree angle.
# Simply do an inversion about the origin
for i in range(len(self.ligand)):
self.ligand[i] = (self.ligand[i].species_and_occu, origin -
(self.ligand[i].coords - origin))
# x - y - shifts
x = self.x_shift
y = self.y_shift
rot = self.rot
if x:
self.ligand.translate_sites(list(range(num_atoms)),
np.array([x, 0, 0]))
if y:
self.ligand.translate_sites(list(range(num_atoms)),
np.array([0, y, 0]))
if rot:
self.ligand.apply_operation(
SymmOp.from_axis_angle_and_translation(
(1, 0, 0),
rot[0],
angle_in_radians=False,
translation_vec=(0, 0, 0)))
self.ligand.apply_operation(
SymmOp.from_axis_angle_and_translation(
(0, 1, 0),
rot[1],
angle_in_radians=False,
translation_vec=(0, 0, 0)))
self.ligand.apply_operation(
SymmOp.from_axis_angle_and_translation(
(0, 0, 1),
rot[2],
angle_in_radians=False,
translation_vec=(0, 0, 0)))
# 3d numpy array
adsorbed_ligands_coords.append(self.ligand.cart_coords)
# extend the slab structure with the adsorbant atoms
adsorbed_ligands_coords = np.array(adsorbed_ligands_coords)
for j in range(len(site_indices)):
[
self.append(self.ligand.species_and_occu[i],
adsorbed_ligands_coords[j, i, :],
coords_are_cartesian=True)
for i in range(num_atoms)
]
def coloumb_configured_interface(iface, random=True,
translations=None,
rotations=None,
samples=10, lowest=5, ecut=None):
"""
Creates Ligand Slab interfaces of user specified translations
and rotations away from the initial guess of binding site
configuration, returns lowest energy structure according to
Coulomb model
Args:
Interface: Interface object: initial interface object
random: True for using Gaussian sampled random numbers for
rotations and translations
translations: list of [x,y,z] translations to be performed
rotation: list of [a,b,c] rotations to be performed w.r.t
Ligand axis
samples: number of interfaces to create
lowest: number of structures to return according to order of
minimum energies
Returns:
list of lowest energy interface objects
"""
ifaces = []
transform = []
for i in range(samples):
if random:
x = np.random.normal() # shift along x direction
y = np.random.normal() # shift along y direction
z = np.random.normal() # shift aling z direction
a = SymmOp.from_axis_angle_and_translation(axis=[1, 0, 0], \
angle=np.random.normal(0, 180))
b = SymmOp.from_axis_angle_and_translation(axis=[0, 1, 0], \
angle=np.random.normal(0, 180))
c = SymmOp.from_axis_angle_and_translation(axis=[0, 0, 1], \
angle=np.random.normal(0, 180))
ligand = iface.ligand
ligand.apply_operation(a)
ligand.apply_operation(b)
ligand.apply_operation(c)
# check if created interface maintains the ligand adsorbed
# over the surface
for j in iface.top_atoms:
if not iface.cart_coords[j][2] + iface.displacement > \
min(ligand.cart_coords[:, 2]):
transform.append(True)
if all(transform):
iface = Interface(iface.strt, hkl=iface.hkl,
min_thick=iface.min_thick,
min_vac=iface.min_vac,
supercell=iface.supercell,
surface_coverage=iface.surface_coverage,
ligand=iface.ligand, displacement=z,
adatom_on_lig=iface.adatom_on_lig,
adsorb_on_species=iface.adsorb_on_species,
primitive=False, from_ase=True,
x_shift=x, y_shift=y)
iface.create_interface()
energy = iface.calc_energy()
iface.sort()
if energy < ecut:
ifaces.append((energy, iface))
# ifaces.zip(energy, iface)
return ifaces
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.mol.apply_operation(op)
self.assertArrayAlmostEqual(self.mol[2].coords,
[0.000000, 1.026719, -0.363000])
def get_grain_boundary_interface(structure=None, hkl_pair= {'hkl': [[1,0,0],[1,1,0]],\
'thickness':[10,10]}, twist = 0, tilt = 0, separation=0):
"""
Args:
structure: pymatgen structure to create grain boundary in
hkl_pair: dict of {'hkl':thickness}
twist: twist in degrees
tilt: tilt in degrees
"""
structure = get_struct_from_mp(structure, MAPI_KEY="")
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
structure = structure_conventional.copy()
structure.sort()
#creation of lower part of grain boundary
lower= Interface(structure,\
hkl = hkl_pair['hkl'][0],
min_thick = hkl_pair['thickness'][0],
min_vac = separation+hkl_pair['thickness'][1],
primitive = False, from_ase = True, center_slab=False)
lower.to(fmt="poscar", filename="POSCAR_lower.vasp")
#creation of upper part of grain boundary
upper= Interface(structure,\
hkl = hkl_pair['hkl'][1],
min_thick = hkl_pair['thickness'][1],
min_vac = 0,
primitive = False, from_ase = True)
#find top atoms reference of lower part of gb
substrate_top_z = np.max(np.array([site.coords for site in lower])[:,2])
# define twist and tilt vectors
twist_shift_normal = lower.lattice.matrix[2,:]/\
np.linalg.norm(lower.lattice.matrix[2,:])
tilt_normal = upper.lattice.matrix[1,:]/\
np.linalg.norm(upper.lattice.matrix[2,:])
#define twist operation SymmOp object
twist_op = SymmOp.from_axis_angle_and_translation(axis= twist_shift_normal,\
angle=twist, angle_in_radians=False,translation_vec=(0, 0, 0))
#define tilt operation SymmOp object
tilt_op = SymmOp.from_axis_angle_and_translation(axis= tilt_normal,\
angle=tilt, angle_in_radians=False,translation_vec=(0, 0, 0))
upper.apply_operation(twist_op)
upper.to(fmt="poscar", filename="POSCAR_upper.vasp")
upper.apply_operation(tilt_op)
#define shift separation along twist vector normal to upper plane
shift = -1*twist_shift_normal/np.linalg.norm(twist_shift_normal) * separation
#define origin to shift w.r.t top of the lower grain
origin = np.array([0,0, substrate_top_z])
#shift sites in upper
for site in upper:
new_coords = site.coords - origin + shift
lower.append(site.specie, new_coords, coords_are_cartesian=True)
return lower
