def setUp(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 12)
self.cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
def test_gen_nodup_exch(self):
lattice = np.array([[5.0, 0.0000000000, 0.0000000000],
[2.5, 4.330127, 0.0000000000],
[0.0000000000, 0.0000000000, 20]])
positions = np.array([[0.666667, 0.000000, 0.5281],
[0.000000, 0.333333, 0.5281],
[0.333333, 0.666667, 0.5281],
[0.000000, 0.000000, 0.6115],
[0.500000, 0.000000, 0.6115],
[0.000000, 0.500000, 0.6115],
[0.500000, 0.500000, 0.6115]])
numbers = np.array([12, 12, 12, 28, 28, 28, 28])
gcell = GeneralCell(lattice, positions, numbers)
ocu_gen = OccupyGenerator(gcell)
nodup_gen = ocu_gen.gen_nodup_exch(Specie('Mg'), Specie('Ni'), 1)
l = [i for i in nodup_gen]
self.assertEqual(len(l), 3)
ocu_gen = OccupyGenerator(gcell)
nodup_gen = ocu_gen.gen_nodup_exch(Specie('Mg'), Specie('Ni'), 2)
l = [i for i in nodup_gen]
self.assertEqual(len(l), 4)
ocu_gen = OccupyGenerator(gcell)
nodup_gen = ocu_gen.gen_nodup_exch(Specie('Mg'), Specie('Ni'), 3)
l = [i for i in nodup_gen]
self.assertEqual(len(l), 2)
def setUp(self):
latt = np.array([[0., 0.5, 0.53333333333], [0.5, 0., 0.56666666667],
[0.5, 0.5, 0.]])
positions = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
numbers = np.array([30, 16])
cell = GeneralCell(latt, positions, numbers)
self.vasp_out = VaspOutput(cell)
def to_general_cell(self):
"""
The function used to convert the superlattice
HermiteLattice to a GeneralCell instance.
input aps for atome_position_s, which are atom positions
of the unit basis.
input numbers are element number of the corespoding positions.
"""
# lat_coeff is represent as column vector
# while ub and latt is row vector
latt = np.matmul(self.lat_coeff, self.ub)
# coor_unit_pos = np.matmul(self.upositions, self.ub)
# o_unit_pos = np.matmul(coor_unit_pos, np.linalg.inv(self.lat_coeff))
########################################################
# Tag: algorithm changed May be harmful!!!!!!!!
########################################################
o_unit_pos = np.matmul(self.upositions, np.linalg.inv(self.lat_coeff))
o_pos = self.get_frac_from_H(self.lat_coeff)
l_of_positions = [
i for i in map(lambda x: x + o_pos, list(o_unit_pos))
]
# pdb.set_trace()
pos = np.concatenate(l_of_positions, axis=0)
n = self.lat_coeff.diagonal().prod()
numbers = np.repeat(self.unumbers, n)
# pdb.set_trace()
return GeneralCell(latt, pos, numbers)
def setUp(self):
a_latt = np.array([[0.5, 0.5, -0.5], [-0.5, 0.5, 0.5],
[0.5, -0.5, 0.5]])
a_pos = np.array([[0, 0, 0]])
a_num = np.array([16])
a_cell = GeneralCell(a_latt, a_pos, a_num)
self.a_yaml = YamlOutput(a_cell, zoom=3)
def setUp(self):
self.bcc_base = np.array([[0.5, 0.5, -0.5], [-0.5, 0.5, 0.5],
[0.5, -0.5, 0.5]])
self.bcc_u_position = np.array([[0, 0, 0]])
self.bcc_u_n = np.array([0])
self.bcc_uc = GeneralCell(self.bcc_base, self.bcc_u_position,
self.bcc_u_n)
def setUp(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([5, 6, 22, 6, 5, 6, 6, 29, 6, 6, 6, 6])
self.p6cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
arr_numbers = np.array([5, 6, 6, 6, 5, 6, 6, 6, 6, 6, 6, 6])
self.p6orsymcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.p6_restrc = SpaceGroupRestriction([6])
self.p6orsym_restrc = SpaceGroupRestriction([6, 47])
def setUp(self):
latt = np.array([[0., 0.5, 0.53333333333], [0.5, 0., 0.56666666667],
[0.5, 0.5, 0.]])
