def cons_max_volume(self, sites, max_volume, min_volume=1, dimension=3, symprec=1e-5):
"""
parameters:
pcell: Cell object, The primitive cell to be extended
sites: disorderd sites infomation.
yield:
Cell object, a list of non-redundant configurations to max volume supercells.
"""
# 该函数产生所有构型用于确定基态相图
for volume in range(min_volume, max_volume + 1):
hnfs = non_dup_hnfs(self._pcell, volume, dimension, symprec)
dict_trans = {} # 记录已经产生过的snf，相同snf的平移操作相同。
for h in hnfs:
hfpg = PermutationGroup(self._pcell, h)
# 此处的平移操作不必每次重新计算，因为相同snf平移操作相同
# 可以用字典来标记查询。若没有这样的操作，那么就没有snf带来的效率提升。
# quotient = hfpg.get_quotient()
# if not quotient in dict_trans:
# dict_trans[quotient] = hfpg.get_pure_translations(symprec)
# trans = dict_trans[quotient]
# rots = hfpg.get_pure_rotations(symprec)
perms = hfpg.get_symmetry_perms(symprec)
supercell = self._pcell.extend(h)
_sites = numpy.repeat(sites, volume, axis=0)
for mol, _ in remove_redundant(supercell.positions, _sites, perms):
c = Cell(supercell.lattice, mol[0], mol[1])
if c.is_primitive(symprec):
yield c
def test_check(self):
lattice = numpy.array([0.0, 2.75, 2.75,
2.75, 0.0, 2.75,
2.75, 2.75, 0.0])
si_pos = [-0.125, -0.125, -0.125,
0.125, 0.125, 0.125]
si_atoms = [14, 14]
cell = Cell(lattice, si_pos, si_atoms)
self.assertTrue(cell.check(limit=0.1))
si_pos = [-0.125, -0.125, -0.125,
0.125, 0.125, 0.125,
0.13, 0.125, 0.125]
si_atoms = [14, 14, 8]
cell = Cell(lattice, si_pos, si_atoms)
self.assertFalse(cell.check(limit=0.1))
# 测试元素
self.assertTrue(cell.check(limit=0.1, elements=['O']))
lattice = numpy.array([1.0, 0.0, 0.0,
0.0, 1.0, 0.0,
0.0, 0.0, 1.0])
si_pos = [-0.01, 0.0, 0.0,
0.01, 0.0, 0.0]
si_atoms = [14, 14]
# 两点之间的距离为0.02<0.05， 但在没有考虑边界条件时距离是0.98
cell = Cell(lattice, si_pos, si_atoms)
self.assertFalse(cell.check(limit=0.05))
def test_get_primitive(self):
fcc_latt = [5, 0, 0, 0, 5, 0, 0, 0, 5]
fcc_pos = [(0, 0, 0), (0, 0.5, 0.5), (0.5, 0, 0.5), (0.5, 0.5, 0)]
fcc_atoms = [0, 0, 0, 0]
con_cell = Cell(fcc_latt, fcc_pos, fcc_atoms)
pcell = con_cell.get_primitive_cell()
self.assertEqual(pcell.atoms, [0])
def test_extend_not_hnf(self):
fcc_latt = [0, 5, 5,
5, 0, 5,
5, 5, 0]
fcc_pos = [(0, 0, 0),
(0.5, 0.5, 0.5)]
fcc_atoms = [1, 2]
fcc_pcell = Cell(fcc_latt, fcc_pos, fcc_atoms)
op_ext = numpy.array([-1, 1, 1,
1, -1, 1,
1, 1, -1]).reshape((3, 3))
ext_fcc = fcc_pcell.extend(op_ext)
wanted_latt = numpy.array([10, 0, 0,
0, 10, 0,
0, 0, 10]).reshape((3, 3))
wanted_pos = numpy.array([(0, 0, 0),
(0.5, 0.5, 0),
(0.5, 0, 0.5),
(0, 0.5, 0.5),
(0.5, 0.5, 0.5),
