def test_get_permutations(self):
pos = numpy.array([
0.5288, 0.1610, 0.9359, 0.0000, 0.0000, 0.0000, 0.2051, 0.8240,
-0.6786, 0.3345, -0.9314, -0.4496, -1.0685, -0.0537, 0.1921
]).reshape((-1, 3))
atoms = ['H', 'C', 'H', 'H', 'H']
methane = Molecule(pos, atoms)
symprec = 1e-2
perm = methane.get_symmetry_permutation(symprec)
num_sym = numpy.shape(perm)[0]
# methane have 12 symmetry operation
expected_num_sym = 12
self.assertEqual(num_sym, expected_num_sym)
def setUp(self):
self.string = '''2
H1He1
H 0.000000 0.000000 0.000000
He 0.250000 0.250000 0.250000
'''
positions = [0., 0., 0., 0.25, 0.25, 0.25]
atoms = ['H', 'He']
self.mol = Molecule(positions, atoms)
def test_write_string(self):
wanted = '''1
H1
H 0.000000 0.000000 0.000000
'''
positions = [0., 0., 0., 2.5, 2.5, 2.5]
atoms = ['H', 'Vacc']
mol = Molecule(positions, atoms)
got = _write_string(mol, long_format=False)
self.assertEqual(got, wanted)
def get_perms(cell,str_type='crystal',symprec=1e-3):
latt = cell.lattice
pos = cell.positions
pos = np.dot(pos,latt)
if str_type == "crystal":
symm = cell.get_symmetry()
trans,rots = symm['translations'],symm['rotations']
perms = np.zeros((np.shape(trans)[0],len(cell.atoms)))
origin_positions = refine_positions(cell.positions)
for ix, rot in enumerate(rots):
for iy,o_pos in enumerate(origin_positions):
new_pos = np.dot(rot,o_pos.T) + trans[ix]
new_pos = np.mod(new_pos,1)
new_pos = refine_positions(new_pos)
idx = np.argmin(np.linalg.norm(new_pos-origin_positions,axis=1))
perms[ix,iy] = idx
perms_table = np.unique(perms,axis=0)
else:
mol = Molecule(pos,cell.atoms)
perms_table = mol.get_symmetry_permutation(symprec)
return perms_table
def test_get_configurations_square_alloy(self):
positions = numpy.array([
0.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 2.0, 0.0, 0.0, 2.0, 2.0, 2.0,
0.0, 0.0, 2.0, 0.0, 2.0, 2.0, 2.0, 0.0, 2.0, 2.0, 2.0
]).reshape((-1, 3))
atoms = ['C'] * 8
molecule = Molecule(positions, atoms)
cg = ConfigurationGenerator(molecule, symprec=0.05)
e_num = (6, 2)
sites = [(5, 6)] * 8
all_type = cg.get_configurations(sites, e_num)
num_confs = len([i for i in all_type])
self.assertEqual(num_confs, 3)
def test_check(self):
# c-c键和c-o键均距离不大于0.1A
cco_pos = [2.0, 0.0, 0.0, -2.0, 0.0, 0.0, 0.0, 0.0, 0.0]
cco_atoms = [6, 6, 8]
mol = Molecule(cco_pos, cco_atoms)
self.assertTrue(mol.check(elements=None, limit=0.1))
# 测试元素c-c距离过近, 但只测o元素时候不会过近
cco_pos = [2.0, 0.0, 0.0, 2.01, 0.0, 0.0, 0.0, 0.0, 0.0]
cco_atoms = [6, 6, 8]
mol = Molecule(cco_pos, cco_atoms)
self.assertFalse(mol.check(elements=['C'], limit=0.1))
self.assertTrue(mol.check(elements=['O'], limit=0.1))
def get_configurations(self, sites, e_num):
'''
get_configurations output specific molecule
for specific concentration.
parameters:
sites: list of (lists or tuples), represent element disorder of each sites
e_num: tuple, number of atoms in disorderd sites.
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.
'''
perms = self.perms
mol_positions = self.mol.positions
for pa, d in remove_redundant(mol_positions, sites, perms,
e_num=e_num):
m = Molecule(pa[0], pa[1])
yield (m, d)
def _read_string(data):
"""
_read_string make io easy to be tested.
parameter: string of xyz input
return: Molecule object
"""
lines = [l for l in data.split('\n') if l.rstrip()]
total_atoms = int(lines[0])
comment = lines[1]
positions = []
atoms = []
for i in range(2, 2 + total_atoms):
s = lines[i].split()
atoms.append(s[0])
vec = float(s[1]), float(s[2]), float(s[3])
positions.append(vec)
return Molecule(positions, atoms)
def get_mole_point_defect(self,
symprec=1e-3,
doped_out='all',
doped_in=['Vac'],
num=[1]):
pos, lat, atoms = self.positions, self.lattice, self.atoms
mole = Molecule(np.dot(pos, lat), atoms)
cg = mole_CG(mole, symprec)
sites = _get_sites(list(mole.atoms),
doped_out=doped_out,
doped_in=doped_in)
if num == None:
confs = cg.get_configurations(sites, e_num=None)
comment = ["-".join(doped_in) + "-all_concentration"]
else:
purity_atom_num = sum(
[1 if len(site) > 1 else 0 for site in sites])
confs = cg.get_configurations(sites,
e_num=[purity_atom_num - sum(num)] +
num)
comment = list(chain(*zip(doped_in, [str(i) for i in num])))
folder = '-'.join(doped_out) + '-' + '-'.join(comment) + '-defect'
if not os.path.exists('./' + folder):
os.mkdir('./' + folder)
else:
rmtree('./' + folder)
os.mkdir('./' + folder)
deg = []
idx = 0
for c, _deg in confs:
c.lattice = lat
c._positions = np.dot(c.positions, np.linalg.inv(lat))
write_poscar(c, folder, idx)
deg.append(_deg)
idx += 1
np.savetxt(os.path.join(folder, "deg.txt"), deg, fmt='%d')
def setUp(self):
molecule = Molecule(positions_c60, atoms_c60)
self.cg = ConfigurationGenerator(molecule, symprec=0.05)
def test_init(self):
positions = [0, 0, 0]
atoms = ['NaN_10']
mole = Molecule(positions, atoms)
self.assertEqual(mole.atoms.tolist(), [1010])