def read_grid(self, name='gridfunc', idx=0, *args, **kwargs):
""" Reads a grid in the current SIESTA.grid.nc file
Enables the reading and processing of the grids created by SIESTA
"""
# Swap as we swap back in the end
sc = self.read_sc().swapaxes(0, 2)
# Create the grid
nx = len(self._dimension('n1'))
ny = len(self._dimension('n2'))
nz = len(self._dimension('n3'))
if name is None:
v = self._variable('gridfunc')
else:
v = self._variable(name)
# Create the grid, SIESTA uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.Periodic, sc=sc,
dtype=v.dtype)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :]
else:
grid.grid = v[idx, :, :, :]
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
return grid.swapaxes(0, 2)
def read_grid(self, name='gridfunc', idx=0, *args, **kwargs):
""" Reads a grid in the current SIESTA.grid.nc file
Enables the reading and processing of the grids created by SIESTA
"""
# Swap as we swap back in the end
sc = self.read_supercell().swapaxes(0, 2)
# Create the grid
nx = len(self._dimension('n1'))
ny = len(self._dimension('n2'))
nz = len(self._dimension('n3'))
if name is None:
v = self._variable('gridfunc')
else:
v = self._variable(name)
# Create the grid, SIESTA uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.Periodic, sc=sc,
dtype=v.dtype)
if len(v.shape) == 3:
grid.grid[:, :, :] = v[:, :, :]
else:
grid.grid[:, :, :] = v[idx, :, :, :]
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
return grid.swapaxes(0, 2)
def read_grid(self, *args, **kwargs):
""" Reads the TranSiesta potential input grid """
# Create the grid
na = len(self._dimension('a'))
nb = len(self._dimension('b'))
nc = len(self._dimension('c'))
v = self._variable('V')
# Create the grid, Siesta uses periodic, always
grid = Grid([nc, nb, na], bc=Grid.PERIODIC, dtype=v.dtype)
grid.grid[:, :, :] = v[:, :, :] / eV2Ry
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
return grid.swapaxes(0, 2)
def read_grid(self, name, idx=0):
""" Reads a grid in the current SIESTA.nc file
Enables the reading and processing of the grids created by SIESTA
"""
# Swap as we swap back in the end
geom = self.read_geom().swapaxes(0, 2)
# Shorthand
g = self.groups['GRID']
# Create the grid
nx = len(g.dimensions['nx'])
ny = len(g.dimensions['ny'])
nz = len(g.dimensions['nz'])
# Shorthand variable name
v = g.variables[name]
# Create the grid, SIESTA uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.Periodic, dtype=v.dtype)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :]
else:
grid.grid = v[idx, :, :, :]
try:
u = v.unit
if u == 'Ry':
# Convert to ev
grid *= Ry2eV
except:
# Simply, we have no units
pass
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
grid = grid.swapaxes(0, 2)
grid.set_geom(geom)
return grid
def read_grid(self, name, idx=0):
""" Reads a grid in the current SIESTA.nc file
Enables the reading and processing of the grids created by SIESTA
"""
# Swap as we swap back in the end
geom = self.read_geom().swapaxes(0, 2)
# Shorthand
g = self.groups['GRID']
# Create the grid
nx = len(g.dimensions['nx'])
ny = len(g.dimensions['ny'])
nz = len(g.dimensions['nz'])
# Shorthand variable name
v = g.variables[name]
# Create the grid, SIESTA uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.Periodic, dtype=v.dtype)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :]
else:
grid.grid = v[idx, :, :, :]
try:
u = v.unit
if u == 'Ry':
# Convert to ev
grid *= Ry2eV
except:
# Simply, we have no units
pass
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
grid = grid.swapaxes(0, 2)
grid.set_geom(geom)
return grid
def read_grid(self, name, spin=0):
""" Reads a grid in the current Siesta.nc file
Enables the reading and processing of the grids created by Siesta
Parameters
----------
name : str
name of the grid variable to read
spin : int or array_like, optional
the spin-index for retrieving one of the components. If a vector
is passed it refers to the fraction per indexed component. I.e.
``[0.5, 0.5]`` will return sum of half the first two components.
Default to the first component.