(0, 0, 0.5),
(0, 0.5, 0),
(0.5, 0, 0)])
wanted_atoms = numpy.array([1, 1, 1, 1, 2, 2, 2, 2])
numpy.testing.assert_almost_equal(ext_fcc.lattice, wanted_latt)
numpy.testing.assert_almost_equal(ext_fcc.positions, wanted_pos)
numpy.testing.assert_almost_equal(ext_fcc.atoms, wanted_atoms)
def test_extend_bug(self):
sc_latt = [4, 0, 0, 0, 4, 0, 0, 0, 4]
sc_pos = [(0, 0, 0)]
sc_atoms = [1]
sc_pcell = Cell(sc_latt, sc_pos, sc_atoms)
op_ext = numpy.array([1, 0, 0, 0, 1, 0, 0, 0, 5]).reshape((3, 3))
ext_sc = sc_pcell.extend(op_ext) # raise ValueError
pass
def test_is_primitive(self):
bcc_latt = [0.5, 0.5, -0.5,
-0.5, 0.5, 0.5,
0.5, -0.5, 0.5]
bcc_pos = [(0, 0, 0)]
bcc_atoms = [0]
bcc_pcell = Cell(bcc_latt, bcc_pos, bcc_atoms)
self.assertTrue(bcc_pcell.is_primitive())
def setUp(self):
# BCC
bcc_latt = [0.5, 0.5, -0.5, -0.5, 0.5, 0.5, 0.5, -0.5, 0.5]
bcc_pos = [(0, 0, 0)]
bcc_atoms = [0]
self.bcc_pcell = Cell(bcc_latt, bcc_pos, bcc_atoms)
# FCC
fcc_latt = [0, 5, 5, 5, 0, 5, 5, 5, 0]
fcc_pos = [(0, 0, 0)]
fcc_atoms = [0]
self.fcc_pcell = Cell(fcc_latt, fcc_pos, fcc_atoms)
def cons_specific_volume(self, sites, volume=2, e_num=None, dimension=3, symprec=1e-5):
"""
parameters:
sites: 2D list, disorderd sites infomation.
volume: int, certain volume with subperiodic.
symprec: float, precision for symmetry find.
yield:
a tuple
tuple[0]: Cell object, a list of non-redundant configurations of certain volume supercell.
tuple[1]: int object, degeneracy of the configuration in all configurations of this volume.
"""
# 该函数产生特定体积下所有构型（包括超胞）和简并度，用于统计平均
hnfs = non_dup_hnfs(self._pcell, volume, dimension, symprec)
dict_trans = {}
for h in hnfs:
hfpg = PermutationGroup(self._pcell, h)
# 此处的平移操作不必每次重新计算，因为相同snf平移操作相同
# 可以用字典来标记查询。若没有这样的操作，那么就没有snf带来的效率提升。
# For hnf with same snf, translations are same.
# quotient = hfpg.get_quotient()
# if not quotient in dict_trans:
# dict_trans[quotient] = hfpg.get_pure_translations(symprec)
# trans = dict_trans[quotient]
# rots = hfpg.get_pure_rotations(symprec)
perms = hfpg.get_symmetry_perms(symprec)
supercell = self._pcell.extend(h)
_sites = numpy.repeat(sites, volume, axis=0)
for mol, d in remove_redundant(supercell.positions, _sites, perms, e_num):
c = Cell(supercell.lattice, mol[0], mol[1])
yield (c, d)
def test_Cart_string(self):
data = '''C2
1.0
4.9208798409 0.0000000000 0.0000000000
-2.4604404879 4.2616066235 0.0000000000
0.0000000000 0.0000000000 10.0000000000
C
8
Cartesian
0.000000000 0.000000000 0.000000000
-1.230220199 2.130803347 0.000000000
