class TestGeometry(object):
def test_objects(self, setup):
str(setup.g)
assert len(setup.g) == 2
assert len(setup.g.xyz) == 2
assert np.allclose(setup.g[0], np.zeros([3]))
assert np.allclose(setup.g[None, 0], setup.g.xyz[:, 0])
i = 0
for ia in setup.g:
i += 1
assert i == len(setup.g)
assert setup.g.no_s == 2 * len(setup.g) * np.prod(setup.g.sc.nsc)
def test_properties(self, setup):
assert 2 == len(setup.g)
assert 2 == setup.g.na
assert 3 * 3 == setup.g.n_s
assert 2 * 3 * 3 == setup.g.na_s
assert 2 * 2 == setup.g.no
assert 2 * 2 * 3 * 3 == setup.g.no_s
def test_iter1(self, setup):
i = 0
for ia in setup.g:
i += 1
assert i == 2
def test_iter2(self, setup):
for ia in setup.g:
assert np.allclose(setup.g[ia], setup.g.xyz[ia, :])
def test_iter3(self, setup):
i = 0
for ia, io in setup.g.iter_orbitals(0):
assert ia == 0
assert io < 2
i += 1
for ia, io in setup.g.iter_orbitals(1):
assert ia == 1
assert io < 2
i += 1
assert i == 4
i = 0
for ia, io in setup.g.iter_orbitals():
assert ia in [0, 1]
assert io < 2
i += 1
assert i == 4
i = 0
for ia, io in setup.g.iter_orbitals(1, local=False):
assert ia == 1
assert io >= 2
i += 1
assert i == 2
@pytest.mark.xfail(raises=ValueError)
def test_tile0(self, setup):
t = setup.g.tile(0, 0)
def test_tile1(self, setup):
cell = np.copy(setup.g.sc.cell)
cell[0, :] *= 2
t = setup.g.tile(2, 0)
assert np.allclose(cell, t.sc.cell)
cell[1, :] *= 2
t = t.tile(2, 1)
assert np.allclose(cell, t.sc.cell)
cell[2, :] *= 2
t = t.tile(2, 2)
assert np.allclose(cell, t.sc.cell)
def test_tile2(self, setup):
cell = np.copy(setup.g.sc.cell)
cell[:, :] *= 2
t = setup.g.tile(2, 0).tile(2, 1).tile(2, 2)
assert np.allclose(cell, t.sc.cell)
def test_sort(self, setup):
t = setup.g.tile(2, 0).tile(2, 1).tile(2, 2)
ts = t.sort()
t = setup.g.tile(2, 1).tile(2, 2).tile(2, 0)
tS = t.sort()
assert np.allclose(ts.xyz, tS.xyz)
def test_tile3(self, setup):
cell = np.copy(setup.g.sc.cell)
cell[:, :] *= 2
t1 = setup.g * 2
cell = np.copy(setup.g.sc.cell)
cell[0, :] *= 2
t1 = setup.g * (2, 0)
assert np.allclose(cell, t1.sc.cell)
t = setup.g * ((2, 0), 'tile')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
cell[1, :] *= 2
t1 = t * (2, 1)
assert np.allclose(cell, t1.sc.cell)
t = t * ((2, 1), 'tile')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
cell[2, :] *= 2
t1 = t * (2, 2)
assert np.allclose(cell, t1.sc.cell)
t = t * ((2, 2), 'tile')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
# Full
t = setup.g * [2, 2, 2]
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
t = setup.g * ([2, 2, 2], 't')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
def test_tile4(self, setup):
t1 = setup.g.tile(2, 0).tile(2, 2)
t = setup.g * ([2, 0], 't') * [2, 2]
assert np.allclose(t1.xyz, t.xyz)
def test_tile5(self, setup):
t = setup.g.tile(2, 0).tile(2, 2)
assert np.allclose(t[:len(setup.g), :], setup.g.xyz)
@pytest.mark.xfail(raises=ValueError)
def test_repeat0(self, setup):
t = setup.g.repeat(0, 0)
def test_repeat1(self, setup):
cell = np.copy(setup.g.sc.cell)
cell[0, :] *= 2
t = setup.g.repeat(2, 0)
assert np.allclose(cell, t.sc.cell)
cell[1, :] *= 2
t = t.repeat(2, 1)
assert np.allclose(cell, t.sc.cell)
cell[2, :] *= 2
t = t.repeat(2, 2)
assert np.allclose(cell, t.sc.cell)
def test_repeat2(self, setup):
cell = np.copy(setup.g.sc.cell)
cell[:, :] *= 2
t = setup.g.repeat(2, 0).repeat(2, 1).repeat(2, 2)
assert np.allclose(cell, t.sc.cell)
def test_repeat3(self, setup):
cell = np.copy(setup.g.sc.cell)
cell[0, :] *= 2
t1 = setup.g.repeat(2, 0)
assert np.allclose(cell, t1.sc.cell)
t = setup.g * ((2, 0), 'repeat')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
cell[1, :] *= 2
t1 = t.repeat(2, 1)
assert np.allclose(cell, t1.sc.cell)
