def test_update_isoset(self):
c = Specie("Cu")
t = Specie("Ti")
m = [[-0.5, -0.5, -0.5],
[-0.5, 0.5, 0.5],
[ 0.5, -0.5, 0.5]]
ele_sea = SitesGrid.sea(2, 2, 2, c)
cell_mother_stru = CStru(m, ele_sea).get_cell()
sym = get_symmetry(cell_mother_stru, symprec=1e-5)
ops = [(r, t) for r, t in zip(sym['rotations'], sym['translations'])]
sym_perm = sogen.get_permutation_cell(cell_mother_stru)
sites_0 = [[[c, c],
[c, c]],
[[c, c],
[t, c]]]
sg_0 = SitesGrid(sites_0)
cstru01 = CStru(m, sg_0)
number01 = cstru01.get_cell()[2]
isoset_init = set()
isoset_init_copy = isoset_init.copy()
isoset_a01 = sogen._update_isoset(isoset_init, number01, sym_perm)
self.assertNotEqual(isoset_a01, isoset_init_copy)
self.assertIsInstance(isoset_a01, set)
isoset_a01_copy = isoset_a01.copy()
isoset_a02 = sogen._update_isoset(isoset_a01, number01, sym_perm)
self.assertEqual(isoset_a02, isoset_a01_copy)
self.assertLessEqual(len(isoset_a01), len(ops))
def gen_nodup_cstru(lattice, sea_ele, size, speckle, num):
d, w, l = size
ele_sea = SitesGrid.sea(d, w, l, sea_ele)
cell_mother_stru = CStru(lattice, ele_sea).get_cell()
sym_perm = get_permutation_cell(cell_mother_stru)
# For testing: Show that the first unit matrix convert to range(num) perm_operator
# print(sym_perm[0])
gen_dup_cstrus = CStru.gen_speckle(lattice, sea_ele, size, speckle, num)
# Add the progress bar when looping
from scipy.special import comb
number_of_structures = comb((d * w * l), num)
bar = ProgressBar(max_value=number_of_structures)
isoset = set()
for cstru in bar(gen_dup_cstrus):
b, pos, atom_num = cstru.get_cell()
#id_cstru = _get_id_seq(pos, atom_num)
id_cstru = _get_atom_seq_identifier(atom_num)
# print(id_cstru)
if id_cstru not in isoset:
# print(len(sym_perm))
# print(len(isoset))
# print(cstru.get_array())
yield cstru
_update_isoset(isoset, atom_num, sym_perm)
def __init__(self, goal_num):
self.goal_num = goal_num
m = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
self.delta = 2.1 # the distance threshold to collect neighbors
sg = SitesGrid([[[GhostSpecie() for _ in range(goal_num)]
for _ in range(goal_num)] for _ in range(goal_num)])
self.bg = CStru(m, sg)
self.start_position = self.bg.get_midpoint()
def setUp(self):
self.m = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
g = GhostSpecie()
b = Specie("B")
self.sites = [[[g, b], [g, g]], [[b, b], [b, g]]]
self.arr = np.array([0, 5, 0, 0, 5, 5, 5, 0]).reshape([2, 2, 2])
self.sg = SitesGrid(self.sites)
self.s = CStru(self.m, self.sg)
def test_gen_speckle(self):
c = Specie("Cu")
t = Specie("Ti")
sites = [[[c, c], [t, t]], [[c, t], [t, c]]]
sg = SitesGrid(sites)
gen = CStru.gen_speckle(self.m, Specie("Cu"), (2, 2, 2), Specie("Ti"),
4)
from collections import Iterator
self.assertIsInstance(gen, Iterator)
self.assertIn(CStru(self.m, sg), gen)
self.assertEqual(next(gen).get_array().sum(), 204)
self.assertEqual(next(gen).get_array().sum(), 204)
def test_equal(self):
m_0 = [[1, 1, 1], [0, 0, 1], [1, 0, 0]]
g = GhostSpecie()
b = Specie("B")
