def test_spin2(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)],
Atom(6, R=1.01),
sc=SuperCell(100, nsc=[3, 3, 1]))
H = Hamiltonian(g, dtype=np.int32, spin=Spin.POLARIZED)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H[0, j] = (i, i * 2)
H2 = Hamiltonian(g, 2, dtype=np.int32)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
H2 = Hamiltonian(g, Spin(Spin.POLARIZED), dtype=np.int32)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
H2 = Hamiltonian(g, Spin('polarized'), dtype=np.int32)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
def test_non_colinear_non_orthogonal(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g,
dtype=np.float64,
orthogonal=False,
spin=Spin.NONCOLINEAR)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
H.S[i, i] = 1.
eig1 = H.eigh()
# Check TimeSelector
for i in range(4):
assert np.allclose(H.eigh(), eig1)
assert len(eig1) == len(H)
H1 = Hamiltonian(g,
dtype=np.float64,
orthogonal=False,
spin=Spin('non-collinear'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
H1.S[i, i] = 1.
assert H1.spsame(H)
eig1 = H1.eigh()
# Check TimeSelector
for i in range(4):
assert np.allclose(H1.eigh(), eig1)
assert np.allclose(H.eigh(), H1.eigh())
es = H1.eigenstate()
assert np.allclose(es.eig, eig1)
es.spin_moment()
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_repeat2(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g.repeat(2, 0).repeat(2, 1).repeat(2, 2))
Hg.construct([R, param])
Hg.finalize()
H = Hamiltonian(self.g)
H.construct([R, param])
H = H.repeat(2, 0).repeat(2, 1).repeat(2, 2, eta=True)
assert_true(Hg.spsame(H))
def test_tile2(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g.tile(2, 0))
Hg.construct([R, param])
Hg.finalize()
H = Hamiltonian(self.g)
H.construct([R, param])
H = H.tile(2, 0)
assert_true(Hg.spsame(H))
def test_spin1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.int32, spin=Spin.POLARIZED)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = (i, i * 2)
H2 = Hamiltonian(g, 2, dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
def test_so1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.float64, spin=Spin.SPINORBIT)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
H[i, i, 4] = 0.1
H[i, i, 5] = 0.1
H[i, i, 6] = 0.1
H[i, i, 7] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
eig1 = H.eigh()
# Check TimeSelector
for i in range(2):
assert np.allclose(H.eigh(), eig1)
assert len(H.eigh()) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('spin-orbit'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
assert H1.spsame(H)
eig1 = H1.eigh()
# Check TimeSelector
for i in range(2):
assert np.allclose(H1.eigh(), eig1)
assert np.allclose(H.eigh(), H1.eigh())
es = H.eigenstate()
assert np.allclose(es.eig, eig1)
es.spin_moment()
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_so1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=SuperCell(100, nsc=[3, 3, 1]))
H = Hamiltonian(g, dtype=np.float64, spin=Spin.SPINORBIT)
for i in range(10):
j = range(i*2, i*2+3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
H[i, i, 4] = 0.1
H[i, i, 5] = 0.1
H[i, i, 6] = 0.1
H[i, i, 7] = 0.1
if i > 0:
H[i, i-1, 0] = 1.
H[i, i-1, 1] = 1.
if i < 9:
H[i, i+1, 0] = 1.
H[i, i+1, 1] = 1.
eig1 = H.eigh(dtype=np.complex64)
assert np.allclose(H.eigh(dtype=np.complex128), eig1)
assert len(H.eigh()) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('spin-orbit'))
for i in range(10):
j = range(i*2, i*2+3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i-1, 0] = 1.
H1[i, i-1, 1] = 1.
if i < 9:
H1[i, i+1, 0] = 1.