t = t * ((2, 1), 'r')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
cell[2, :] *= 2
t1 = t.repeat(2, 2)
assert np.allclose(cell, t1.sc.cell)
t = t * ((2, 2), 'repeat')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
# Full
t = setup.g * ([2, 2, 2], 'r')
assert np.allclose(cell, t.sc.cell)
assert np.allclose(t1.xyz, t.xyz)
def test_repeat4(self, setup):
t1 = setup.g.repeat(2, 0).repeat(2, 2)
t = setup.g * ([2, 0], 'repeat') * ([2, 2], 'r')
assert np.allclose(t1.xyz, t.xyz)
def test_repeat5(self, setup):
t = setup.g.repeat(2, 0).repeat(2, 2)
assert np.allclose(t.xyz[::4, :], setup.g.xyz)
def test_a2o1(self, setup):
assert 0 == setup.g.a2o(0)
assert setup.g.atom[0].no == setup.g.a2o(1)
assert setup.g.no == setup.g.a2o(setup.g.na)
def test_sub1(self, setup):
assert len(setup.g.sub([0])) == 1
assert len(setup.g.sub([0, 1])) == 2
assert len(setup.g.sub([-1])) == 1
def test_sub2(self, setup):
assert len(setup.g.sub(range(1))) == 1
assert len(setup.g.sub(range(2))) == 2
def test_fxyz(self, setup):
fxyz = setup.g.fxyz
assert np.allclose(fxyz, [[0, 0, 0], [1. / 3, 1. / 3, 0]])
assert np.allclose(np.dot(fxyz, setup.g.cell), setup.g.xyz)
def test_axyz(self, setup):
assert np.allclose(setup.g[:], setup.g.xyz[:])
assert np.allclose(setup.g[0], setup.g.xyz[0, :])
assert np.allclose(setup.g[2], setup.g.axyz(2))
isc = setup.g.a2isc(2)
off = setup.g.sc.offset(isc)
assert np.allclose(setup.g.xyz[0] + off, setup.g.axyz(2))
def test_rij1(self, setup):
assert np.allclose(setup.g.rij(0, 1), 1.42)
assert np.allclose(setup.g.rij(0, [0, 1]), [0., 1.42])
def test_orij1(self, setup):
assert np.allclose(setup.g.orij(0, 2), 1.42)
assert np.allclose(setup.g.orij(0, [0, 2]), [0., 1.42])
def test_Rij1(self, setup):
assert np.allclose(setup.g.Rij(0, 1), [1.42, 0, 0])
def test_oRij1(self, setup):
assert np.allclose(setup.g.oRij(0, 1), [0., 0, 0])
assert np.allclose(setup.g.oRij(0, 2), [1.42, 0, 0])
assert np.allclose(setup.g.oRij(0, [0, 1, 2]),
[[0., 0, 0], [0., 0, 0], [1.42, 0, 0]])
assert np.allclose(setup.g.oRij(0, 2), [1.42, 0, 0])
def test_cut(self, setup):
with pytest.warns(SislWarning) as warns:
assert len(setup.g.cut(1, 1)) == 2
assert len(setup.g.cut(2, 1)) == 1
assert len(setup.g.cut(2, 1, 1)) == 1
assert len(warns) == 2
def test_cut2(self, setup):
with pytest.warns(SislWarning) as warns:
c1 = setup.g.cut(2, 1)
c2 = setup.g.cut(2, 1, 1)
assert len(warns) == 2
assert np.allclose(c1.xyz[0, :], setup.g.xyz[0, :])
assert np.allclose(c2.xyz[0, :], setup.g.xyz[1, :])
def test_cut3(self, setup):
nr = range(2, 5)
g = setup.g.copy()
for x in nr:
gx = g.tile(x, 0)
for y in nr:
gy = gx.tile(y, 1)
for z in nr:
gz = gy.tile(z, 2)
G = gz.cut(z, 2)
assert np.allclose(G.xyz, gy.xyz)
assert np.allclose(G.cell, gy.cell)
G = gy.cut(y, 1)
assert np.allclose(G.xyz, gx.xyz)
assert np.allclose(G.cell, gx.cell)
G = gx.cut(x, 0)
assert np.allclose(G.xyz, g.xyz)
assert np.allclose(G.cell, g.cell)
def test_remove1(self, setup):
assert len(setup.g.remove([0])) == 1
assert len(setup.g.remove([])) == 2
assert len(setup.g.remove([-1])) == 1
assert len(setup.g.remove([-0])) == 1
def test_remove2(self, setup):
assert len(setup.g.remove(range(1))) == 1
assert len(setup.g.remove(range(0))) == 2
def test_copy(self, setup):
assert setup.g == setup.g.copy()
def test_nsc1(self, setup):
sc = setup.g.sc.copy()
nsc = np.copy(sc.nsc)
sc.set_nsc([5, 5, 0])
assert np.allclose([5, 5, 1], sc.nsc)
assert len(sc.sc_off) == np.prod(sc.nsc)
def test_nsc2(self, setup):
sc = setup.g.sc.copy()
nsc = np.copy(sc.nsc)
sc.set_nsc([0, 1, 0])
assert np.allclose([1, 1, 1], sc.nsc)
assert len(sc.sc_off) == np.prod(sc.nsc)
def test_rotation1(self, setup):
rot = setup.g.rotate(180, [0, 0, 1])
rot.sc.cell[2, 2] *= -1
assert np.allclose(-rot.sc.cell, setup.g.sc.cell)