sites_0 = [[[b, b], [g, g]], [[b, g], [g, b]]]
sg_0 = SitesGrid(sites_0)
diff_m = CStru(m_0, self.sg)
diff_s = CStru(self.m, sg_0)
self.assertEqual(self.s, self.s)
self.assertNotEqual(diff_m, self.s)
self.assertNotEqual(diff_s, self.s)
def test_gen_nodup_cstru(self):
c = Specie("Cu")
t = Specie("Ti")
m = [[-0.5, -0.5, -0.5],
[-0.5, 0.5, 0.5],
[ 0.5, -0.5, 0.5]]
ele_sea = SitesGrid.sea(2, 2, 2, c)
cell_mother_stru = CStru(m, ele_sea).get_cell()
sym = get_symmetry(cell_mother_stru, symprec=1e-3)
ops = [(r, t) for r, t in zip(sym['rotations'], sym['translations'])]
sites_0 = [[[c, c],
[c, c]],
[[c, c],
[t, c]]]
sg_0 = SitesGrid(sites_0)
cstru01 = CStru(m, sg_0)
gen_01 = sogen.gen_nodup_cstru(m, c, (2,2,2), t, 1)
nodup_01 = [stru for stru in gen_01]
self.assertEqual(len(nodup_01), 1)
gen_02 = sogen.gen_nodup_cstru(m, c, (1,2,8), t, 4)
nodup_02 = [stru for stru in gen_02]
# eq_(len(nodup_02), 51)
m_tri = [[0, 0, 20],
[1, 0, 0],
[0.5, 0.8660254, 0]]
ele_sea = SitesGrid.sea(1, 3, 3, c)
cell_mother_stru = CStru(m, ele_sea).get_cell()
sym = get_symmetry(cell_mother_stru, symprec=1e-3)
ops = [(r, t) for r, t in zip(sym['rotations'], sym['translations'])]
sites_0 = [[[c, c, c],
[c, c, c],
[c, c, c]]]
sg_0 = SitesGrid(sites_0)
cstru01 = CStru(m, sg_0)
gen_01 = sogen.gen_nodup_cstru(m_tri, c, (1,3,3), t, 2)
nodup_01 = [stru for stru in gen_01]
self.assertEqual(len(nodup_01), 2)
gen_02 = sogen.gen_nodup_cstru(m_tri, c, (1,3,3), t, 3)
nodup_02 = [stru for stru in gen_02]
self.assertEqual(len(nodup_02), 4)
gen_03 = sogen.gen_nodup_cstru(m_tri, c, (1,5,5), t, 2)
nodup_03 = [stru for stru in gen_03]
self.assertEqual(len(nodup_03), 4)
def test_get_cell(self):
c = Specie("Cu")
t = Specie("Ti")
m = [[-0.5, -0.5, -0.5], [-0.5, 0.5, 0.5], [0.5, -0.5, 0.5]]
sites01 = [[[c]]]
sites02 = [[[t, c, t], [t, t, c]]]
sg01 = SitesGrid(sites01)
sg02 = SitesGrid(sites02)
cstru01 = CStru(m, sg01)
cstru02 = CStru(m, sg02)
lat01, pos01, num01 = cstru01.get_cell()
lat02, pos02, num02 = cstru02.get_cell()
self.assertTrue(
np.allclose(
lat01,
np.array([[-0.5, -0.5, -0.5], [-0.5, 0.5, 0.5],
[0.5, -0.5, 0.5]])))
self.assertTrue(np.allclose(pos01, np.array([[0, 0, 0]])))
self.assertTrue(np.allclose(num01, np.array([29])))
self.assertTrue(
np.allclose(
lat02,
np.array([[-0.5, -0.5, -0.5], [-1, 1, 1], [1.5, -1.5, 1.5]])))
self.assertTrue(
np.allclose(
pos02,
np.array([[0, 0, 0], [0, 0, 1 / 3], [0, 0,
2 / 3], [0, 1 / 2, 0],
[0, 1 / 2, 1 / 3], [0, 1 / 2, 2 / 3]])))
self.assertTrue(np.allclose(num02, np.array([22, 29, 22, 22, 22, 29])))
def test_is_speckle_disjunct(self):
g = GhostSpecie()
b = Specie('B')
m = [[0, 0, 20],
[1, 0, 0],
[0.5, 0.8660254, 0]]
# ele_sea = SitesGrid.sea(4, 4, 1, b)
# cell_mother_stru = CStru(m, ele_sea).get_cell()
# sym = get_symmetry(cell_mother_stru, symprec=1e-3)
# ops = [(r, t) for r, t in zip(sym['rotations'], sym['translations'])]
sites_0 = [[[g, g, b, b],
[b, b, b, b],
[b, b, b, b],
[b, b, b, b]]]
sg_0 = SitesGrid(sites_0)
cstru00 = CStru(m, sg_0)
self.assertFalse(sogen.is_speckle_disjunct(cstru00, g))