2.460439920 0.000000000 0.000000000
1.230219722 2.130803347 0.000000000
1.230232477 0.710260868 0.000000000
0.000012159 2.841064692 0.000000000
3.690671921 0.710260868 0.000000000
2.460451603 2.841064692 0.000000000
'''
latt = [[4.9208798409, 0.0000000000, 0.0000000000],
[-2.4604404879, 4.2616066235, 0.0000000000],
[0.0000000000, 0.0000000000, 10.0000000000]]
positions = [[0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[1.32703105e-08, 5.00000008e-01, 0.00000000e+00],
[5.00000000e-01, 0.00000000e+00, 0.00000000e+00],
[5.00000013e-01, 5.00000008e-01, 0.00000000e+00],
[3.33335086e-01, 1.66665047e-01, 0.00000000e+00],
[3.33335131e-01, 6.66665167e-01, 0.00000000e+00],
[8.33334989e-01, 1.66665047e-01, 0.00000000e+00],
[8.33335035e-01, 6.66665167e-01, 0.00000000e+00]]
atoms = ['C' for i in range(8)]
wanted = Cell(latt, positions, atoms)
got = _read_string(data)
self.assertLess(numpy.sum(abs(got.positions - wanted.positions)), 1e-4)
def setUp(self):
lattice = numpy.array([7.1, 0, 0, 0, 7.1, 0, 0, 0, 7.1]).reshape(
(3, 3))
positions = numpy.array([
0.00, 0.00, 0.00, 0.00, 0.00, 0.50, 0.00, 0.50, 0.00, 0.00, 0.50,
0.50, 0.50, 0.00, 0.00, 0.50, 0.00, 0.50, 0.50, 0.50, 0.00, 0.50,
0.50, 0.50, 0.00, 0.25, 0.25, 0.00, 0.25, 0.75, 0.00, 0.75, 0.25,
0.00, 0.75, 0.75, 0.50, 0.25, 0.25, 0.50, 0.25, 0.75, 0.50, 0.75,
0.25, 0.50, 0.75, 0.75, 0.25, 0.00, 0.25, 0.25, 0.00, 0.75, 0.25,
0.50, 0.25, 0.25, 0.50, 0.75, 0.75, 0.00, 0.25, 0.75, 0.00, 0.75,
0.75, 0.50, 0.25, 0.75, 0.50, 0.75, 0.25, 0.25, 0.00, 0.25, 0.25,
0.50, 0.25, 0.75, 0.00, 0.25, 0.75, 0.50, 0.75, 0.25, 0.00, 0.75,
0.25, 0.50, 0.75, 0.75, 0.00, 0.75, 0.75, 0.50
])
atoms = numpy.array([28] * 32)
cell = Cell(lattice, positions, atoms)
mcell = cell_to_mcell(cell)
mcell.set_site(0, ([0, 0, 0], 'Co'))
mcell.set_site(16, ([0.25, 0, 0.25], 'Co'))
self.cell_nearest_1 = mcell.to_cell()
mcell = cell_to_mcell(cell)
mcell.set_site(0, ([0, 0, 0], 'Co'))
mcell.set_site(21, ([0.75, 0, 0.75], 'Co'))
self.cell_nearest_2 = mcell.to_cell()
mcell = cell_to_mcell(cell)
mcell.set_site(1, ([0, 0, 0.5], 'Co'))
mcell.set_site(5, ([0.5, 0, 0.5], 'Co'))
self.cell_far = mcell.to_cell()
def cons_specific_cell(self, sites, e_num=None, symprec=1e-5):
"""
cons_specific_cell_and_c generate configurations of specific cell
and specific concentration.
parameters:
sites: list of (lists or tuples), represent element disorder of each sites
e_num: tuple, number of atoms in disorderd sites.
e_num 特指无序位点的浓度，也就是原子比，而不是整体构型的元素原子比。有可能其他位点存在相同构型。
!!限制，无序位点的组成必须是相同的，而上面几个函数的无序位点是可以不同的。!!
