class TestAtom(object):
def setUp(self):
self.C = Atom['C']
self.C3 = Atom('C', orbs=3)
self.Au = Atom['Au']
self.PT = PeriodicTable()
def tearDown(self):
del self.C
del self.Au
del self.C3
del self.PT
def test1(self):
assert_true(self.C == Atom['C'])
assert_true(self.C == Atom[self.C])
assert_true(self.C == Atom[Atom['C']])
assert_true(self.C == Atom[Atom(6)])
assert_true(self.Au == Atom['Au'])
assert_true(self.Au != self.C)
assert_false(self.Au == self.C)
assert_true(self.Au == self.Au.copy())
def test2(self):
C = Atom('C', R=20)
assert_false(self.C == C)
Au = Atom('Au', R=20)
assert_false(self.C == Au)
C = Atom['C']
assert_false(self.Au == C)
Au = Atom['Au']
assert_false(self.C == Au)
def test3(self):
assert_true(self.C.symbol == 'C')
assert_true(self.Au.symbol == 'Au')
def test4(self):
assert_true(self.C.mass > 0)
assert_true(self.Au.mass > 0)
def test5(self):
assert_true(Atom(Z=1, mass=12).mass == 12)
assert_true(Atom(Z=31, mass=12).mass == 12)
assert_true(Atom(Z=31, mass=12).Z == 31)
def test6(self):
assert_true(Atom(Z=1, orbs=3).orbs == 3)
assert_true(len(Atom(Z=1, orbs=3)) == 3)
assert_true(Atom(Z=1, R=1.4).R == 1.4)
assert_true(Atom(Z=1, R=1.4).maxR() == 1.4)
assert_true(Atom(Z=1, R=[1.4, 1.8]).orbs == 2)
assert_true(Atom(Z=1, R=[1.4, 1.8]).maxR() == 1.8)
def test7(self):
assert_true(Atom(Z=1, orbs=3).radius() > 0.)
assert_true(len(str(Atom(Z=1, orbs=3))))
def test8(self):
a = self.PT.Z([1, 2])
assert_true(len(a) == 2)
assert_true(a[0] == 1)
assert_true(a[1] == 2)
def test9(self):
a = self.PT.Z_label(['H', 2])
assert_true(len(a) == 2)
assert_true(a[0] == 'H')
assert_true(a[1] == 'He')
a = self.PT.Z_label(1)
assert_true(a == 'H')
def test10(self):
assert_equal(self.PT.atomic_mass(1), self.PT.atomic_mass('H'))
assert_true(np.allclose(self.PT.atomic_mass([1, 2]), self.PT.atomic_mass(['H', 'He'])))
def test11(self):
PT = self.PT
for m in ['calc', 'empirical', 'vdw']:
assert_equal(PT.radius(1, method=m), PT.radius('H', method=m))
assert_true(np.allclose(PT.radius([1, 2], method=m), PT.radius(['H', 'He'], method=m)))
@raises(KeyError)
def test12(self):
a = Atom(1.2)
def test_pickle(self):
import pickle as p
sC = p.dumps(self.C)
sC3 = p.dumps(self.C3)
sAu = p.dumps(self.Au)
C = p.loads(sC)
C3 = p.loads(sC3)
Au = p.loads(sAu)
assert_false(Au == C)
assert_true(Au != C)
assert_true(C == self.C)
assert_true(C3 == self.C3)
assert_false(C == self.Au)
assert_true(Au == self.Au)
assert_true(Au != self.C)
class TestAtom(object):
def setUp(self):
self.C = Atom['C']
self.C3 = Atom('C', orbs=3)
self.Au = Atom['Au']
self.PT = PeriodicTable()
def tearDown(self):
del self.C
del self.Au
del self.C3
del self.PT
def test1(self):
assert_true(self.C == Atom['C'])
assert_true(self.Au == Atom['Au'])
assert_true(self.Au != self.C)
assert_false(self.Au == self.C)
assert_true(self.Au == self.Au.copy())
def test2(self):
C = Atom('C', R=20)
assert_false(self.C == C)
Au = Atom('Au', R=20)
assert_false(self.C == Au)
C = Atom['C']
assert_false(self.Au == C)
Au = Atom['Au']
assert_false(self.C == Au)
def test3(self):
assert_true(self.C.symbol == 'C')
assert_true(self.Au.symbol == 'Au')
def test4(self):
assert_true(self.C.mass > 0)
assert_true(self.Au.mass > 0)
def test5(self):
assert_true(Atom(Z=1, mass=12).mass == 12)
assert_true(Atom(Z=31, mass=12).mass == 12)
assert_true(Atom(Z=31, mass=12).Z == 31)
def test6(self):
assert_true(Atom(Z=1, orbs=3).orbs == 3)
assert_true(len(Atom(Z=1, orbs=3)) == 3)
assert_true(Atom(Z=1, R=1.4).R == 1.4)
assert_true(Atom(Z=1, R=1.4).dR == 1.4)
assert_true(Atom(Z=1, R=[1.4, 1.8]).orbs == 2)
def test7(self):
assert_true(Atom(Z=1, orbs=3).radius() > 0.)
