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