H1[i, i+1, 1] = 1.
assert H1.spsame(H)
eig1 = H1.eigh(dtype=np.complex64)
assert np.allclose(H1.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(dtype=np.complex64), H1.eigh(dtype=np.complex128))
es = H.eigenstate(dtype=np.complex128)
assert np.allclose(es.eig, eig1)
sm = es.spin_moment()
om = es.spin_orbital_moment()
assert np.allclose(sm, om.sum(1))
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_repeat2(self, setup):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(setup.g.repeat(2, 0).repeat(2, 1).repeat(2, 2))
Hg.construct([R, param])
Hg.finalize()
H = Hamiltonian(setup.g)
H.construct([R, param])
H = H.repeat(2, 0).repeat(2, 1).repeat(2, 2)
assert Hg.spsame(H)
H.finalize()
Hg.finalize()
assert np.allclose(H._csr._D, Hg._csr._D)
def test_non_colinear_non_orthogonal(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=SuperCell(100, nsc=[3, 3, 1]))
H = Hamiltonian(g, dtype=np.float64, orthogonal=False, spin=Spin.NONCOLINEAR)
for i in range(10):
j = range(i*2, i*2+3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
if i > 0:
H[i, i-1, 0] = 1.
H[i, i-1, 1] = 1.
if i < 9:
H[i, i+1, 0] = 1.
H[i, i+1, 1] = 1.
H.S[i, i] = 1.
eig1 = H.eigh(dtype=np.complex64)
assert np.allclose(H.eigh(dtype=np.complex128), eig1)
assert len(eig1) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, orthogonal=False, spin=Spin('non-collinear'))
for i in range(10):
j = range(i*2, i*2+3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i-1, 0] = 1.
H1[i, i-1, 1] = 1.
if i < 9:
H1[i, i+1, 0] = 1.
H1[i, i+1, 1] = 1.
H1.S[i, i] = 1.
assert H1.spsame(H)
eig1 = H1.eigh(dtype=np.complex64)
assert np.allclose(H1.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(dtype=np.complex64), H1.eigh(dtype=np.complex128))
es = H1.eigenstate(dtype=np.complex128)
assert np.allclose(es.eig, eig1)
sm = es.spin_moment()
om = es.spin_orbital_moment()
assert np.allclose(sm, om.sum(1))
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_op4(self, setup):
g = Geometry([[i, 0, 0] for i in range(100)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.int32)
# Create initial stuff
for i in range(10):
j = range(i*4, i*4+3)
H[0, j] = i
h = 1 + H
assert h.dtype == np.int32
h = 1. + H
assert h.dtype == np.float64
h = 1.j + H
assert h.dtype == np.complex128
h = 1 - H
assert h.dtype == np.int32
h = 1. - H
assert h.dtype == np.float64
h = 1.j - H
assert h.dtype == np.complex128
h = 1 * H
assert h.dtype == np.int32
h = 1. * H
assert h.dtype == np.float64
h = 1.j * H
assert h.dtype == np.complex128
h = 1 ** H
assert h.dtype == np.int32
h = 1. ** H
assert h.dtype == np.float64
h = 1.j ** H
assert h.dtype == np.complex128
def test_wrap_kwargs(arg):
from sisl import geom, Hamiltonian
g = geom.graphene()
H = Hamiltonian(g)
H.construct([[0.1, 1.44], [0, -2.7]])
bz = MonkhorstPack(H, [2, 2, 2], trs=False)
assert len(bz) == 2 ** 3
def wrap_none(arg):
return arg
def wrap_kwargs(arg, parent, k, weight):
return arg * weight
E = np.linspace(-2, 2, 100)
asarray1 = (bz.asarray().DOS(E, wrap=wrap_none) * bz.weight.reshape(-1, 1)).sum(0)
asarray2 = bz.asarray().DOS(E, wrap=wrap_kwargs).sum(0)
aslist1 = (np.array(bz.aslist().DOS(E, wrap=wrap_none)) * bz.weight.reshape(-1, 1)).sum(0)
aslist2 = np.array(bz.aslist().DOS(E, wrap=wrap_kwargs)).sum(0)
asyield1 = (np.array([a for a in bz.asyield().DOS(E, wrap=wrap_none)]) * bz.weight.reshape(-1, 1)).sum(0)
asyield2 = np.array([a for a in bz.asyield().DOS(E, wrap=wrap_kwargs)]).sum(0)
asaverage = bz.asaverage().DOS(E, wrap=wrap_none)
assum = bz.assum().DOS(E, wrap=wrap_kwargs)
assert np.allclose(asarray1, asaverage)
assert np.allclose(asarray2, asaverage)
assert np.allclose(aslist1, asaverage)
assert np.allclose(aslist2, asaverage)
assert np.allclose(asyield1, asaverage)
assert np.allclose(asyield2, asaverage)
assert np.allclose(assum, asaverage)
def test_pathos(self):
try:
import pathos
except ImportError:
pytest.skip("pathos not available")
from sisl import geom, Hamiltonian
g = geom.graphene()
H = Hamiltonian(g)
H.construct([[0.1, 1.44], [0, -2.7]])
bz = MonkhorstPack(H, [2, 2, 2], trs=False)
# We need to ensure that all functions does the same
apply = bz.apply
papply = bz.papply
for method in ["iter", "average", "sum", "array", "list", "oplist"]:
# TODO One should be careful with zip
# zip will stop when it hits the final element in the first
# list.
# So if a generator has some clean-up code one has to use zip_longest
# regardless of method
for v1, v2 in zip(papply[method].eigh(), apply[method].eigh()):
assert np.allclose(v1, v2)
def test_sub1(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
H = Hamiltonian(self.g)
H.construct([R, param])
H.finalize()
# Tiling in this direction will not introduce
# any new connections.
# So tiling and removing is a no-op (but
# increases vacuum in 3rd lattice vector)
Hg = Hamiltonian(self.g.tile(2, 2))
Hg.construct([R, param])
Hg = Hg.sub(range(len(self.g)))
Hg.finalize()
assert_true(Hg.spsame(H))
def test_real_space_SE_fail_nsc_semi():
sq = Geometry([0] * 3, Atom(1, 1.01), [1])
sq.set_nsc([3, 5, 3])
H = Hamiltonian(sq)
H.construct([(0.1, 1.1), (4, -1)])
RSE = RealSpaceSE(H, 1, 0, (3, 4, 1), dk=100)
def test_read_write_hamiltonian(self):
G = self.g.rotatec(-30)
H = Hamiltonian(G)
H.construct([[0.1, 1.45], [0.1, -2.7]])
print(H)
f = mkstemp(dir=self.d)[1]
read_hamiltonian = get_siles(['read_hamiltonian'])
for sile in get_siles(['write_hamiltonian']):
if not sile in read_hamiltonian:
continue
# Write
sile(f, mode='w').write_hamiltonian(H)
# Read 1
try:
h = sile(f, mode='r').read_hamiltonian()
assert_true(H.spsame(h))
except UnicodeDecodeError as e:
pass
# Read 2
try:
h = Hamiltonian.read(sile(f, mode='r'))
assert_true(H.spsame(h))
except UnicodeDecodeError as e:
pass
# Clean-up file
os.remove(f)
def test_read_write_hamiltonian_overlap(self, sisl_tmp, sisl_system, sile):
if issubclass(sile, _gfSileSiesta):
return
G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :])
H = Hamiltonian(G, orthogonal=False)
H.construct([[0.1, 1.45], [(0.1, 1), (-2.7, 0.1)]])
f = sisl_tmp("test_read_write_hamiltonian_overlap.win", _dir)
# Write
with sile(f, mode='w') as s:
s.write_hamiltonian(H)
# Read 1
try:
with sile(f, mode='r') as s:
h = s.read_hamiltonian()
assert H.spsame(h)
except UnicodeDecodeError as e:
pass
# Read 2
try:
with sile(f, mode='r') as s:
h = Hamiltonian.read(s)
assert H.spsame(h)
except UnicodeDecodeError as e:
pass
def test_real_space_SE_fail_k_semi_same():
sq = Geometry([0] * 3, Atom(1, 1.01), [1])
sq.set_nsc([3] * 3)
H = Hamiltonian(sq)
H.construct([(0.1, 1.1), (4, -1)])
RSE = RealSpaceSE(H, 0, 0, (3, 4, 1))
def sisl_system():
""" A preset list of geometries/Hamiltonians. """
class System:
pass
d = System()
alat = 1.42
sq3h = 3.**.5 * 0.5
C = Atom(Z=6, R=1.42)
sc = SuperCell(np.array([[1.5, sq3h, 0.],
[1.5, -sq3h, 0.],
[0., 0., 10.]], np.float64) * alat,
nsc=[3, 3, 1])
d.g = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * alat,
atom=C, sc=sc)
d.R = np.array([0.1, 1.5])
d.t = np.array([0., 2.7])
d.tS = np.array([(0., 1.0),
(2.7, 0.)])