pos = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
numbers = np.array([30, 16])
gcell = GeneralCell(latt, pos, numbers)
self.vasp_out = VaspOutput(gcell)
self.yaml_out = YamlOutput(gcell)
self.io_s = GeneralIO(gcell)
def gen_dup_unitary(self, n, sp):
init_numbers = self.init_cell.numbers
num_count = init_numbers.size # number of atoms in structure
i_speckle = sp.Z
from itertools import combinations
for comb_index in combinations(range(num_count), n):
numbers = init_numbers.copy()
for index in comb_index:
numbers[index] = i_speckle
yield GeneralCell(self.lattice, self.positions, numbers)
def gen_dup(self, wy, n, sp):
init_numbers = self.init_cell.numbers
i_speckle = sp.Z
wyckoffs = self.wyckoffs
sp_ind = [i for i, w in enumerate(wyckoffs) if w is wy]
# pdb.set_trace()
for comb_index in combinations(sp_ind, n):
numbers = init_numbers.copy()
for index in comb_index:
numbers[index] = i_speckle
yield GeneralCell(self.lattice, self.positions, numbers)
def test_get_cartesian(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 12)
cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
cart_coor = cell.get_cartesian()
cart_ans = np.array([[0., 0., 0.], [0., 1., 0.], [0.49998, 0.5, 0.5],
[0.49998, 1.5, 0.5], [0.99999, 0., 0.],
[0.99999, 1., 0.], [1.5, 0.5, 0.5],
[1.5, 1.5, 0.5], [1.99998, 0., 0.],
[1.99998, 1., 0.], [2.49999, 0.5, 0.5],
[2.49999, 1.5, 0.5]])
self.assertTrue(np.allclose(cart_coor, cart_ans))
arr_numbers = np.array([6, 6, 6, 5, 6, 5, 6, 6, 6, 6, 6, 6])
cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
cart_coor = cell.get_cartesian(Specie('B'))
cart_ans = np.array([[0.49998, 1.5, 0.5], [0.99999, 1., 0.]])
def gen_dup_of_ele(self, ele, n, sp):
# ele is a Specie instance
ele_num = ele.Z
init_numbers = self.init_cell.numbers
i_speckle = sp.Z
sp_ind = [i for i, e in enumerate(init_numbers) if e == ele_num]
for comb_index in combinations(sp_ind, n):
numbers = init_numbers.copy()
for index in comb_index:
numbers[index] = i_speckle
yield GeneralCell(self.lattice, self.positions, numbers)
def gen_add_one_speckle(self, gen, wy, sp):
atom = sp.Z
id_db = dict()
for cell in gen:
wy_ele = zip(self.wyckoffs, cell.numbers)
for index, tuple_w_e in enumerate(wy_ele):
numbers_new = cell.numbers.copy()
if tuple_w_e[0] == wy and atom != tuple_w_e[1]:
numbers_new[index] = atom
num_id = numbers2id(numbers_new)
if num_id not in id_db:
yield GeneralCell(cell.lattice, cell.positions,
numbers_new)
id_db[num_id] = None
def gen_dup_exch(self, sp1, sp2, n):
init_numbers = self.init_cell.numbers
n_sp1 = sp1.Z
n_sp2 = sp2.Z
sp1_ind = [i for i, e in enumerate(init_numbers) if e == n_sp1]
sp2_ind = [i for i, e in enumerate(init_numbers) if e == n_sp2]
for ex_sp1 in combinations(sp1_ind, n):