"""
lat_cell = self._cell.lattice
lat_pcell = self._pcell.lattice
mat = numpy.matmul(lat_cell, numpy.linalg.inv(lat_pcell))
if is_int_np_array(mat):
mat = numpy.around(mat).astype('intc')
else:
print("cell:\n", lat_cell)
print("primitive cell:\n", lat_pcell)
raise ValueError(
"cell lattice and its primitive cell lattice not convertable")
hfpg = PermutationGroup(self._pcell, mat)
perms = hfpg.get_symmetry_perms(symprec)
supercell = self._pcell.extend(mat)
for mol, d in remove_redundant(supercell.positions, sites, perms, e_num=e_num):
c = Cell(supercell.lattice, mol[0], mol[1])
yield (c, d)
def get_max_volume(pcell, sites, max_volume, min_volume=1, dimension=3, symprec=1e-5):
for volume in range(min_volume, max_volume + 1):
hnfs = non_dup_hnfs(pcell, volume, dimension, symprec)
dict_trans = {} # 记录已经产生过的snf，相同snf的平移操作相同。
for h in hnfs:
hfpg = PG(pcell, h)
perms = hfpg.get_symmetry_perms(symprec)
if dimension == 2:
supercell = pcell.extend(h)._get_niggli_2D()
else:
supercell = pcell.extend(h)._get_niggli_3D()
_sites = np.repeat(sites, volume, axis=0)
for mol, _ in remove_redundant(supercell.positions, _sites, perms):
c = Cell(supercell.lattice, mol[0], mol[1])
if c.is_primitive(symprec):
yield c
def setUp(self):
fcc_latt = [0, 5, 5,
5, 0, 5,
5, 5, 0]
fcc_pos = [(0, 0, 0), (0.5, 0.5, 0.5)]
fcc_atoms = [1, 2]
self.fcc_pcell = Cell(fcc_latt, fcc_pos, fcc_atoms)
def read(ase_atoms):
if isinstance(ase_atoms, Atoms):
lattice = ase_atoms.get_cell(complete=False)
positions = ase_atoms.get_positions(wrap=False)
atoms = ase_atoms.get_atomic_numbers()
return Cell(lattice, positions, atoms)
else:
raise TypeError("The value is not an ase.Atoms object")
def setUp(self):
lattice = numpy.array([5.5, 0, 0, 0, 5.5, 0, 0, 0, 5.5]).reshape(
(3, 3))
positions = numpy.array([
0.0, 0.0, 0.0, 0.0, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.0, 0.5,
0.5, 0.5, 0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.5
])
atoms = numpy.array([11, 11, 11, 11, 17, 17, 17, 17])
self.cell = Cell(lattice, positions, atoms)
def test_cons_specific_cell_and_c(self):
# FCC conventional cell
fcc_latt = [5, 0, 0,
0, 5, 0,
0, 0, 5]
fcc_pos = [(0, 0, 0),
(0, 0.5, 0.5),
(0.5, 0, 0.5),
(0.5, 0.5, 0)]
fcc_atoms = [0, 0, 0, 0]
con_cell = Cell(fcc_latt, fcc_pos, fcc_atoms)
cg = CG(con_cell)
con = cg.cons_specific_cell(
[(2, 3, 4), (2, 3, 4), (2, 3, 4), (2, 3, 4)], e_num=(2, 1, 1))
# number of all configurations
wanted = 1
got = len([i for i in con])
self.assertEqual(got, wanted)
# Zinc-blende conventional cell
fcc_latt = [5, 0, 0,
0, 5, 0,
0, 0, 5]
fcc_pos = [(0, 0, 0),
(0, 0.5, 0.5),
(0.5, 0, 0.5),
(0.5, 0.5, 0),
(0.25, 0.25, 0.25),
(0.75, 0.75, 0.25),
(0.75, 0.25, 0.75),
(0.25, 0.75, 0.75)]
fcc_atoms = [0, 0, 0, 0, 1, 1, 1, 1]
con_cell = Cell(fcc_latt, fcc_pos, fcc_atoms)
cg = CG(con_cell)
con = cg.cons_specific_cell(
[(2, 3, 4), (2, 3, 4), (2, 3, 4), (2, 3, 4), (1, ), (1, ), (1, ), (1,)], e_num=(2, 1, 1))