sites_1 = [[[g, b, b, g],
[b, b, b, b],
[b, b, b, b],
[b, b, b, b]]]
sg_1 = SitesGrid(sites_1)
cstru01 = CStru(m, sg_1)
self.assertFalse(sogen.is_speckle_disjunct(cstru01, g))
sites_2 = [[[g, b, b, b],
[b, g, b, b],
[b, b, b, b],
[b, b, b, b]]]
sg_2 = SitesGrid(sites_2)
cstru02 = CStru(m, sg_2)
self.assertTrue(sogen.is_speckle_disjunct(cstru02, g))
class FCC3dArrangeProblem(arrange.ArrangeProblem):
def __init__(self, goal_num):
self.goal_num = goal_num
m = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
self.delta = 2.1 # the distance threshold to collect neighbors
sg = SitesGrid([[[GhostSpecie() for _ in range(goal_num)]
for _ in range(goal_num)] for _ in range(goal_num)])
self.bg = CStru(m, sg)
self.start_position = self.bg.get_midpoint()
def get_start_position(self):
return self.start_position
def is_goal(self, len_path):
is_goal = len_path == self.goal_num
return is_goal
def get_neighbors(self, position):
# neighbors is a list contain positions
neighbors = self.bg.get_neighbors(position, self.delta)
return neighbors
def test_write_file(self):
""".
The function is tested by save structure
to a POSCAR file, and then read from it.
Compare the parameters read from to the
origin input parameter. Using almostEqual
"""
bcu_arr = np.array([[[5, 29, 5, 5, 5, 5], [5, 5, 5, 5, 5, 5],
[5, 5, 29, 5, 5, 5]]])
latt = [[0, 0, 20], [1, 0, 0], [0.5, sqrt(3) / 2, 0]]
bcu_stru = CStru.from_array(latt, bcu_arr)
poscar_bcu = VaspPOSCAR(bcu_stru.get_gcell(), zoom=4)
tmp_file = "POSCAR.testing"
poscar_bcu.write(tmp_file)
with open(tmp_file, 'r') as testing_file:
data = testing_file.read()
self.assertEqual(data, str(poscar_bcu))
os.remove(tmp_file)
class testCStru(unittest.TestCase):
def setUp(self):
self.m = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
g = GhostSpecie()
b = Specie("B")
self.sites = [[[g, b], [g, g]], [[b, b], [b, g]]]
self.arr = np.array([0, 5, 0, 0, 5, 5, 5, 0]).reshape([2, 2, 2])
self.sg = SitesGrid(self.sites)
self.s = CStru(self.m, self.sg)
def test_get_property(self):
self.assertEqual(self.s.m, self.m)
# eq_(self.s.depth, 2)
# eq_(self.s.width, 2)
# eq_(self.s.length, 2)
# eq_(self.s.get_grid, self.sites)
# arr = [[[0, 5],
# [0, 0]],
# [[5, 5],
# [5, 0]]]
# eq_(self.s.get_array(), arr)
def test_equal(self):
m_0 = [[1, 1, 1], [0, 0, 1], [1, 0, 0]]
g = GhostSpecie()
b = Specie("B")
sites_0 = [[[b, b], [g, g]], [[b, g], [g, b]]]
sg_0 = SitesGrid(sites_0)
diff_m = CStru(m_0, self.sg)
diff_s = CStru(self.m, sg_0)
self.assertEqual(self.s, self.s)
self.assertNotEqual(diff_m, self.s)
self.assertNotEqual(diff_s, self.s)
def test_from_array(self):
ss = CStru.from_array(self.m, self.arr)
self.assertEqual(ss, self.s)
def test_get_array(self):
self.assertTrue(np.allclose(self.s.get_array(), self.arr))
def test_gen_speckle(self):
c = Specie("Cu")
t = Specie("Ti")
sites = [[[c, c], [t, t]], [[c, t], [t, c]]]
sg = SitesGrid(sites)
gen = CStru.gen_speckle(self.m, Specie("Cu"), (2, 2, 2), Specie("Ti"),
4)
from collections import Iterator
