sisl.io.siesta.gridncSileSiesta

class sisl.io.siesta.gridncSileSiesta(filename, mode='r', lvl=0, access=1, *args, **kwargs)

Bases: SileCDFSiesta

NetCDF real-space grid file

The grid sile will automatically convert the units from Siesta units (Bohr, Ry) to sisl units (Ang, eV) provided the correct extension is present.

Methods

base_directory([relative_to])	Retrieve the base directory of the file, relative to the path relative_to
close()
dir_file([filename, filename_base])	File of the current Sile
iter([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_grid([index, name])	Reads a grid in the current Siesta.grid.nc file
read_lattice()	Returns a Lattice object from a Siesta.grid.nc file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_grid(grid[, spin, nspin])	Write a grid to the grid.nc file
write_lattice(lattice)	Write a supercell to the grid.nc file
base_file	File of the current Sile
file	File of the current Sile
plot	Handles all plotting possibilities for a class

__init__(filename, mode='r', lvl=0, access=1, *args, **kwargs)

Just to pass away the args and kwargs

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

property base_file

File of the current Sile

close()

dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

iter(group=True, dimension=True, variable=True, levels=-1, root=None)

Iterator on all groups, variables and dimensions.

This iterator iterates through all groups, variables and dimensions in the Dataset

The generator sequence will _always_ be:

1. Group

2. Dimensions in group

3. Variables in group

As the dimensions are generated before the variables it is possible to copy groups, dimensions, and then variables such that one always ensures correct dependencies in the generation of a new SileCDF.

Parameters:

• group (bool (True)) – whether the iterator yields Group instances

• dimension (bool (True)) – whether the iterator yields Dimension instances

• variable (bool (True)) – whether the iterator yields Variable instances

• levels (int (-1)) – number of levels to traverse, with respect to root variable, i.e. number of sub-groups this iterator will return.

• root (str (None)) – the base root to start iterating from.

Examples

Script for looping and checking each instance.

>>> for gv in self.iter():
...     if self.isGroup(gv):
...         # is group
...     elif self.isDimension(gv):
...         # is dimension
...     elif self.isVariable(gv):
...         # is variable

plot

Handles all plotting possibilities for a class

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

Parameters:

kwargs – keyword arguments will try and search for the attribute read_<> and call it with the remaining **kwargs as arguments.

read_grid(index=0, name='gridfunc', *args, **kwargs) → Grid

Reads a grid in the current Siesta.grid.nc file

Enables the reading and processing of the grids created by Siesta

Parameters:

• index (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.

• 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

• spin (optional) – same as index argument. spin argument has precedence.

Return type:

Grid

read_lattice() → Lattice

Returns a Lattice object from a Siesta.grid.nc file

Return type:

Lattice

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Parameters:

**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining **kwargs as arguments.

write_grid(grid, spin=0, nspin=None, **kwargs)

Write a grid to the grid.nc file

write_lattice(lattice)

Write a supercell to the grid.nc file