assert np.allclose(-rot.xyz, setup.g.xyz)
rot = setup.g.rotate(np.pi, [0, 0, 1], rad=True)
rot.sc.cell[2, 2] *= -1
assert np.allclose(-rot.sc.cell, setup.g.sc.cell)
assert np.allclose(-rot.xyz, setup.g.xyz)
rot = rot.rotate(180, [0, 0, 1])
rot.sc.cell[2, 2] *= -1
assert np.allclose(rot.sc.cell, setup.g.sc.cell)
assert np.allclose(rot.xyz, setup.g.xyz)
def test_rotation2(self, setup):
rot = setup.g.rotate(180, [0, 0, 1], only='abc')
rot.sc.cell[2, 2] *= -1
assert np.allclose(-rot.sc.cell, setup.g.sc.cell)
assert np.allclose(rot.xyz, setup.g.xyz)
rot = setup.g.rotate(np.pi, [0, 0, 1], rad=True, only='abc')
rot.sc.cell[2, 2] *= -1
assert np.allclose(-rot.sc.cell, setup.g.sc.cell)
assert np.allclose(rot.xyz, setup.g.xyz)
rot = rot.rotate(180, [0, 0, 1], only='abc')
rot.sc.cell[2, 2] *= -1
assert np.allclose(rot.sc.cell, setup.g.sc.cell)
assert np.allclose(rot.xyz, setup.g.xyz)
def test_rotation3(self, setup):
rot = setup.g.rotate(180, [0, 0, 1], only='xyz')
assert np.allclose(rot.sc.cell, setup.g.sc.cell)
assert np.allclose(-rot.xyz, setup.g.xyz)
rot = setup.g.rotate(np.pi, [0, 0, 1], rad=True, only='xyz')
assert np.allclose(rot.sc.cell, setup.g.sc.cell)
assert np.allclose(-rot.xyz, setup.g.xyz)
rot = rot.rotate(180, [0, 0, 1], only='xyz')
assert np.allclose(rot.sc.cell, setup.g.sc.cell)
assert np.allclose(rot.xyz, setup.g.xyz)
def test_rotation4(self, setup):
rot = setup.g.rotatea(180, only='xyz')
rot = setup.g.rotateb(180, only='xyz')
rot = setup.g.rotatec(180, only='xyz')
def test_rotation5(self, setup):
g = setup.g.copy()
rot = g.rotatea(180, origo=g.center(what='xyz'), only='xyz')
def test_translate(self, setup):
t = setup.g.translate([0, 0, 1])
assert np.allclose(setup.g.xyz[:, 0], t.xyz[:, 0])
assert np.allclose(setup.g.xyz[:, 1], t.xyz[:, 1])
assert np.allclose(setup.g.xyz[:, 2] + 1, t.xyz[:, 2])
t = setup.g.move([0, 0, 1])
assert np.allclose(setup.g.xyz[:, 0], t.xyz[:, 0])
assert np.allclose(setup.g.xyz[:, 1], t.xyz[:, 1])
assert np.allclose(setup.g.xyz[:, 2] + 1, t.xyz[:, 2])
def test_iter_block1(self, setup):
for i, iaaspec in enumerate(setup.g.iter_species()):
ia, a, spec = iaaspec
assert i == ia
assert setup.g.atom[ia] == a
for ia, a, spec in setup.g.iter_species([1]):
assert 1 == ia
assert setup.g.atom[ia] == a
for ia in setup.g:
assert ia >= 0
i = 0
for ias, idx in setup.g.iter_block():
for ia in ias:
i += 1
assert i == len(setup.g)
i = 0
for ias, idx in setup.g.iter_block(atom=1):
for ia in ias:
i += 1
assert i == 1
@pytest.mark.slow
def test_iter_block2(self, setup):
g = setup.g.tile(30, 0).tile(30, 1)
i = 0
for ias, _ in g.iter_block():
i += len(ias)
assert i == len(g)
def test_iter_shape1(self, setup):
i = 0
for ias, _ in setup.g.iter_block(method='sphere'):
i += len(ias)
assert i == len(setup.g)
i = 0
for ias, _ in setup.g.iter_block(method='cube'):
i += len(ias)
assert i == len(setup.g)
@pytest.mark.slow
def test_iter_shape2(self, setup):
g = setup.g.tile(30, 0).tile(30, 1)
i = 0
for ias, _ in g.iter_block(method='sphere'):
i += len(ias)
assert i == len(g)
i = 0
for ias, _ in g.iter_block(method='cube'):
i += len(ias)
assert i == len(g)
i = 0
for ias, _ in g.iter_block_shape(Cube(g.maxR() * 20)):
i += len(ias)
assert i == len(g)
@pytest.mark.slow
def test_iter_shape3(self, setup):
g = setup.g.tile(50, 0).tile(50, 1)
i = 0
for ias, _ in g.iter_block(method='sphere'):
i += len(ias)
assert i == len(g)
i = 0
for ias, _ in g.iter_block(method='cube'):
i += len(ias)
assert i == len(g)
i = 0
for ias, _ in g.iter_block_shape(Sphere(g.maxR() * 20)):
i += len(ias)
assert i == len(g)
def test_swap(self, setup):
s = setup.g.swap(0, 1)
for i in [0, 1, 2]:
assert np.allclose(setup.g.xyz[::-1, i], s.xyz[:, i])
def test_append1(self, setup):