self.assertIsInstance(gen, Iterator)
self.assertIn(CStru(self.m, sg), gen)
self.assertEqual(next(gen).get_array().sum(), 204)
self.assertEqual(next(gen).get_array().sum(), 204)
def test_get_cell(self):
c = Specie("Cu")
t = Specie("Ti")
m = [[-0.5, -0.5, -0.5], [-0.5, 0.5, 0.5], [0.5, -0.5, 0.5]]
sites01 = [[[c]]]
sites02 = [[[t, c, t], [t, t, c]]]
sg01 = SitesGrid(sites01)
sg02 = SitesGrid(sites02)
cstru01 = CStru(m, sg01)
cstru02 = CStru(m, sg02)
lat01, pos01, num01 = cstru01.get_cell()
lat02, pos02, num02 = cstru02.get_cell()
self.assertTrue(
np.allclose(
lat01,
np.array([[-0.5, -0.5, -0.5], [-0.5, 0.5, 0.5],
[0.5, -0.5, 0.5]])))
self.assertTrue(np.allclose(pos01, np.array([[0, 0, 0]])))
self.assertTrue(np.allclose(num01, np.array([29])))
self.assertTrue(
np.allclose(
lat02,
np.array([[-0.5, -0.5, -0.5], [-1, 1, 1], [1.5, -1.5, 1.5]])))
self.assertTrue(
np.allclose(
pos02,
np.array([[0, 0, 0], [0, 0, 1 / 3], [0, 0,
2 / 3], [0, 1 / 2, 0],
[0, 1 / 2, 1 / 3], [0, 1 / 2, 2 / 3]])))
self.assertTrue(np.allclose(num02, np.array([22, 29, 22, 22, 22, 29])))
def test_from_array(self):
ss = CStru.from_array(self.m, self.arr)
self.assertEqual(ss, self.s)
def test_get_string(self):
boron_arr = np.array([[[5, 0, 5, 5, 5, 5], [5, 5, 5, 5, 5, 5],
[5, 5, 0, 5, 5, 5]]])
latt = [[0, 0, 20], [1, 0, 0], [0.5, sqrt(3) / 2, 0]]
boron_stru = CStru.from_array(latt, boron_arr)
poscar = VaspPOSCAR(boron_stru.get_gcell(), zoom=4)
expected_str = '''B16
4
0.000000 0.000000 20.000000
3.000000 0.000000 0.000000
3.000000 5.196152 0.000000
B
16
direct
0.000000 0.000000 0.000000 B
0.000000 0.000000 0.333333 B
0.000000 0.000000 0.500000 B
0.000000 0.000000 0.666667 B
0.000000 0.000000 0.833333 B
0.000000 0.333333 0.000000 B
0.000000 0.333333 0.166667 B
0.000000 0.333333 0.333333 B
0.000000 0.333333 0.500000 B
0.000000 0.333333 0.666667 B
0.000000 0.333333 0.833333 B
0.000000 0.666667 0.000000 B
0.000000 0.666667 0.166667 B
0.000000 0.666667 0.500000 B
0.000000 0.666667 0.666667 B
0.000000 0.666667 0.833333 B
'''
self.assertEqual(str(poscar), expected_str)
bcu_arr = np.array([[[5, 29, 5, 5, 5, 5], [5, 5, 5, 5, 5, 5],
[5, 5, 29, 5, 5, 5]]])
latt = [[0, 0, 20], [1, 0, 0], [0.5, sqrt(3) / 2, 0]]
bcu_stru = CStru.from_array(latt, bcu_arr)
poscar_bcu = VaspPOSCAR(bcu_stru.get_gcell(), zoom=4)
expected_str_bcu = '''B16Cu2
4
0.000000 0.000000 20.000000
3.000000 0.000000 0.000000
3.000000 5.196152 0.000000
B Cu
16 2
direct
0.000000 0.000000 0.000000 B
0.000000 0.000000 0.333333 B
0.000000 0.000000 0.500000 B
0.000000 0.000000 0.666667 B
0.000000 0.000000 0.833333 B
0.000000 0.333333 0.000000 B
0.000000 0.333333 0.166667 B
0.000000 0.333333 0.333333 B
0.000000 0.333333 0.500000 B
0.000000 0.333333 0.666667 B
0.000000 0.333333 0.833333 B
0.000000 0.666667 0.000000 B
0.000000 0.666667 0.166667 B
0.000000 0.666667 0.500000 B
0.000000 0.666667 0.666667 B
0.000000 0.666667 0.833333 B
0.000000 0.000000 0.166667 Cu
0.000000 0.666667 0.333333 Cu
'''
self.assertEqual(str(poscar_bcu), expected_str_bcu)