def test_imaginary_fail_geometry(sisl_tmp):
fr = sisl_tmp('GRID_real.cube', _dir)
fi = sisl_tmp('GRID_imag.cube', _dir)
geom = Geometry(np.random.rand(10, 3), np.random.randint(1, 70, 10), sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom, dtype=np.complex128)
grid.grid = np.random.rand(*grid.shape) + 1j*np.random.rand(*grid.shape)
grid.write(fr)
# Assert it fails on geometry
grid2 = Grid(0.3, dtype=np.complex128)
grid2.write(fi, imag=True)
grid.read(fr, imag=fi)
def test_read_write_grid(self, sisl_tmp, sisl_system, sile):
g = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :])
G = Grid([10, 11, 12])
G[:, :, :] = np.random.rand(10, 11, 12)
f = sisl_tmp("test_read_write_grid.win", _dir)
# Write
try:
with sile(f, mode="w") as s:
s.write_grid(G)
except SileError:
with sile(f, mode="wb") as s:
s.write_grid(G)
# Read 1
try:
with sile(f, mode="r") as s:
g = s.read_grid()
assert np.allclose(g.grid, G.grid, atol=1e-5)
except UnicodeDecodeError as e:
pass
# Read 2
try:
with sile(f, mode='r') as s:
g = Grid.read(s)
assert np.allclose(g.grid, G.grid, atol=1e-5)
except UnicodeDecodeError as e:
pass
def test_default_size(sisl_tmp):
f = sisl_tmp('GRID.cube', _dir)
grid = Grid(0.2, sc=2.0)
grid.grid = np.random.rand(*grid.shape)
grid.write(f)
read = grid.read(f)
assert np.allclose(grid.grid, read.grid)
assert grid.geometry is None
assert len(read.geometry) == 1
def test_geometry(sisl_tmp):
f = sisl_tmp('GRID.cube', _dir)
geom = Geometry(np.random.rand(10, 3), np.random.randint(1, 70, 10), sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom)
grid.grid = np.random.rand(*grid.shape)
grid.write(f)
read = grid.read(f)
assert np.allclose(grid.grid, read.grid)
assert not grid.geometry is None
assert not read.geometry is None
assert grid.geometry == read.geometry
def test_imaginary(sisl_tmp):
fr = sisl_tmp('GRID_real.cube', _dir)
fi = sisl_tmp('GRID_imag.cube', _dir)
geom = Geometry(np.random.rand(10, 3), np.random.randint(1, 70, 10), sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom, dtype=np.complex128)
grid.grid = np.random.rand(*grid.shape) + 1j*np.random.rand(*grid.shape)
grid.write(fr)
grid.write(fi, imag=True)
read = grid.read(fr)
read_i = grid.read(fi)
read.grid = read.grid + 1j*read_i.grid
assert np.allclose(grid.grid, read.grid)
assert not grid.geometry is None
assert not read.geometry is None
assert grid.geometry == read.geometry
read = grid.read(fr, imag=fi)
assert np.allclose(grid.grid, read.grid)
read = grid.read(fr, imag=read_i)
assert np.allclose(grid.grid, read.grid)
def test_read_write_grid(self, sisl_tmp, sisl_system, sile):
g = sisl_system.g.rotatec(-30)
G = Grid([10, 11, 12])
G[:, :, :] = np.random.rand(10, 11, 12)
f = sisl_tmp('test_read_write_grid.win', _dir)
# Write
try:
sile(f, mode='w').write_grid(G)
except SileError:
sile(f, mode='wb').write_grid(G)
# Read 1
try:
g = sile(f, mode='r').read_grid()
assert np.allclose(g.grid, G.grid, atol=1e-5)
except UnicodeDecodeError as e:
pass
# Read 2
try:
g = Grid.read(sile(f, mode='r'))
assert np.allclose(g.grid, G.grid, atol=1e-5)
except UnicodeDecodeError as e:
pass
def read_grid(self, imag=None):
""" Returns `Grid` object from the CUBE file
Parameters
----------
imag : str or Sile or Grid
the imaginary part of the grid. If the geometries does not match
an error will be raised.
"""
if not imag is None:
if not isinstance(imag, Grid):
imag = Grid.read(imag)
geom = self.read_geometry()
if geom is None:
self.fh.seek(0)
sc = self.read_supercell()
else:
sc = geom.sc
# Now seek behind to read grid sizes
self.fh.seek(0)
# Skip headers and origin
self.readline()
self.readline()
na = int(self.readline().split()[0])
ngrid = [0] * 3
for i in [0, 1, 2]:
tmp = self.readline().split()
ngrid[i] = int(tmp[0])
# Read past the atoms
for i in range(na):
self.readline()
if geom is None:
grid = Grid(ngrid, dtype=np.float64, sc=sc)
else:
grid = Grid(ngrid, dtype=np.float64, geometry=geom)
grid.grid.shape = (-1, )
# TODO check performance of this
# We are currently doing this to enable reading
# 1-column data and 6-column data.
lines = [
item for sublist in self.fh.readlines()
for item in sublist.split()
]
grid.grid[:] = np.array(lines).astype(grid.dtype)
grid.grid.shape = ngrid
if imag is None:
return grid
# We are expecting an imaginary part
if not grid.geometry.equal(imag.geometry):
raise SislError(
str(self) + ' and its imaginary part does not have the same '
'geometry. Hence a combined complex Grid cannot be formed.')
if grid != imag:
raise SislError(
str(self) + ' and its imaginary part does not have the same '
'shape. Hence a combined complex Grid cannot be formed.')
# Now we have a complex grid
grid.grid = grid.grid + 1j * imag.grid
return grid