d.C = Atom(Z=6, R=max(d.R))
d.sc = SuperCell(np.array([[1.5, sq3h, 0.],
[1.5, -sq3h, 0.],
[0., 0., 10.]], np.float64) * alat,
nsc=[3, 3, 1])
d.gtb = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * alat,
atom=C, sc=sc)
d.ham = Hamiltonian(d.gtb)
d.ham.construct([(0.1, 1.5), (0.1, 2.7)])
return d
def test_as_wrap(self):
from sisl import geom, Hamiltonian
g = geom.graphene()
H = Hamiltonian(g)
H.construct([[0.1, 1.44], [0, -2.7]])
bz = MonkhorstPack(H, [2, 2, 2], trs=False)
assert len(bz) == 2**3
# Check with a wrap function
def wrap(arg):
return arg[::-1]
# Assert that as* all does the same
asarray = bz.apply.array.eigh(wrap=wrap)
aslist = np.array(bz.apply.list.eigh(wrap=wrap))
asyield = np.array([a for a in bz.apply.iter.eigh(wrap=wrap)])
asaverage = bz.apply.average.eigh(wrap=wrap)
assert np.allclose(asarray, aslist)
assert np.allclose(asarray, asyield)
assert np.allclose((asarray / len(bz)).sum(0), asaverage)
# Now we should check whether the reverse is doing its magic!
mylist = [wrap(H.eigh(k=k)) for k in bz]
assert np.allclose(aslist, mylist)
def test_wrap_unzip(self):
from sisl import geom, Hamiltonian
g = geom.graphene()
H = Hamiltonian(g)
H.construct([[0.1, 1.44], [0, -2.7]])
bz = MonkhorstPack(H, [2, 2, 2], trs=False)
# Check with a wrap function
E = np.linspace(-2, 2, 20)
def wrap(es):
return es.eig, es.DOS(E)
eig0, DOS0 = zip(*bz.apply.list.eigenstate(wrap=wrap))
with bz.apply.renew(unzip=True) as k_unzip:
eig1, DOS1 = k_unzip.list.eigenstate(wrap=wrap)
eig2, DOS2 = k_unzip.array.eigenstate(wrap=wrap)
#eig0 and DOS0 are generators, and not list's
#eig1 and DOS1 are generators, and not list's
assert isinstance(eig2, np.ndarray)
assert isinstance(DOS2, np.ndarray)
assert np.allclose(eig0, eig1)
assert np.allclose(DOS0, DOS1)
assert np.allclose(eig0, eig2)
assert np.allclose(DOS0, DOS2)
def test_shift2(self, setup):
R, param = [0.1, 1.5], [(1., 1.), (0.1, 0.1)]
H = Hamiltonian(setup.g.copy(), orthogonal=False)
H.construct([R, param])
eig0 = H.eigh()[0]
H.shift(0.2)
assert H.eigh()[0] == pytest.approx(eig0 + 0.2)
def test_repeat4(self, setup):
def func(self, ia, idxs, idxs_xyz=None):
idx = self.geom.close(ia, R=[0.1, 1.43], idx=idxs)
io = self.geom.a2o(ia)
# Set on-site on first and second orbital
odx = self.geom.a2o(idx[0])
self[io, odx] = -1.
self[io + 1, odx + 1] = 1.
# Set connecting
odx = self.geom.a2o(idx[1])
self[io, odx] = 0.2
self[io, odx + 1] = 0.01
self[io + 1, odx] = 0.01
self[io + 1, odx + 1] = 0.3
setup.H2.construct(func)
Hbig = setup.H2.repeat(3, 0).repeat(3, 1)
gbig = setup.H2.geom.repeat(3, 0).repeat(3, 1)
H = Hamiltonian(gbig)
H.construct(func)
assert H.spsame(Hbig)
H.finalize()
Hbig.finalize()
assert np.allclose(H._csr._D, Hbig._csr._D)
setup.H2.empty()
def test_shift1(self, setup):
R, param = [0.1, 1.5], [1., 0.1]
H = Hamiltonian(setup.g.copy())
H.construct([R, param])
eig0 = H.eigh()[0]
H.shift(0.2)
assert H.eigh()[0] == pytest.approx(eig0 + 0.2)
def get_H(orthogonal=True, *args):
gr = geom.graphene(orthogonal=orthogonal)
H = Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
for axis, rep in zip(args[::2], args[1::2]):
H = H.tile(rep, axis)
return H
def __init__(self):
bond = 1.42
sq3h = 3.**.5 * 0.5
self.sc = SuperCell(np.array([[1.5, sq3h, 0.],
[1.5, -sq3h, 0.],
[0., 0., 10.]], np.float64) * bond, nsc=[3, 3, 1])
C = Atom(Z=6, R=[bond * 1.01])
self.g = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * bond,
atom=C, sc=self.sc)
self.H = Hamiltonian(self.g)
func = self.H.create_construct([0.1, bond+0.1], [0., -2.7])
self.H.construct(func)
self.HS = Hamiltonian(self.g, orthogonal=False)
func = self.HS.create_construct([0.1, bond+0.1], [(0., 1.), (-2.7, 0.)])