"""
# Swap as we swap back in the end
geom = self.read_geometry().swapaxes(0, 2)
# Shorthand
g = self.groups['GRID']
# Create the grid
nx = len(g.dimensions['nx'])
ny = len(g.dimensions['ny'])
nz = len(g.dimensions['nz'])
# Shorthand variable name
v = g.variables[name]
# Create the grid, Siesta uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.PERIODIC, dtype=v.dtype)
# Unit-conversion
BohrC2AngC = Bohr2Ang**3
unit = {
'Rho': 1. / BohrC2AngC,
'RhoInit': 1. / BohrC2AngC,
'RhoTot': 1. / BohrC2AngC,
'RhoDelta': 1. / BohrC2AngC,
'RhoXC': 1. / BohrC2AngC,
'RhoBader': 1. / BohrC2AngC,
'Chlocal': 1. / BohrC2AngC,
}.get(name, 1.)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :] * unit
elif isinstance(spin, Integral):
grid.grid = v[spin, :, :, :] * unit
else:
if len(spin) > v.shape[0]:
raise SileError(
self.__class__.__name__ +
'.read_grid requires spin to be an integer or '
'an array of length equal to the number of spin components.'
)
grid.grid[:, :, :] = v[0, :, :, :] * (spin[0] * unit)
for i, scale in enumerate(spin[1:]):
grid.grid[:, :, :] += v[1 + i, :, :, :] * (scale * unit)
try:
if v.unit == 'Ry':
# Convert to ev
grid *= Ry2eV
except:
# Allowed pass due to pythonic reading
pass
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
grid = grid.swapaxes(0, 2)
grid.set_geom(geom)
return grid
def read_grid(self, spin=0, name='gridfunc', *args, **kwargs):
""" Reads a grid in the current Siesta.grid.nc file
Enables the reading and processing of the grids created by Siesta
Parameters
----------
spin : int or array_like, optional
specify the retrieved values
name : str, optional
the name for the grid-function (do not supply for standard Siesta output)
geometry: Geometry, optional
add the Geometry to the Grid
"""
# Default to *index* variable
spin = kwargs.get('index', spin)
# Determine the name of this file
f = osp.basename(self.file)
# File names are made up of
# ElectrostaticPotential.grid.nc
# So the first one should be ElectrostaticPotential
try:
# <>.grid.nc
base = f.split('.')[-3]
except:
base = 'None'
# Unit-conversion
BohrC2AngC = Bohr2Ang**3
unit = {
'Rho': 1. / BohrC2AngC,
'DeltaRho': 1. / BohrC2AngC,
'RhoXC': 1. / BohrC2AngC,
'RhoInit': 1. / BohrC2AngC,
'Chlocal': 1. / BohrC2AngC,
'TotalCharge': 1. / BohrC2AngC,
'BaderCharge': 1. / BohrC2AngC,
'ElectrostaticPotential': Ry2eV,
'TotalPotential': Ry2eV,
'Vna': Ry2eV,
}.get(base, None)
# Fall-back
if unit is None:
unit = 1.
show_info = True
else:
show_info = False
# Swap as we swap back in the end
sc = self.read_supercell().swapaxes(0, 2)
# Create the grid
nx = len(self._dimension('n1'))
ny = len(self._dimension('n2'))
nz = len(self._dimension('n3'))
if name is None:
v = self._variable('gridfunc')
else:
v = self._variable(name)
# Create the grid, Siesta uses periodic, always
grid = Grid([nz, ny, nx],
bc=Grid.PERIODIC,
sc=sc,
dtype=v.dtype,
geometry=kwargs.get("geometry", None))
if v.ndim == 3:
grid.grid[:, :, :] = v[:, :, :] * unit
elif isinstance(spin, Integral):
grid.grid[:, :, :] = v[spin, :, :, :] * unit
else:
if len(spin) > v.shape[0]:
raise SileError(
f"{self.__class__.__name__}.read_grid requires spin to be an integer or "
"an array of length equal to the number of spin components."
)
grid.grid[:, :, :] = v[0, :, :, :] * spin[0] * unit
for i, scale in enumerate(spin[1:]):
grid.grid[:, :, :] += v[1 + i, :, :, :] * scale * unit
if show_info:
info(
f"{self.__class__.__name__}.read_grid cannot determine the units of the grid. "
"The units may not be in sisl units.")
