def test_read_write_geometry(self, sisl_tmp, sisl_system, sile):
G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :])
G.set_nsc([1, 1, 1])
f = sisl_tmp("test_read_write_geom.win", _dir)
# These files does not store the atomic species
if issubclass(sile, (_ncSileTBtrans, deltancSileTBtrans)):
return
if sys.platform.startswith("win") and issubclass(sile, chgSileVASP):
pytest.xfail(
"Windows reading/writing supercell fails for some unknown reason"
)
# Write
sile(f, mode="w").write_geometry(G)
# Read 1
try:
with sile(f, mode='r') as s:
g = s.read_geometry()
assert g.equal(
G, R=False,
tol=1e-3) # pdb files have 8.3 for atomic coordinates
except UnicodeDecodeError as e:
pass
# Read 2
try:
with sile(f, mode='r') as s:
g = Geometry.read(s)
assert g.equal(G, R=False, tol=1e-3)
except UnicodeDecodeError as e:
pass
def test_read_write_geom(self):
G = self.g.rotatec(-30)
G.set_nsc([1, 1, 1])
f = mkstemp(dir=self.d)[1]
read_geometry = get_siles(['read_geometry'])
for sile in get_siles(['write_geometry']):
if not sile in read_geometry:
continue
# It is not yet an instance, hence issubclass
if issubclass(sile, (HamiltonianSile, tbtncSileSiesta, dHncSileSiesta)):
continue
# Write
sile(f, mode='w').write_geometry(G)
# Read 1
try:
g = sile(f, mode='r').read_geometry()
assert_true(g.equal(G, R=False))
except UnicodeDecodeError as e:
pass
# Read 2
try:
g = Geometry.read(sile(f, mode='r'))
assert_true(g.equal(G, R=False))
except UnicodeDecodeError as e:
pass
# Clean-up file
os.remove(f)
def test_read_write_geom(self, sisl_tmp, sisl_system, sile):
G = sisl_system.g.rotatec(-30)
G.set_nsc([1, 1, 1])
f = sisl_tmp('test_read_write_geom.win', _dir)
# These files does not store the atomic species
if issubclass(sile, (_ncSileTBtrans, deltancSileTBtrans)):
return
# Write
sile(f, mode='w').write_geometry(G)
# Read 1
try:
g = sile(f, mode='r').read_geometry()
assert g.equal(G, R=False)
except UnicodeDecodeError as e:
pass
# Read 2
try:
g = Geometry.read(sile(f, mode='r'))
assert g.equal(G, R=False)
except UnicodeDecodeError as e:
pass
def test_read_write_geometry(self, sisl_tmp, sisl_system, sile):
G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :])
G.set_nsc([1, 1, 1])
f = sisl_tmp("test_read_write_geom.win", _dir)
# These files does not store the atomic species
if issubclass(sile, (_ncSileTBtrans, deltancSileTBtrans)):
return
# Write
sile(f, mode="w").write_geometry(G)
# Read 1
try:
g = sile(f, mode="r").read_geometry()
assert g.equal(G, R=False, tol=1e-3) # pdb files have 8.3 for atomic coordinates
except UnicodeDecodeError as e:
pass
# Read 2
try:
g = Geometry.read(sile(f, mode="r"))
assert g.equal(G, R=False, tol=1e-3)
except UnicodeDecodeError as e:
pass