assert_true(len(str(Atom(Z=1, orbs=3))))
def test8(self):
a = self.PT.Z([1, 2])
assert_true(len(a) == 2)
assert_true(a[0] == 1)
assert_true(a[1] == 2)
def test9(self):
a = self.PT.Z_label(['H', 2])
assert_true(len(a) == 2)
assert_true(a[0] == 'H')
assert_true(a[1] == 'He')
a = self.PT.Z_label(1)
assert_true(a == 'H')
def test_pickle(self):
import pickle as p
sC = p.dumps(self.C)
sC3 = p.dumps(self.C3)
sAu = p.dumps(self.Au)
C = p.loads(sC)
C3 = p.loads(sC3)
Au = p.loads(sAu)
assert_false(Au == C)
assert_true(Au != C)
assert_true(C == self.C)
assert_true(C3 == self.C3)
assert_false(C == self.Au)
assert_true(Au == self.Au)
assert_true(Au != self.C)
def _r_geometry_multiple(self, steps, ret_data=False, squeeze=False):
asteps = steps
steps = dict((step, i) for i, step in enumerate(steps))
# initialize all things
cell = [None] * len(steps)
cell_set = [False] * len(steps)
xyz_set = [False] * len(steps)
atom = [None for _ in steps]
xyz = [None for _ in steps]
data = [None for _ in steps]
data_set = [not ret_data for _ in steps]
line = " "
all_loaded = False
pt = PeriodicTable()
while line != '' and not all_loaded:
line = self.readline()
if line.isspace():
continue
kw = line.split()[0]
if kw not in ("CONVVEC", "PRIMVEC", "PRIMCOORD"):
continue
step = _get_kw_index(line)
if step != -1 and step not in steps:
continue
if step not in steps and step == -1:
step = idstep = istep = None
else:
idstep = steps[step]
istep = idstep
if kw == "CONVVEC":
if step is None:
if not any(cell_set):
cell_set = [True] * len(cell_set)
else:
continue
elif cell_set[istep]:
continue
else:
cell_set[istep] = True
icell = _a.zerosd([3, 3])
for i in range(3):
line = self.readline()
icell[i] = line.split()
if step is None:
cell = [icell] * len(cell)
else:
cell[istep] = icell
elif kw == "PRIMVEC":
if step is None:
cell_set = [True] * len(cell_set)
else:
cell_set[istep] = True
icell = _a.zerosd([3, 3])
for i in range(3):
line = self.readline()
icell[i] = line.split()
if step is None:
cell = [icell] * len(cell)
else:
cell[istep] = icell
elif kw == "PRIMCOORD":
if step is None:
raise ValueError(f"{self.__class__.__name__}"
" contains an unindexed (or somehow malformed) 'PRIMCOORD'"
" section but you've asked for a particular index. This"
f" shouldn't happen. line:\n {line}"
)
iatom = []
ixyz = []
idata = []
line = self.readline().split()
for _ in range(int(line[0])):
line = self.readline().split()
if not xyz_set[istep]:
iatom.append(pt.Z(line[0]))
ixyz.append([float(x) for x in line[1:4]])
if ret_data and len(line) > 4:
idata.append([float(x) for x in line[4:]])
if not xyz_set[istep]:
atom[istep] = iatom
xyz[istep] = ixyz
xyz_set[istep] = True
data[idstep] = idata
data_set[idstep] = True
all_loaded = all(xyz_set) and all(cell_set) and all(data_set)
if not all(xyz_set):
which = [asteps[i] for i in np.flatnonzero(xyz_set)]
raise ValueError(f"{self.__class__.__name__} file did not contain atom coordinates for the following requested index: {which}")
if ret_data:
data = _a.arrayd(data)
if data.size == 0:
data.shape = (len(steps), len(xyz[0]), 0)
xyz = _a.arrayd(xyz)
cell = _a.arrayd(cell)
atom = _a.arrayi(atom)
geoms = []
for istep in range(len(steps)):
if len(atom) == 0:
geoms.append(Geometry(xyz[istep], sc=SuperCell(cell[istep])))
elif len(atom[0]) == 1 and atom[0][0] == -999:
# should we perhaps do AtomUnknown?
geoms.append(None)
else:
geoms.append(Geometry(xyz[istep], atoms=atom[istep], sc=SuperCell(cell[istep])))
if squeeze and len(steps) == 1:
geoms = geoms[0]
if ret_data:
data = data[0]
if ret_data:
return geoms, data
return geoms