for axis in [0, 1, 2]:
s = setup.g.append(setup.g, axis)
assert len(s) == len(setup.g) * 2
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
s = setup.g.prepend(setup.g, axis)
assert len(s) == len(setup.g) * 2
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
s = setup.g.append(setup.g.sc, axis)
assert len(s) == len(setup.g)
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
s = setup.g.prepend(setup.g.sc, axis)
assert len(s) == len(setup.g)
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
assert np.allclose(s.cell[axis, :], setup.g.cell[axis, :] * 2)
def test_swapaxes(self, setup):
s = setup.g.swapaxes(0, 1)
assert np.allclose(setup.g.xyz[:, 0], s.xyz[:, 1])
assert np.allclose(setup.g.xyz[:, 1], s.xyz[:, 0])
assert np.allclose(setup.g.cell[0, :], s.cell[1, :])
assert np.allclose(setup.g.cell[1, :], s.cell[0, :])
def test_center(self, setup):
one = setup.g.center(atom=[0])
assert np.allclose(setup.g[0], one)
al = setup.g.center()
assert np.allclose(np.mean(setup.g.xyz, axis=0), al)
al = setup.g.center(what='mass')
al = setup.g.center(what='mm(xyz)')
@pytest.mark.xfail(raises=ValueError)
def test_center_raise(self, setup):
al = setup.g.center(what='unknown')
def test___add1__(self, setup):
n = len(setup.g)
double = setup.g + setup.g + setup.g.sc
assert len(double) == n * 2
assert np.allclose(setup.g.cell * 2, double.cell)
assert np.allclose(setup.g.xyz[:n, :], double.xyz[:n, :])
double = (setup.g, 1) + setup.g
d = setup.g.prepend(setup.g, 1)
assert len(double) == n * 2
assert np.allclose(setup.g.cell[::2, :], double.cell[::2, :])
assert np.allclose(double.xyz, d.xyz)
double = setup.g + (setup.g, 1)
d = setup.g.append(setup.g, 1)
assert len(double) == n * 2
assert np.allclose(setup.g.cell[::2, :], double.cell[::2, :])
assert np.allclose(double.xyz, d.xyz)
def test___add2__(self, setup):
g1 = setup.g.rotatec(15)
g2 = setup.g.rotatec(30)
assert g1 != g2
assert g1 + g2 == g1.add(g2)
assert g1 + g2 != g2.add(g1)
assert g2 + g1 == g2.add(g1)
assert g2 + g1 != g1.add(g2)
for i in range(3):
assert g1 + (g2, i) == g1.append(g2, i)
assert (g1, i) + g2 == g2.append(g1, i)
def test___mul__(self, setup):
g = setup.g.copy()
assert g * 2 == g.tile(2, 0).tile(2, 1).tile(2, 2)
assert g * [2, 1] == g.tile(2, 1)
assert g * (2, 2, 2) == g.tile(2, 0).tile(2, 1).tile(2, 2)
assert g * [1, 2, 2] == g.tile(1, 0).tile(2, 1).tile(2, 2)
assert g * [1, 3, 2] == g.tile(1, 0).tile(3, 1).tile(2, 2)
assert g * ([1, 3, 2], 'r') == g.repeat(1, 0).repeat(3, 1).repeat(2, 2)
assert g * ([1, 3, 2], 'repeat') == g.repeat(1,
0).repeat(3,
1).repeat(2, 2)
assert g * ([1, 3, 2], 'tile') == g.tile(1, 0).tile(3, 1).tile(2, 2)
assert g * ([1, 3, 2], 't') == g.tile(1, 0).tile(3, 1).tile(2, 2)
assert g * ([3, 2], 't') == g.tile(3, 2)
assert g * ([3, 2], 'r') == g.repeat(3, 2)
def test_add(self, setup):
double = setup.g.add(setup.g)
assert len(double) == len(setup.g) * 2
assert np.allclose(setup.g.cell, double.cell)
double = setup.g.add(setup.g).add(setup.g.sc)
assert len(double) == len(setup.g) * 2
assert np.allclose(setup.g.cell * 2, double.cell)
def test_insert(self, setup):
double = setup.g.insert(0, setup.g)
assert len(double) == len(setup.g) * 2
assert np.allclose(setup.g.cell, double.cell)
def test_a2o(self, setup):
# There are 2 orbitals per C atom
assert setup.g.a2o(1) == setup.g.atom[0].no
assert np.all(setup.g.a2o(1, True) == [2, 3])
setup.g.reorder()
def test_o2a(self, setup):
# There are 2 orbitals per C atom
assert setup.g.o2a(2) == 1
assert setup.g.o2a(3) == 1
assert setup.g.o2a(4) == 2
assert np.all(setup.g.o2a([0, 2, 4]) == [0, 1, 2])
def test_angle(self, setup):
# There are 2 orbitals per C atom
g = Geometry([[0] * 3, [1, 0, 0]])
g.angle([0])
g.angle([0], ref=1)
def test_2uc(self, setup):
