def setUp(self):
g = GhostSpecie()
b = Specie("B")
self.sites = [[[b, b], [g, g]], [[b, g], [g, b]]]
self.sg = SitesGrid(self.sites)
self.allg0 = SitesGrid.sea(2, 2, 2, GhostSpecie())
self.allg = SitesGrid.sea(4, 2, 2, GhostSpecie())
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_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 test_equal(self):
other = SitesGrid.sea(4, 2, 2, Specie("Ti"))
self.assertNotEqual(other, self.allg)
self.assertNotEqual(None, self.allg)