for ex_sp2 in combinations(sp2_ind, n):
numbers = init_numbers.copy()
for ind_sp1, ind_sp2 in zip(ex_sp1, ex_sp2):
numbers[ind_sp1] = n_sp2
numbers[ind_sp2] = n_sp1
yield GeneralCell(self.lattice, self.positions, numbers)
def setUp(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([5, 6, 6, 6, 5, 6, 6, 6, 6, 6, 6, 6])
self.cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.carbon_restrc = MinDistanceRestriction((Specie('C'), 0.85))
self.boron_restrc = MinDistanceRestriction((Specie('B'), 1.01))
def test_is_equivalent(self):
# perm_sym = self.cell.get_symmetry_permutation()
self.assertTrue(self.ocu_gen.is_equivalent(self.cell_a, self.cell_b))
# cell_3A = GeneralCell(self.arr_lat, self.arr_positions, self.numbers_3A)
# cell_3B = GeneralCell(self.arr_lat, self.arr_positions, self.numbers_3B)
# cell_3C = GeneralCell(self.arr_lat, self.arr_positions, self.numbers_3C)
# cell_3D = GeneralCell(self.arr_lat, self.arr_positions, self.numbers_3D)
# self.assertTrue(self.ocu_gen.is_equivalent(cell_3A, cell_3B))
# self.assertTrue(self.ocu_gen.is_equivalent(cell_3C, cell_3D))
tri_num_A = np.array([28, 28, 28, 28, 51, 51, 50, 50, 22, 22, 22, 22])
tri_num_B = np.array([28, 28, 28, 28, 51, 50, 50, 51, 22, 22, 22, 22])
trinary_cell_A = GeneralCell(self.trinary_lat, self.trinary_positions, tri_num_A)
trinary_cell_B = GeneralCell(self.trinary_lat, self.trinary_positions, tri_num_B)
self.assertTrue(self.trinary_ocu_gen.is_equivalent(trinary_cell_A, trinary_cell_B))
bin_num_A = np.array([30, 30, 30, 30, 30, 30, 30, 30, 50, 50, 16, 16, 16, 16, 16, 16])
bin_num_B = np.array([30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 50, 50, 16, 16, 16, 16])
bin_cell_A = GeneralCell(self.binary_lat, self.binary_positions, bin_num_A)
bin_cell_B = GeneralCell(self.binary_lat, self.binary_positions, bin_num_B)
self.assertTrue(self.binary_ocu_gen.is_equivalent(bin_cell_A, bin_cell_B))
def gen_add_one_speckle_of_ele(self, gen, ele, sp):
ele_Z = ele.Z
atom = sp.Z
id_db = dict()
for cell in gen:
# site_ele = zip(self.wyckoffs, cell.numbers)
for index, e in enumerate(cell.numbers):
numbers_new = cell.numbers.copy()
if e == ele_Z and e != atom:
numbers_new[index] = atom
num_id = numbers2id(numbers_new)
if num_id not in id_db:
yield GeneralCell(cell.lattice, cell.positions,
numbers_new)
id_db[num_id] = None
def __init__(self, settings, comment, element, speckle, nspeckle, zoom,
trs, refined, outmode, mpr):
# read comment & zoom from setting file first
# if not exist, read from cmd args, then default
if zoom is None:
try:
zoom = settings['zoom']
except:
zoom = 1
self.zoom = zoom
if comment is None:
try:
comment = settings['comment']
except:
comment = 'default'
self.comment = comment