# number of all configurations
wanted = 1
got = len([i for i in con])
self.assertEqual(got, wanted)
def setUp(self):
lattice = [3.0, 0, 0, 0, 2.0, 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)]
atoms = ['C'] * 12
self.cell = Cell(lattice, positions, atoms)
def setUp(self):
# BCC
bcc_latt = [1, 1, -1, -1, 1, 1, 1, -1, 1]
bcc_pos = [(0, 0, 0)]
bcc_atoms = [0]
self.bcc_pcell = Cell(bcc_latt, bcc_pos, bcc_atoms)
# FCC
fcc_latt = [0, 5, 5, 5, 0, 5, 5, 5, 0]
fcc_pos = [(0, 0, 0)]
fcc_atoms = [0]
self.fcc_pcell = Cell(fcc_latt, fcc_pos, fcc_atoms)
# HCP
hcp_b = [
2.51900005, 0., 0., -1.25950003, 2.18151804, 0., 0., 0., 4.09100008
]
hcp_positions = [(0.33333334, 0.66666669, 0.25),
(0.66666663, 0.33333331, 0.75)]
hcp_numbers = [0, 0]
self.hcp_pcell = Cell(hcp_b, hcp_positions, hcp_numbers)
def test_cell_to_mcell(self):
si_pos = [(-0.125, -0.125, -0.125), (0.125, 0.125, 0.125)]
si_atoms = [14, 14]
c = Cell(self.lattice, si_pos, si_atoms)
mc = cell_to_mcell(c)
self.assertTrue(isinstance(mc, MutableCell))
# 转换回去，并测试返回后的数据结构
c = mc.to_cell()
numpy.testing.assert_almost_equal(
c.positions,
numpy.array([0.875, 0.875, 0.875, 0.125, 0.125, 0.125]).reshape(
(2, 3)))
numpy.testing.assert_almost_equal(c.atoms, numpy.array([14, 14]))
def setUp(self):
self.string = '''H1 He1
1.000000
0.000000 0.500000 0.533333
0.500000 0.000000 0.566667
0.500000 0.500000 0.000000
H He
1 1
Direct
0.000000 0.000000 0.000000 H
0.250000 0.250000 0.250000 He
'''
latt = [0., 0.5, 0.53333333333, 0.5, 0., 0.56666666667, 0.5, 0.5, 0.]
positions = [0., 0., 0., 0.25, 0.25, 0.25]
atoms = ['H', 'He']
self.cell = Cell(latt, positions, atoms)
def test_cons_specific_cell(self):
fcc_latt = [5, 0, 0,
0, 5, 0,
0, 0, 5]
fcc_pos = [(0, 0, 0),
(0, 0.5, 0.5),
(0.5, 0, 0.5),
(0.5, 0.5, 0)]
fcc_atoms = [0, 0, 0, 0]
con_cell = Cell(fcc_latt, fcc_pos, fcc_atoms)
cg = CG(con_cell)
con = cg.cons_specific_cell([(2, 3), (2, 3), (2, 3), (2, 3)])
# number of all configurations
wanted = 5
got = len([i for i in con])
self.assertEqual(got, wanted)
def test_from_cell(self):
lattice = numpy.copy(self.lattice)
positions = numpy.array([0.0, 0.0, 0.0,
0.25, 0.25, 0.25]).reshape((2, 3))
atoms = numpy.array([6, 6])
origin_lattice = numpy.copy(lattice)
origin_positions = numpy.copy(positions)
origin_atoms = numpy.copy(atoms)
cell = Cell(lattice, positions, atoms)
mcell = MutableCell.from_cell(cell)
self.assertTrue(isinstance(mcell, MutableCell))
# Make sure mcell modified not change the cell
mcell.remove_site(0)
numpy.testing.assert_almost_equal(cell.lattice, origin_lattice)
numpy.testing.assert_almost_equal(cell.positions, origin_positions)
numpy.testing.assert_almost_equal(cell.atoms, origin_atoms)
def test_write_string_vacc(self):
wanted = '''H1
1.000000
0.000000 0.500000 0.533333
0.500000 0.000000 0.566667
0.500000 0.500000 0.000000
H
1
Direct
0.000000 0.000000 0.000000 H
'''
latt = [0., 0.5, 0.53333333333, 0.5, 0., 0.56666666667, 0.5, 0.5, 0.]