# functions for any-thing to UC
assert setup.g.sc2uc(2) == 0
assert np.all(setup.g.sc2uc([2, 3]) == [0, 1])
assert setup.g.asc2uc(2) == 0
assert np.all(setup.g.asc2uc([2, 3]) == [0, 1])
assert setup.g.osc2uc(4) == 0
assert setup.g.osc2uc(5) == 1
assert np.all(setup.g.osc2uc([4, 5]) == [0, 1])
def test_2sc(self, setup):
# functions for any-thing to SC
c = setup.g.cell
print(setup)
# check indices
assert np.all(setup.g.a2isc([1, 2]) == [[0, 0, 0], [-1, -1, 0]])
assert np.all(setup.g.a2isc(2) == [-1, -1, 0])
assert np.allclose(setup.g.a2sc(2), -c[0, :] - c[1, :])
assert np.all(setup.g.o2isc([1, 5]) == [[0, 0, 0], [-1, -1, 0]])
assert np.all(setup.g.o2isc(5) == [-1, -1, 0])
assert np.allclose(setup.g.o2sc(5), -c[0, :] - c[1, :])
# Check off-sets
assert np.allclose(setup.g.a2sc([1, 2]),
[[0., 0., 0.], -c[0, :] - c[1, :]])
assert np.allclose(setup.g.o2sc([1, 5]),
[[0., 0., 0.], -c[0, :] - c[1, :]])
def test_reverse(self, setup):
rev = setup.g.reverse()
assert len(rev) == 2
assert np.allclose(rev.xyz[::-1, :], setup.g.xyz)
rev = setup.g.reverse(atom=list(range(len(setup.g))))
assert len(rev) == 2
assert np.allclose(rev.xyz[::-1, :], setup.g.xyz)
def test_scale1(self, setup):
two = setup.g.scale(2)
assert len(two) == len(setup.g)
assert np.allclose(two.xyz[:, :] / 2., setup.g.xyz)
def test_close1(self, setup):
three = range(3)
for ia in setup.mol:
i = setup.mol.close(ia, R=(0.1, 1.1), idx=three)
if ia < 3:
assert len(i[0]) == 1
else:
assert len(i[0]) == 0
# Will only return results from [0,1,2]
# but the fourth atom connects to
# the third
if ia in [0, 2, 3]:
assert len(i[1]) == 1
elif ia == 1:
assert len(i[1]) == 2
else:
assert len(i[1]) == 0
def test_close2(self, setup):
mol = range(3, 5)
for ia in setup.mol:
i = setup.mol.close(ia, R=(0.1, 1.1), idx=mol)
assert len(i) == 2
i = setup.mol.close([100, 100, 100], R=0.1)
assert len(i) == 0
i = setup.mol.close([100, 100, 100], R=0.1, ret_rij=True)
for el in i:
assert len(el) == 0
i = setup.mol.close([100, 100, 100], R=0.1, ret_rij=True, ret_xyz=True)
for el in i:
assert len(el) == 0
@pytest.mark.slow
def test_close4(self, setup):
# 2 * 200 ** 2
g = setup.g * (200, 200, 1)
i = g.close(0, R=(0.1, 1.43))
print(i)
assert len(i) == 2
assert len(i[0]) == 1
assert len(i[1]) == 3
def test_close_within1(self, setup):
three = range(3)
for ia in setup.mol:
shapes = [Sphere(0.1, setup.mol[ia]), Sphere(1.1, setup.mol[ia])]
i = setup.mol.close(ia, R=(0.1, 1.1), idx=three)
ii = setup.mol.within(shapes, idx=three)
assert np.all(i[0] == ii[0])
assert np.all(i[1] == ii[1])
def test_close_within2(self, setup):
g = setup.g.repeat(6, 0).repeat(6, 1)
for ia in g:
shapes = [Sphere(0.1, g[ia]), Sphere(1.5, g[ia])]
i = g.close(ia, R=(0.1, 1.5))
ii = g.within(shapes)
assert np.all(i[0] == ii[0])
assert np.all(i[1] == ii[1])
def test_close_within3(self, setup):
g = setup.g.repeat(6, 0).repeat(6, 1)
args = {'ret_xyz': True, 'ret_rij': True}
for ia in g:
shapes = [Sphere(0.1, g[ia]), Sphere(1.5, g[ia])]
i, xa, d = g.close(ia, R=(0.1, 1.5), **args)
ii, xai, di = g.within(shapes, **args)
for j in [0, 1]:
assert np.all(i[j] == ii[j])
assert np.allclose(xa[j], xai[j])
assert np.allclose(d[j], di[j])
def test_within_inf1(self, setup):
g = setup.g.translate([0.05] * 3)
sc_3x3 = g.sc.tile(3, 0).tile(3, 1)
assert len(g.within_inf(sc_3x3)[0]) == len(g) * 3**2
def test_within_inf2(self, setup):
g = setup.mol.translate([0.05] * 3)
sc = SuperCell(1.5)
for o in range(10):
origo = [o - 0.5, -0.5, -0.5]
sc.origo = origo
idx = g.within_inf(sc)[0]
assert len(idx) == 1
assert idx[0] == o
def test_within_inf_duplicates(self, setup):
g = setup.g.copy()
sc_3x3 = g.sc.tile(3, 0).tile(3, 1)
assert len(
g.within_inf(sc_3x3)[0]
