sisl.io.siesta.ionncSileSiesta

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

Bases: SileCDFSiesta

Basis set information in NetCDF files

Note that the ion.nc files are equivalent to the ion.xml files.

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_basis()

Returns data associated with the ion.xml file

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

base_file

File of the current Sile

file

File of the current Sile

__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
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_basis()[source]

Returns data associated with the ion.xml file

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.