lat = np.array(settings['lattice'])
pos = np.array(settings['positions'])
num = np.array(settings['numbers'])
self.cell = GeneralCell(lat * self.zoom, pos, num)
self.element = element
# Get number and index of target element
if element is None:
tgt_ele = int(num[1])
else:
tgt_ele = Specie(element).Z
tgt_ele_index = np.where(num == tgt_ele)[0]
self.s1, self.s2 = speckle
self.n1, self.n2 = nspeckle
# self.ele for function all-speckle-gen-of-ele in run
self.ele = Specie.from_num(tgt_ele)
# if there no restriction given then no restriction
if trs != ():
self.tr = trs[0]
else:
self.tr = None
self.refined = refined
self.outmode = outmode
self.mpr = mpr
self.n0 = tgt_ele_index.size - self.n1 - self.n2
def _gen_dup_trinary_alloy(self, sp1, n1, sp2, n2):
init_numbers = self.init_cell.numbers
isp1 = sp1.Z
isp2 = sp2.Z
sp_ind_origin = [i for i, s in enumerate(init_numbers)]
for sp1_comb_index in combinations(sp_ind_origin, n1):
sp_ind_bin = [x for x in sp_ind_origin if x not in sp1_comb_index]
for sp2_comb_index in combinations(sp_ind_bin, n2):
numbers = init_numbers.copy()
for i1, i2 in zip_longest(sp1_comb_index, sp2_comb_index):
if i1 is not None:
numbers[i1] = isp1
if i2 is not None:
numbers[i2] = isp2
yield GeneralCell(self.lattice, self.positions, numbers)
def test_supercell(self):
scale_mat = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 2]])
scell = self.cell.supercell(scale_mat)
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 2.0]])
positions = [[0., 0., 0.], [0., 0., 0.5], [0., 0.5,
0.], [0., 0.5, 0.5],
[0.16666, 0.25, 0.25], [0.16666, 0.25, 0.75],
[0.16666, 0.75, 0.25], [0.16666, 0.75, 0.75],
[0.33333, 0., 0.], [0.33333, 0., 0.5], [0.33333, 0.5, 0.],
[0.33333, 0.5, 0.5], [0.5, 0.25, 0.25], [0.5, 0.25, 0.75],
[0.5, 0.75, 0.25], [0.5, 0.75, 0.75], [0.66666, 0., 0.],
[0.66666, 0., 0.5], [0.66666, 0.5, 0.],
[0.66666, 0.5, 0.5], [0.83333, 0.25, 0.25],
[0.83333, 0.25, 0.75], [0.83333, 0.75, 0.25],
[0.83333, 0.75, 0.75]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 24)
ans_scell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertTrue(np.allclose(scell.positions, arr_positions))
def gen_add_one_speckle_unitary(self, gen, sp):
"""
input a structure generator __ spg_cell(mostly nonduplicate)
output a generator with one more speckle.
This a method give duplicate structures which have one more speckle
than the input structures.
"""
atom = sp.Z
id_db = dict()
for cell in gen:
for index, val in enumerate(cell.numbers):
numbers_new = cell.numbers.copy()
if atom != val:
numbers_new[index] = atom
num_id = numbers2id(numbers_new)
if num_id not in id_db:
yield GeneralCell(cell.lattice, cell.positions,
numbers_new)
id_db[num_id] = None
def test_HNFs_from_n(self):