) == len(g) * 3**2 + 7 # 3 per vector and 1 in the upper right corner
def test_close_sizes(self, setup):
point = 0
# Return index
idx = setup.mol.close(point, R=.1)
assert len(idx) == 1
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1))
assert len(idx) == 2
assert len(idx[0]) == 1
assert not isinstance(idx[0], list)
# Longer
idx = setup.mol.close(point, R=(.1, 1.1, 2.1))
assert len(idx) == 3
assert len(idx[0]) == 1
# Return index
idx = setup.mol.close(point, R=.1, ret_xyz=True)
assert len(idx) == 2
assert len(idx[0]) == 1
assert len(idx[1]) == 1
assert idx[1].shape[0] == 1 # equivalent to above
assert idx[1].shape[1] == 3
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1), ret_xyz=True)
# [[idx-1, idx-2], [coord-1, coord-2]]
assert len(idx) == 2
assert len(idx[0]) == 2
assert len(idx[1]) == 2
# idx-1
assert len(idx[0][0].shape) == 1
assert idx[0][0].shape[0] == 1
# idx-2
assert idx[0][1].shape[0] == 1
# coord-1
assert len(idx[1][0].shape) == 2
assert idx[1][0].shape[1] == 3
# coord-2
assert idx[1][1].shape[1] == 3
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1), ret_xyz=True, ret_rij=True)
# [[idx-1, idx-2], [coord-1, coord-2], [dist-1, dist-2]]
assert len(idx) == 3
assert len(idx[0]) == 2
assert len(idx[1]) == 2
# idx-1
assert len(idx[0][0].shape) == 1
assert idx[0][0].shape[0] == 1
# idx-2
assert idx[0][1].shape[0] == 1
# coord-1
assert len(idx[1][0].shape) == 2
assert idx[1][0].shape[1] == 3
# coord-2
assert idx[1][1].shape[1] == 3
# dist-1
assert len(idx[2][0].shape) == 1
assert idx[2][0].shape[0] == 1
# dist-2
assert idx[2][1].shape[0] == 1
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1), ret_rij=True)
# [[idx-1, idx-2], [dist-1, dist-2]]
assert len(idx) == 2
assert len(idx[0]) == 2
assert len(idx[1]) == 2
# idx-1
assert len(idx[0][0].shape) == 1
assert idx[0][0].shape[0] == 1
# idx-2
assert idx[0][1].shape[0] == 1
# dist-1
assert len(idx[1][0].shape) == 1
assert idx[1][0].shape[0] == 1
# dist-2
assert idx[1][1].shape[0] == 1
def test_close_sizes_none(self, setup):
point = [100., 100., 100.]
# Return index
idx = setup.mol.close(point, R=.1)
assert len(idx) == 0
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1))
assert len(idx) == 2
assert len(idx[0]) == 0
assert not isinstance(idx[0], list)
# Longer
idx = setup.mol.close(point, R=(.1, 1.1, 2.1))
assert len(idx) == 3
assert len(idx[0]) == 0
# Return index
idx = setup.mol.close(point, R=.1, ret_xyz=True)
assert len(idx) == 2
assert len(idx[0]) == 0
assert len(idx[1]) == 0
assert idx[1].shape[0] == 0 # equivalent to above
assert idx[1].shape[1] == 3
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1), ret_xyz=True)
# [[idx-1, idx-2], [coord-1, coord-2]]
assert len(idx) == 2
assert len(idx[0]) == 2
assert len(idx[1]) == 2
# idx-1
assert len(idx[0][0].shape) == 1
assert idx[0][0].shape[0] == 0
# idx-2
assert idx[0][1].shape[0] == 0
# coord-1
assert len(idx[1][0].shape) == 2
assert idx[1][0].shape[1] == 3
# coord-2
assert idx[1][1].shape[1] == 3
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1), ret_xyz=True, ret_rij=True)
# [[idx-1, idx-2], [coord-1, coord-2], [dist-1, dist-2]]
assert len(idx) == 3
assert len(idx[0]) == 2
assert len(idx[1]) == 2
# idx-1
assert len(idx[0][0].shape) == 1
assert idx[0][0].shape[0] == 0
# idx-2
assert idx[0][1].shape[0] == 0
# coord-1
assert len(idx[1][0].shape) == 2
assert idx[1][0].shape[0] == 0
assert idx[1][0].shape[1] == 3
# coord-2
assert idx[1][1].shape[0] == 0
assert idx[1][1].shape[1] == 3
# dist-1
assert len(idx[2][0].shape) == 1
assert idx[2][0].shape[0] == 0
# dist-2
assert idx[2][1].shape[0] == 0
# Return index of two things
idx = setup.mol.close(point, R=(.1, 1.1), ret_rij=True)
# [[idx-1, idx-2], [dist-1, dist-2]]
assert len(idx) == 2
assert len(idx[0]) == 2