self.HS.construct(func)
def test_cut1(self):
# Test of eigenvalues using a cut
# Hamiltonian
dR, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g)
Hg.construct([dR, param])
g = self.g.tile(2, 0).tile(2, 1)
H = Hamiltonian(g)
H.construct([dR, param])
# Create cut Hamiltonian
Hc = H.cut(2, 1).cut(2, 0)
eigc = Hc.eigh()
eigg = Hg.eigh()
assert_true(np.allclose(Hg.eigh(), Hc.eigh()))
del Hc, H
def test_berry_phase_fail_loop(self, setup):
g = setup.g.tile(2, 0).tile(2, 1).tile(2, 2)
H = Hamiltonian(g)
bz = BandStructure.param_circle(H,
20,
0.01, [0, 0, 1], [1 / 3] * 3,
loop=True)
elec.berry_phase(bz)
def test_fermi_level(self, setup):
R, param = [0.1, 1.5], [(1., 1.), (2.1, 0.1)]
H = Hamiltonian(setup.g.copy(), orthogonal=False)
H.construct([R, param])
bz = MonkhorstPack(H, [10, 10, 1])
Ef = H.fermi_level(bz, q=1)
H.shift(-Ef)
assert H.fermi_level(bz, q=1) == pytest.approx(0., abs=1e-6)
def test_real_space_SE_fail_nsc_semi_fully_periodic():
sq = Geometry([0] * 3, Atom(1, 1.01), [1])
sq.set_nsc([3, 5, 3])
H = Hamiltonian(sq)
H.construct([(0.1, 1.1), (4, -1)])
with pytest.raises(ValueError):
RSE = RealSpaceSE(H, 1, 0, (3, 4, 1), dk=100)
def test_pathos(self):
pytest.skip(
"BrillouinZone.apply(pool=True|int) scales extremely bad and may cause stall"
)
pytest.importorskip("pathos", reason="pathos not available")
from sisl import geom, Hamiltonian
g = geom.graphene()
H = Hamiltonian(g)
H.construct([[0.1, 1.44], [0, -2.7]])
bz = MonkhorstPack(H, [2, 2, 2], trs=False)
# try and determine a sensible
import os
try:
import psutil
nprocs = len(psutil.Process().cpu_affinity()) // 2
except Exception:
nprocs = os.cpu_count() // 2
omp_num_threads = os.environ.get("OMP_NUM_THREADS")
# Check that the ObjectDispatcher works
apply = bz.apply
papply = bz.apply.renew(pool=nprocs)
assert str(apply) != str(papply)
for method in ["iter", "average", "sum", "array", "list", "oplist"]:
# TODO One should be careful with zip
# zip will stop when it hits the final element in the first
# list.
# So if a generator has some clean-up code one has to use zip_longest
# regardless of method
os.environ["OMP_NUM_THREADS"] = "1"
V1 = papply[method].eigh()
if omp_num_threads is None:
del os.environ["OMP_NUM_THREADS"]
else:
os.environ["OMP_NUM_THREADS"] = omp_num_threads
V2 = apply[method].eigh()
for v1, v2 in zip(V1, V2):
assert np.allclose(v1, v2)
# Check that the MethodDispatcher works
apply = bz.apply.eigh
papply = bz.apply.renew(pool=True).eigh
assert str(apply) != str(papply)
for method in ["iter", "average", "sum", "array", "list", "oplist"]:
# TODO One should be careful with zip
# zip will stop when it hits the final element in the first
# list.
# So if a generator has some clean-up code one has to use zip_longest
# regardless of method
for v1, v2 in zip(papply[method](), apply[method]()):
assert np.allclose(v1, v2)