positions = [0., 0., 0., 0.25, 0.25, 0.25]
atoms = ['H', 'Vacc']
cell = Cell(latt, positions, atoms)
got = _write_string(cell, long_format=False)
self.assertEqual(got, wanted)
def get_tetrahedral_defect(self,
isunique=False,
doped_in='H',
min_d=1.5,
folder='tetrahedral-defect'):
all_basis = generate_all_basis(1, 1, 1)
direct_lattice = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
extend_S = np.zeros((0, 3))
for basis in all_basis:
new_basis = np.sum([(direct_lattice[ii] * basis[ii]).tolist()
for ii in range(3)],
axis=0)
extend_S = np.vstack(
(extend_S,
self.positions + np.tile(new_basis, len(self.atoms)).reshape(
(-1, 3))))
idx = np.sum((extend_S <= 1.2) & (extend_S >= -0.2), axis=1)
idx = np.where(idx == 3)[0]
extend_S = np.dot(extend_S[idx], self.lattice)
n = extend_S.shape[0]
d = np.zeros((n, n))
for ii in range(n):
d[ii, ii + 1:] = np.linalg.norm(extend_S[ii] - extend_S[ii + 1:],
axis=1)
d = d + d.T
first_tetra, sec_tetra, third_tetra = [], [], []
for ii in range(n):
temp_d = sorted(d[ii])
idx = np.where(abs(d[ii] - temp_d[1]) < min_d)[0]
if len(idx) < 3:
continue
for comb in combinations(idx, 3):
comb_list = list(comb)
tmp = d[comb_list][:, comb_list]
comb_list.append(ii)
if np.std(tmp[tmp > 0]) < 0.01:
if abs(tmp[0, 1] - temp_d[1]) < 0.1:
first_tetra.append(comb_list)
else:
sec_tetra.append(comb_list)
else:
tmp = d[comb_list][:, comb_list]
tmp = np.triu(tmp)
tmp = sorted(tmp[tmp > 0])
if (np.std(tmp[0:4]) < 0.1 or np.std(tmp[1:5]) < 0.1
or np.std(tmp[2:]) < 0.1) and np.std(tmp) < 0.5:
third_tetra.append(comb_list)
all_tetra = []
if len(first_tetra) != 0:
first_tetra = np.unique(np.sort(first_tetra, axis=1), axis=0)
first_tetra = refine_points(first_tetra,
extend_S,
self.lattice,
min_d=min_d)
all_tetra.append(first_tetra)
if len(sec_tetra) != 0:
sec_tetra = np.unique(np.sort(sec_tetra, axis=1), axis=0)
sec_tetra = refine_points(sec_tetra,
extend_S,
self.lattice,
min_d=min_d)
all_tetra.append(sec_tetra)
if len(third_tetra) != 0:
third_tetra = np.unique(np.sort(third_tetra, axis=1), axis=0)
third_tetra = refine_points(third_tetra,
extend_S,
self.lattice,
min_d=min_d)
all_tetra.append(third_tetra)
if isunique:
if not os.path.exists(folder):
os.mkdir(folder)
else:
rmtree(folder)
os.mkdir(folder)
idx = 0
# deg = []
for tetra in all_tetra:
if len(tetra) == 0:
continue
new_pos = np.vstack((self.positions, tetra))
new_atoms = np.hstack((self.atoms, s2n(doped_in) * np.ones(
(tetra.shape[0], ))))
new_cell = Cell(self.lattice, new_pos, new_atoms)
equi_atoms = new_cell.get_symmetry()['equivalent_atoms']
purity_atom_type = np.unique(equi_atoms[-tetra.shape[0]:])
for atom_type in purity_atom_type:
new_uniq_pos = np.vstack(
(self.positions, new_pos[atom_type]))
new_uniq_atoms = np.hstack(
(self.atoms, s2n(doped_in) * np.ones((1, ))))
new_uniq_cell = Cell(self.lattice, new_uniq_pos,