assert len(idx[1]) == 2
# idx-1
assert len(idx[0][0].shape) == 1
assert idx[0][0].shape[0] == 0
# idx-2
assert idx[0][1].shape[0] == 0
# dist-1
assert len(idx[1][0].shape) == 1
assert idx[1][0].shape[0] == 0
# dist-2
assert idx[1][1].shape[0] == 0
def test_sparserij1(self, setup):
rij = setup.g.sparserij()
def test_bond_correct(self, setup):
# Create ribbon
rib = setup.g.tile(2, 1)
# Convert the last atom to a H atom
rib.atom[-1] = Atom[1]
ia = len(rib) - 1
# Get bond-length
idx, d = rib.close(ia, R=(.1, 1000), ret_rij=True)
i = np.argmin(d[1])
d = d[1][i]
rib.bond_correct(ia, idx[1][i])
idx, d2 = rib.close(ia, R=(.1, 1000), ret_rij=True)
i = np.argmin(d2[1])
d2 = d2[1][i]
assert d != d2
# Calculate actual radius
assert d2 == (Atom[1].radius() + Atom[6].radius())
def test_unit_cell_estimation1(self, setup):
# Create new geometry with only the coordinates
# and atoms
geom = Geometry(setup.g.xyz, Atom[6])
# Only check the two distances we know have sizes
for i in range(2):
# It cannot guess skewed axis
assert not np.allclose(geom.cell[i, :], setup.g.cell[i, :])
def test_unit_cell_estimation2(self, setup):
# Create new geometry with only the coordinates
# and atoms
s1 = SuperCell([2, 2, 2])
g1 = Geometry([[0, 0, 0], [1, 1, 1]], sc=s1)
g2 = Geometry(np.copy(g1.xyz))
assert np.allclose(g1.cell, g2.cell)
# Assert that it correctly calculates the bond-length in the
# directions of actual distance
g1 = Geometry([[0, 0, 0], [1, 1, 0]], atom='H', sc=s1)
g2 = Geometry(np.copy(g1.xyz))
for i in range(2):
assert np.allclose(g1.cell[i, :], g2.cell[i, :])
assert not np.allclose(g1.cell[2, :], g2.cell[2, :])
@pytest.mark.xfail(raises=ValueError)
def test_distance1(self, setup):
geom = Geometry(setup.g.xyz, Atom[6])
# maxR is undefined
d = geom.distance()
@pytest.mark.xfail(raises=ValueError)
def test_distance2(self, setup):
geom = Geometry(setup.g.xyz, Atom[6])
d = geom.distance(R=1.42, method='unknown_numpy_function')
def test_distance3(self, setup):
geom = setup.g.copy()
d = geom.distance()
assert len(d) == 1
assert np.allclose(d, [1.42])
def test_distance4(self, setup):
geom = setup.g.copy()
d = geom.distance(method=np.min)
assert len(d) == 1
assert np.allclose(d, [1.42])
d = geom.distance(method=np.max)
assert len(d) == 1
assert np.allclose(d, [1.42])
d = geom.distance(method='max')
assert len(d) == 1
assert np.allclose(d, [1.42])
def test_distance5(self, setup):
geom = setup.g.copy()
d = geom.distance(R=np.inf)
assert len(d) == 6
d = geom.distance(0, R=1.42)
assert len(d) == 1
assert np.allclose(d, [1.42])
def test_distance6(self, setup):
# Create a 1D chain
geom = Geometry([0] * 3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 1, 1])
d = geom.distance(0)
assert len(d) == 1
assert np.allclose(d, [1.])
# Do twice
d = geom.distance(R=2)
assert len(d) == 2
assert np.allclose(d, [1., 2.])
# Do all
d = geom.distance(R=np.inf)
assert len(d) == 77 // 2
# Add one due arange not adding the last item
assert np.allclose(d, range(1, 78 // 2))
# Create a 2D grid
geom.set_nsc([3, 3, 1])
d = geom.distance(R=2, tol=[.4, .3, .2, .1])
assert len(d) == 2 # 1, sqrt(2)
# Add one due arange not adding the last item
assert np.allclose(d, [1, 2**.5])
# Create a 2D grid
geom.set_nsc([5, 5, 1])
d = geom.distance(R=2, tol=[.4, .3, .2, .1])
assert len(d) == 3 # 1, sqrt(2), 2
# Add one due arange not adding the last item
assert np.allclose(d, [1, 2**.5, 2])
def test_distance7(self, setup):
# Create a 1D chain
geom = Geometry([0] * 3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 1, 1])
# Try with a short R and a long tolerance list
# We know that the tolerance list prevails, because
d = geom.distance(R=1, tol=np.ones(10) * .5)
assert len(d) == 1
assert np.allclose(d, [1.])