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
return grid.swapaxes(0, 2)
class TestGrid(object):
def setUp(self):
alat = 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) *
alat,
nsc=[3, 3, 1])
self.g = Grid([10, 10, 100], sc=self.sc)
def tearDown(self):
del self.sc
del self.g
def test_append(self):
g = self.g.append(self.g, 0)
assert_true(np.allclose(g.grid.shape, [20, 10, 100]))
g = self.g.append(self.g, 1)
assert_true(np.allclose(g.grid.shape, [10, 20, 100]))
g = self.g.append(self.g, 2)
assert_true(np.allclose(g.grid.shape, [10, 10, 200]))
def test_size(self):
assert_true(np.allclose(self.g.grid.shape, [10, 10, 100]))
def test_item(self):
assert_true(
np.allclose(self.g[1:2, 1:2, 2:3], self.g.grid[1:2, 1:2, 2:3]))
def test_dcell(self):
assert_true(np.all(self.g.dcell * self.g.cell >= 0))
def test_dvol(self):
assert_true(self.g.dvol > 0)
def test_shape(self):
assert_true(np.all(self.g.shape == self.g.grid.shape))
def test_dtype(self):
assert_true(self.g.dtype == self.g.grid.dtype)
def test_copy(self):
assert_true(self.g.copy() == self.g)
def test_swapaxes(self):
g = self.g.swapaxes(0, 1)
assert_true(np.allclose(self.g.cell[0, :], g.cell[1, :]))
assert_true(np.allclose(self.g.cell[1, :], g.cell[0, :]))
def test_interp(self):
shape = np.array(self.g.shape, np.int32)
g = self.g.interp(shape * 2)
g1 = g.interp(shape)
assert_true(np.allclose(self.g.grid, g1.grid))
def test_index1(self):
mid = np.array(self.g.shape, np.int32) // 2
idx = self.g.index(self.sc.center())
print(mid, idx)
assert_true(np.all(mid == idx))
def test_sum(self):
for i in range(3):
assert_true(self.g.sum(i).shape[i] == 1)
def test_mean(self):
for i in range(3):
assert_true(self.g.mean(i).shape[i] == 1)
def test_cross_section(self):
for i in range(3):
assert_true(self.g.cross_section(1, i).shape[i] == 1)
def test_remove_part(self):
for i in range(3):
assert_true(self.g.remove_part(1, i, above=True).shape[i] == 1)
def test_sub_part(self):
for i in range(3):
assert_true(self.g.sub_part(1, i, above=False).shape[i] == 1)
def test_sub(self):
for i in range(3):
assert_true(self.g.sub(1, i).shape[i] == 1)
for i in range(3):
assert_true(self.g.sub([1, 2], i).shape[i] == 2)
def test_remove(self):
for i in range(3):
assert_true(self.g.remove(1, i).shape[i] == self.g.shape[i] - 1)
for i in range(3):
assert_true(
self.g.remove([1, 2], i).shape[i] == self.g.shape[i] - 2)
def test_argumentparser(self):
self.g.ArgumentParser()
class TestGrid(object):
def setUp(self):
alat = 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) * alat, nsc=[3, 3, 1])
self.g = Grid([10, 10, 100], sc=self.sc)
def tearDown(self):
del self.sc
del self.g
def test_append(self):
g = self.g.append(self.g, 0)
assert_true(np.allclose(g.grid.shape, [20, 10, 100]))
g = self.g.append(self.g, 1)
assert_true(np.allclose(g.grid.shape, [10, 20, 100]))
g = self.g.append(self.g, 2)
assert_true(np.allclose(g.grid.shape, [10, 10, 200]))
def test_size(self):
assert_true(np.allclose(self.g.grid.shape, [10, 10, 100]))
def test_item(self):
assert_true(np.allclose(self.g[1:2, 1:2, 2:3], self.g.grid[1:2, 1:2, 2:3]))
def test_dcell(self):
assert_true(np.all(self.g.dcell*self.g.cell >= 0))
def test_dvol(self):
assert_true(self.g.dvol > 0)
def test_shape(self):
assert_true(np.all(self.g.shape == self.g.grid.shape))
def test_dtype(self):
assert_true(self.g.dtype == self.g.grid.dtype)
def test_copy(self):
assert_true(self.g.copy() == self.g)
def test_swapaxes(self):
g = self.g.swapaxes(0, 1)
assert_true(np.allclose(self.g.cell[0,:], g.cell[1,:]))
assert_true(np.allclose(self.g.cell[1,:], g.cell[0,:]))
def test_interp(self):
shape = np.array(self.g.shape, np.int32)
g = self.g.interp(shape * 2)
g1 = g.interp(shape)
assert_true(np.allclose(self.g.grid, g1.grid))
def test_index1(self):
mid = np.array(self.g.shape, np.int32) // 2
idx = self.g.index(self.sc.center())
print(mid, idx)
assert_true(np.all(mid == idx))
def test_sum(self):
for i in range(3):
assert_true(self.g.sum(i).shape[i] == 1)
def test_mean(self):
for i in range(3):
assert_true(self.g.mean(i).shape[i] == 1)
def test_cross_section(self):
for i in range(3):
assert_true(self.g.cross_section(1, i).shape[i] == 1)
def test_remove_part(self):
for i in range(3):
assert_true(self.g.remove_part(1, i, above=True).shape[i] == 1)
def test_sub_part(self):
for i in range(3):
assert_true(self.g.sub_part(1, i, above=False).shape[i] == 1)
def test_sub(self):
for i in range(3):
assert_true(self.g.sub(1, i).shape[i] == 1)
for i in range(3):
assert_true(self.g.sub([1,2], i).shape[i] == 2)
def test_remove(self):
for i in range(3):
assert_true(self.g.remove(1, i).shape[i] == self.g.shape[i]-1)
for i in range(3):
assert_true(self.g.remove([1,2], i).shape[i] == self.g.shape[i]-2)
def test_argumentparser(self):
self.g.ArgumentParser()
class TestGrid(object):
def setUp(self):
alat = 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) *
alat,
nsc=[3, 3, 1])
self.g = Grid([10, 10, 100], sc=self.sc)
self.g[:, :, :] = 2.