new_uniq_atoms)
# deg.append(len(np.where(equi_atoms == atom_type)[0]))
write_poscar(new_uniq_cell, folder, idx)
idx += 1
# np.savetxt(folder+'/deg.txt',deg,fmt='%d')
else:
if not os.path.exists(folder):
os.mkdir(folder)
else:
rmtree(folder)
os.mkdir(folder)
idx = 0
for tetra in all_tetra:
if len(tetra) == 0:
continue
new_pos = np.vstack((self.positions, tetra))
new_atoms = np.hstack((self.atoms, s2n(doped_in) * np.ones(
(tetra.shape[0], ))))
new_cell = Cell(self.lattice, new_pos, new_atoms)
write_poscar(new_cell, folder, idx)
idx += 1
neig_list = np.zeros((n, 6))
for ii in range(pos.shape[0]):
d = np.linalg.norm(pos[ii] - extend_pos, axis=1)
idx = np.where(abs(d - d[np.argsort(d)[1]]) < 0.01)[0]
neig_list[ii] = idx % n
pos = np.dot(pos, np.linalg.inv(latt))
vac_str = [np.array([0])]
for vac in range(2, 6):
last_vac_str = vac_str[-1]
tmp_vac_str = []
n_prev = last_vac_str.shape[0]
for i in range(n_prev):
each_str = last_vac_str[i]
idx = np.setdiff1d(np.setdiff1d(range(n), each_str),
neig_list[each_str][:])
for ii in idx:
tmp_vac_str.append(get_min_serial(perms, np.hstack(
(each_str, ii))))
vac_str.append(np.unique(tmp_vac_str, axis=0))
idx = 0
os.makedirs('vac-' + str(vac))
for _str in vac_str[-1]:
_pos = pos[np.setdiff1d(range(n), _str), :]
_latt, _atoms = latt, np.ones((n - vac, )) * 5
write_vasp(Cell(_latt, _pos, _atoms),
'vac-' + str(vac) + '/POSCAR' + str(idx))
idx += 1
print(vac_str[-1].shape)
class TestHnf(unittest.TestCase):
def test(self):
pass
def setUp(self):
# BCC
bcc_latt = [1, 1, -1, -1, 1, 1, 1, -1, 1]
bcc_pos = [(0, 0, 0)]
bcc_atoms = [0]
self.bcc_pcell = Cell(bcc_latt, bcc_pos, bcc_atoms)
# FCC
fcc_latt = [0, 5, 5, 5, 0, 5, 5, 5, 0]
fcc_pos = [(0, 0, 0)]
fcc_atoms = [0]
self.fcc_pcell = Cell(fcc_latt, fcc_pos, fcc_atoms)
# HCP
hcp_b = [
2.51900005, 0., 0., -1.25950003, 2.18151804, 0., 0., 0., 4.09100008
]
hcp_positions = [(0.33333334, 0.66666669, 0.25),
(0.66666663, 0.33333331, 0.75)]
hcp_numbers = [0, 0]
self.hcp_pcell = Cell(hcp_b, hcp_positions, hcp_numbers)
def test_hnf_cells(self):
# Results from <PHYSICAL REVIEW B 80, 014120 (2009)>
# BCC
wanted = [1, 2, 3, 7, 5, 10, 7]
got = [len(non_dup_hnfs(self.bcc_pcell, i)) for i in range(1, 8)]
# for h in non_dup_hnfs(self.bcc_pcell, 7):
# print(h)
self.assertEqual(got, wanted)
# FCC
wanted = [1, 2, 3, 7, 5, 10, 7]
got = [len(non_dup_hnfs(self.fcc_pcell, i)) for i in range(1, 8)]
self.assertEqual(got, wanted)
# HCP
wanted = [1, 3, 5, 11, 7, 19, 11, 34]
got = [len(non_dup_hnfs(self.hcp_pcell, i)) for i in range(1, 9)]
self.assertEqual(got, wanted)
def test_is_hnf_dup(self):
hnf_x = numpy.array([[1, 0, 0], [0, 1, 0], [0, 0, 2]])
hnf_y = numpy.array([[1, 0, 0], [0, 2, 0], [0, 0, 1]])
rot_syms = self.bcc_pcell.get_rotations(1e-3)
is_dup = _is_hnf_dup(hnf_x, hnf_y, rot_syms, prec=1e-3)
self.assertTrue(is_dup)