def test_distance8(self, setup):
geom = Geometry([0] * 3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 1, 1])
d = geom.distance(0, method='min')
assert len(d) == 1
d = geom.distance(0, method='median')
assert len(d) == 1
d = geom.distance(0, method='mode')
assert len(d) == 1
def test_optimize_nsc1(self, setup):
# Create a 1D chain
geom = Geometry([0] * 3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc(), [3, 3, 3])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc(1), [77, 3, 77])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc([0, 2]), [3, 77, 3])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc([0, 2], R=2.00000001), [5, 77, 5])
geom.set_nsc([1, 1, 1])
assert np.allclose(geom.optimize_nsc([0, 2], R=2.0000001), [5, 1, 5])
geom.set_nsc([5, 1, 5])
assert np.allclose(geom.optimize_nsc([0, 2], R=0.9999), [1, 1, 1])
def test_optimize_nsc2(self, setup):
# 2 ** 0.5 ensures lattice vectors with length 1
geom = sisl_geom.fcc(2**0.5, Atom(1, R=1.0001))
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc(), [3, 3, 3])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc(1), [77, 3, 77])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc([0, 2]), [3, 77, 3])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc([0, 2], R=2.000001), [5, 77, 5])
geom.set_nsc([1, 1, 1])
assert np.allclose(geom.optimize_nsc([0, 2], R=2.0000001), [5, 1, 5])
geom.set_nsc([5, 1, 5])
assert np.allclose(geom.optimize_nsc([0, 2], R=0.9999), [1, 1, 1])
def test_argumentparser1(self, setup):
setup.g.ArgumentParser()
setup.g.ArgumentParser(**setup.g._ArgumentParser_args_single())
def test_argumentparser2(self, setup, **kwargs):
p, ns = setup.g.ArgumentParser(**kwargs)
# Try all options
opts = [
'--origin',
'--center-of',
'mass',
'--center-of',
'xyz',
'--center-of',
'position',
'--center-of',
'cell',
'--unit-cell',
'translate',
'--unit-cell',
'mod',
'--rotate',
'90',
'x',
'--rotate',
'90',
'y',
'--rotate',
'90',
'z',
'--add',
'0,0,0',
'6',
'--swap',
'0',
'1',
'--repeat',
'2',
'x',
'--repeat',
'2',
'y',
'--repeat',
'2',
'z',
'--tile',
'2',
'x',
'--tile',
'2',
'y',
'--tile',
'2',
'z',
'--cut',
'2',
'z',
'--cut',
'2',
'y',
'--cut',
'2',
'x',
]
if kwargs.get('limit_arguments', True):
opts.extend([
'--rotate', '-90', 'x', '--rotate', '-90', 'y', '--rotate',
'-90', 'z'
])
else:
opts.extend([
'--rotate-x', ' -90', '--rotate-y', ' -90', '--rotate-z',
' -90', '--repeat-x', '2', '--repeat-y', '2', '--repeat-z', '2'
])
args = p.parse_args(opts, namespace=ns)
if len(kwargs) == 0:
self.test_argumentparser2(setup,
**setup.g._ArgumentParser_args_single())
def test_set_sc(self, setup):
# Create new geometry with only the coordinates
# and atoms
s1 = SuperCell([2, 2, 2])
g1 = Geometry([[0, 0, 0], [1, 1, 1]], sc=[2, 2, 1])
g1.set_sc(s1)
assert g1.sc == s1
def test_attach1(self, setup):
g = setup.g.attach(0, setup.mol, 0, dist=1.42, axis=2)
g = setup.g.attach(0, setup.mol, 0, dist='calc', axis=2)
g = setup.g.attach(0, setup.mol, 0, dist=[0, 0, 1.42])
def test_mirror1(self, setup):
for plane in ['xy', 'xz', 'yz']:
setup.g.mirror(plane)
def test_pickle(self, setup):
import pickle as p
s = p.dumps(setup.g)
n = p.loads(s)
assert n == setup.g
def test_geometry_names(self):
g = sisl_geom.graphene()
assert len(g.names) == 0
g['A'] = 1
assert len(g.names) == 1
g['B'] = [1, 2]
assert len(g.names) == 2
g.names.delete_name('B')
assert len(g.names) == 1
# Add new group
g['B'] = [0, 2]
for name in g.names:
assert name in ['A', 'B']
str(g)
assert np.allclose(g['B'], g[[0, 2], :])
assert np.allclose(g.axyz('B'), g[[0, 2], :])
del g.names['B']
assert len(g.names) == 1
@pytest.mark.xfail(raises=SislError)
def test_geometry_groups_raise(self):
g = sisl_geom.graphene()
g['A'] = 1
g['A'] = [1, 2]
@pytest.mark.parametrize("geometry", [
sisl_geom.graphene(),
sisl_geom.diamond(),
sisl_geom.sc(1.4, Atom[1]),
sisl_geom.fcc(1.4, Atom[1]),
sisl_geom.bcc(1.4, Atom[1]),
sisl_geom.hcp(1.4, Atom[1])
])
def test_geometry_as_primary(self, geometry):
prod = itertools.product
x_reps = [1, 4, 3]
y_reps = [1, 4, 5]
z_reps = [1, 4, 6]
tile_rep = ['r', 't']
na_primary = len(geometry)
for x, y, z in prod(x_reps, y_reps, z_reps):
if x == y == z == 1:
continue
for a, b, c in prod(tile_rep, tile_rep, tile_rep):
G = ((geometry * ([x, 1, 1], a)) *
([1, y, 1], b)) * ([1, 1, z], c)
p = G.as_primary(na_primary)
assert np.allclose(p.xyz, geometry.xyz)
assert np.allclose(p.cell, geometry.cell)
def test_geometry_as_primary_without_super(self):
g = sisl_geom.graphene()
p = g.as_primary(len(g))
assert g == p
G = g.tile(2, 0).tile(3, 1)
p, supercell = G.as_primary(len(g), ret_super=True)
assert np.allclose(p.xyz, g.xyz)
assert np.allclose(p.cell, g.cell)
assert np.all(supercell == [2, 3, 1])
def get_H():
s = geom.sc(1., Atom(1, 1.001))
H = Hamiltonian(s)
H.construct([(0.1, 1.001), (0.1, 0.5)])
return H.tile(2, 0).tile(2, 1).tile(2, 2)