# use bcc data from <PHYSICAL REVIEW B 80, 014120 (2009)>
# to test...
results = [2, 3, 7, 5, 10, 7]
for i, result in zip(range(2, 8), results):
nodup_hnfs = SuperLatticeGenerator.hnfs_from_n(self.bcc_uc, i)
self.assertEqual(len(nodup_hnfs), result)
# hcp test
hcp_b = np.array([[2.51900005, 0., 0.], [-1.25950003, 2.18151804, 0.],
[0., 0., 4.09100008]])
hcp_positions = np.array([[0.33333334, 0.66666669, 0.25],
[0.66666663, 0.33333331, 0.75]])
hcp_numbers = np.array([0, 0])
hcp_uc = GeneralCell(hcp_b, hcp_positions, hcp_numbers)
# import pdb; pdb.set_trace()
result = [
len(SuperLatticeGenerator.hnfs_from_n(hcp_uc, i))
for i in range(1, 10)
]
self.assertEqual(result, [1, 3, 5, 11, 7, 19, 11, 34, 23])
def test_to_general_cell(self):
hnfs = SuperLatticeGenerator.hnfs_from_n_dups(self.bcc_uc, 4)
hnf = hnfs[2]
cell = hnf.to_general_cell()
# print(cell.spg_cell)
self.assertEqual(len(cell.spg_cell[2]), 4)
zb_b = np.array([[3.82863, 0., 0.], [1.91431, 3.31569, 0.],
[1.91431, 1.10523, 3.12606]])
zb_pos = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
zb_num = np.array([30, 16])
zb_uc = GeneralCell(zb_b, zb_pos, zb_num)
zbs = SuperLatticeGenerator.hnfs_from_n(zb_uc, 3)
one_zb = zbs[1]
cell = one_zb.to_general_cell()
# print(cell.spg_cell)
self.assertEqual(len(cell.spg_cell[2]), 6)
h = np.array([[1, 0, 3], [0, 2, 2], [0, 0, 4]])
strange_hnf = SuperLatticeCell(self.bcc_uc, h)
shnf = strange_hnf.to_general_cell()
self.assertEqual(len(shnf.spg_cell[2]), 8)
def test_degeneracy(self):
sym_perm = self.cell.get_symmetry_permutation()
self.assertEqual(self.cell.get_degeneracy(sym_perm), 1)
### more complex test
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 12)
arr_numbers = np.array([5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 6)
def test_from_to_gcell(self):
gcell = GeneralCell(self.latt, self.pos, self.numbers)
modcell = ModifiedCell.from_gcell(gcell)
new_gcell = modcell.to_gcell()
self.assertTrue(np.allclose(new_gcell.positions, gcell.positions))
class testGeneralCell(unittest.TestCase):
def setUp(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 12)
self.cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# def test_eq(self):
# arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([6]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertEqual(cell, self.cell)
#
# arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([6]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertEqual(cell, self.cell)
#
# arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([4]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertNotEqual(cell, self.cell)
#
# arr_lat = np.array([[2.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([6]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertNotEqual(cell, self.cell)
def test_get_speckle_num(self):
self.assertEqual(self.cell.get_speckle_num(Specie("B")), 0)
self.assertEqual(self.cell.get_speckle_num(Specie("C")), 12)
def test_property(self):
np.testing.assert_equal(self.cell.numbers, np.array([6] * 12))
self.assertEqual(self.cell.comment, 'C12')
def test_get_symmetry(self):
sym = self.cell.get_spacegroup()
self.assertEqual(sym, 'Im-3m (229)')
def test_get_symmetry_permutation(self):
sym_num = len(self.cell.get_symmetry_permutation())
self.assertEqual(sym_num, 96)
def test_is_primitive(self):
self.assertFalse(self.cell.is_primitive())
def test_degeneracy(self):
sym_perm = self.cell.get_symmetry_permutation()
self.assertEqual(self.cell.get_degeneracy(sym_perm), 1)
### more complex test
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 12)
arr_numbers = np.array([5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 6)
def test_get_cartesian(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 12)
cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
cart_coor = cell.get_cartesian()
cart_ans = np.array([[0., 0., 0.], [0., 1., 0.], [0.49998, 0.5, 0.5],
[0.49998, 1.5, 0.5], [0.99999, 0., 0.],
[0.99999, 1., 0.], [1.5, 0.5, 0.5],
[1.5, 1.5, 0.5], [1.99998, 0., 0.],
[1.99998, 1., 0.], [2.49999, 0.5, 0.5],
[2.49999, 1.5, 0.5]])
self.assertTrue(np.allclose(cart_coor, cart_ans))
arr_numbers = np.array([6, 6, 6, 5, 6, 5, 6, 6, 6, 6, 6, 6])
cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
cart_coor = cell.get_cartesian(Specie('B'))
cart_ans = np.array([[0.49998, 1.5, 0.5], [0.99999, 1., 0.]])