g = Grid(sc=self.sc)
def tearDown(self):
del self.sc
del self.g
def test_append(self):
g = self.g.append(self.g, 0)
assert_true(np.allclose(g.grid.shape, [20, 10, 100]))
g = self.g.append(self.g, 1)
assert_true(np.allclose(g.grid.shape, [10, 20, 100]))
g = self.g.append(self.g, 2)
assert_true(np.allclose(g.grid.shape, [10, 10, 200]))
def test_set(self):
v = self.g[0, 0, 0]
self.g[0, 0, 0] = 3
assert_true(self.g.grid[0, 0, 0] == 3)
assert_true(self.g[0, 0, 0] == 3)
self.g[0, 0, 0] = v
assert_true(self.g[0, 0, 0] == v)
def test_size(self):
assert_true(np.allclose(self.g.grid.shape, [10, 10, 100]))
def test_item(self):
assert_true(
np.allclose(self.g[1:2, 1:2, 2:3], self.g.grid[1:2, 1:2, 2:3]))
def test_dcell(self):
assert_true(np.all(self.g.dcell * self.g.cell >= 0))
def test_dvol(self):
assert_true(self.g.dvol > 0)
def test_shape(self):
assert_true(np.all(self.g.shape == self.g.grid.shape))
def test_dtype(self):
assert_true(self.g.dtype == self.g.grid.dtype)
def test_copy(self):
assert_true(self.g.copy() == self.g)
assert_false(self.g.copy() != self.g)
def test_add(self):
g = self.g + self.g
assert_true(np.allclose(g.grid, (self.g * 2).grid))
g = self.g.copy()
g *= 2
assert_true(np.allclose(g.grid, (self.g * 2).grid))
g = self.g.copy()
g /= 2
assert_true(np.allclose(g.grid, (self.g / 2).grid))
def test_swapaxes(self):
g = self.g.swapaxes(0, 1)
assert_true(np.allclose(self.g.cell[0, :], g.cell[1, :]))
assert_true(np.allclose(self.g.cell[1, :], g.cell[0, :]))
def test_interp(self):
shape = np.array(self.g.shape, np.int32)
g = self.g.interp(shape * 2)
g1 = g.interp(shape)
# Sadly the interpolation does not work as it really
# should...
# One cannot interp down/up and retrieve the same
# grid... Perhaps this is ok, but not good... :(
assert_true(np.allclose(self.g.grid, g1.grid))
def test_index1(self):
mid = np.array(self.g.shape, np.int32) // 2
idx = self.g.index(self.sc.center())
assert_true(np.all(mid == idx))
def test_sum(self):
for i in range(3):
assert_true(self.g.sum(i).shape[i] == 1)
def test_mean(self):
for i in range(3):
assert_true(self.g.mean(i).shape[i] == 1)
def test_cross_section(self):
for i in range(3):
assert_true(self.g.cross_section(1, i).shape[i] == 1)
def test_remove_part(self):
for i in range(3):
assert_true(self.g.remove_part(1, i, above=True).shape[i] == 1)
def test_sub_part(self):
for i in range(3):
assert_true(self.g.sub_part(1, i, above=False).shape[i] == 1)
assert_true(
self.g.sub_part(1, i, above=True).shape[i] == self.g.shape[i] -
1)
def test_sub(self):
for i in range(3):
assert_true(self.g.sub(1, i).shape[i] == 1)
for i in range(3):
assert_true(self.g.sub([1, 2], i).shape[i] == 2)
def test_remove(self):
for i in range(3):
assert_true(self.g.remove(1, i).shape[i] == self.g.shape[i] - 1)
for i in range(3):
assert_true(
self.g.remove([1, 2], i).shape[i] == self.g.shape[i] - 2)
def test_argumentparser(self):
self.g.ArgumentParser()