# debug for compare method
# numpy.mod problem!
hnf_x = numpy.array([[1, 0, 0], [0, 1, 2], [0, 0, 5]])
hnf_y = numpy.array([[1, 0, 3], [0, 1, 3], [0, 0, 5]])
rot_syms = self.bcc_pcell.get_rotations(1e-3)
is_dup = _is_hnf_dup(hnf_x, hnf_y, rot_syms, prec=1e-5)
self.assertTrue(is_dup)
# debug for compare method
# numpy.astype problem!
hnf_x = numpy.array([[1, 0, 6], [0, 1, 6], [0, 0, 7]])
hnf_y = numpy.array([[1, 0, 3], [0, 1, 6], [0, 0, 7]])
rot_syms = self.bcc_pcell.get_rotations(1e-3)
is_dup = _is_hnf_dup(hnf_x, hnf_y, rot_syms, prec=1e-5)
self.assertTrue(is_dup)
def _read_string(data):
"""
_read_string make io easy to be tested.
parameter: string of vasp input
return: Cell object
"""
lines = [l for l in data.split('\n') if l.rstrip()]
name = lines[0]
lattice_scale = float(lines[1].split()[0])
# lattice vectors
lattice = []
for i in [2, 3, 4]:
s = lines[i].split()
vec = float(s[0]), float(s[1]), float(s[2])
lattice.append(vec)
lattice = numpy.array(lattice)
if lattice_scale < 0:
# In vasp , a negative scale factor is treated as a volume.
# http://pymatgen.org/_modules/pymatgen/io/vasp/inputs.html#POSCAR
vol = abs(numpy.linalg.det(lattice))
lattice *= (-lattice_scale / vol)**(1 / 3)
else:
lattice *= lattice_scale
# atoms
vasp5 = False
_fifth_line = lines[5].split()
# VASP 5.x use the fifth line to represent atomic symbols
try:
for i in _fifth_line:
int(i)
numofatoms = _fifth_line
except ValueError:
vasp5 = True
atomtypes = _fifth_line
numofatoms = lines[6].split() # list of string here
if not vasp5:
warnings.warn(
"symbols of elements in fifth line are missing, "
"all atoms are init to NaN_i (i=0,1,2...)",
UserWarning,
stacklevel=2)
atomtypes = [str("NaN_{:}".format(i)) for i in range(len(numofatoms))]
atoms = []
for i, num in enumerate(numofatoms):
# https://gitlab.com/ase/ase/blob/master/ase/io/vasp.py
numofatoms[i] = int(num)
[atoms.append(atomtypes[i]) for na in range(numofatoms[i])]
if not vasp5:
line_coortype = 6
else:
line_coortype = 7
# TODO: Supporting Cartesian coordinates vasp input
coortype = lines[line_coortype].split()[0]
if coortype[0] in "sS":
warnings.warn("Sorry! Selective dynamics "
"are not supported now",
FutureWarning,
stacklevel=2)
line_coortype += 1
coortype = lines[line_coortype].split()[0]
if coortype[0] in "cCkK":
line_first_pos = line_coortype + 1
iscart = True
else:
iscart = False
if coortype[0] in "dD":
line_first_pos = line_coortype + 1
positions = []
total_atoms = sum(numofatoms)
for i in range(line_first_pos, line_first_pos + total_atoms):
s = lines[i].split()
vec = float(s[0]), float(s[1]), float(s[2])
positions.append(vec)
if iscart:
positions = numpy.dot(numpy.array(positions),
numpy.linalg.inv(lattice))
return Cell(lattice, positions, atoms)
def test_init(self):
lattice = [1.0, 0, 0, 0, 1.0, 0, 0, 0, 1.0]
positions = [0, 0, 0]
atoms = ['NaN_10']
cell = Cell(lattice, positions, atoms)
self.assertEqual(cell.atoms.tolist(), [1010])