def test_supercell(self):
scale_mat = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 2]])
scell = self.cell.supercell(scale_mat)
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 2.0]])
positions = [[0., 0., 0.], [0., 0., 0.5], [0., 0.5,
0.], [0., 0.5, 0.5],
[0.16666, 0.25, 0.25], [0.16666, 0.25, 0.75],
[0.16666, 0.75, 0.25], [0.16666, 0.75, 0.75],
[0.33333, 0., 0.], [0.33333, 0., 0.5], [0.33333, 0.5, 0.],
[0.33333, 0.5, 0.5], [0.5, 0.25, 0.25], [0.5, 0.25, 0.75],
[0.5, 0.75, 0.25], [0.5, 0.75, 0.75], [0.66666, 0., 0.],
[0.66666, 0., 0.5], [0.66666, 0.5, 0.],
[0.66666, 0.5, 0.5], [0.83333, 0.25, 0.25],
[0.83333, 0.25, 0.75], [0.83333, 0.75, 0.25],
[0.83333, 0.75, 0.75]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 24)
ans_scell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertTrue(np.allclose(scell.positions, arr_positions))
def setUp(self):
self.arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [
[0.00000, 0.00000, 0.00000],
[0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000],
[0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000],
[0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000],
[0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000],
[0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000],
[0.83333, 0.75000, 0.50000]
]
self.arr_positions = np.array(positions)
arr_numbers_0 = np.array([6]*12)
self.cell = GeneralCell(self.arr_lat, self.arr_positions, arr_numbers_0)
self.ocu_gen = OccupyGenerator(self.cell)
tmp = arr_numbers_0.copy()
tmp[0] = 5
arr_numbers_a = tmp
tmp = arr_numbers_0.copy()
tmp[1] = 5
arr_numbers_b = tmp
self.cell_a = GeneralCell(self.arr_lat, self.arr_positions, arr_numbers_a)
self.cell_b = GeneralCell(self.arr_lat, self.arr_positions, arr_numbers_b)
# self.numbers_3A = np.array([5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6])
# self.numbers_3B = np.array([5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 5, 6])
# self.numbers_3C = np.array([5, 5, 6, 6, 5, 6, 6, 6, 6, 6, 6, 6])
# self.numbers_3D = np.array([5, 5, 6, 6, 6, 6, 6, 6, 5, 6, 6, 6])
self.trinary_lat = np.array([[1.5, 0., 0.], [0., 1.5, 0.], [0., 0., 1.5]])
self.trinary_positions = np.array([[0.25, 0.25, 0.25],
[0.25, 0.75, 0.75],
[0.75, 0.25, 0.75],
[0.75, 0.75, 0.25],
[0.00, 0.00, 0.00],
[0.50, 0.50, 0.00],
[0.50, 0.00, 0.50],
[0.00, 0.50, 0.50],
[0.75, 0.75, 0.75],
[0.75, 0.25, 0.25],
[0.25, 0.75, 0.25],
[0.25, 0.25, 0.75]])
self.trinary_numbers = np.array([28, 28, 28, 28, 50, 50, 50, 50, 22, 22, 22, 22])
self.trinary_cell = GeneralCell(self.trinary_lat, self.trinary_positions, self.trinary_numbers)
self.trinary_ocu_gen = OccupyGenerator(self.trinary_cell)
import os
test_dir = os.path.join(os.path.dirname(__file__), 'test_files')
file_name = os.path.join(test_dir, 'zns_f43m2x.yaml')
zns2x = open(file_name, "r")
binary = yaml.load(zns2x)
self.binary_lat = np.array(binary["lattice"])
self.binary_positions = np.array(binary["positions"])
self.binary_numbers = np.array(binary["numbers"])
self.binary_cell = GeneralCell(self.binary_lat, self.binary_positions, self.binary_numbers)
self.binary_ocu_gen = OccupyGenerator(self.binary_cell)
def get_cell(self):
return GeneralCell(self.latt, self.pos, self.numbers)
def test_test(self):
zb_b = np.array([[3.82863, 0., 0.], [1.91431, 3.31569, 0.],
[1.91431, 1.10523, 3.12606]])
zb_pos = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
zb_num = np.array([30, 16])
zb_uc = GeneralCell(zb_b, zb_pos, zb_num)