sisl.io.siesta.siesta module¶
Sile object for reading/writing SIESTA binary files
-
class
sisl.io.siesta.siesta.
ncSileSiesta
(filename, mode='r', lvl=0, access=1, _open=True)[source]¶ Bases:
sisl.io.siesta.sile.SileCDFSIESTA
SIESTA file object
Attributes
file
Filename of the current Sile
Methods
ArgumentParser
(*args, **kwargs)Returns the arguments that is available for this Sile ArgumentParser_out
([parser])Appends additional arguments based on the output of the file grids
()Return a list of available grids in this file. isDataset
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisDimension
(obj)Return true if obj
is an instance of the NetCDF4Dimension
typeisGroup
(obj)Return true if obj
is an instance of the NetCDF4Group
typeisRoot
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisVariable
(obj)Return true if obj
is an instance of the NetCDF4Variable
typeiter
([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_es
(**kwargs)Returns a tight-binding model from the underlying NetCDF file read_geom
()Returns Geometry object from a SIESTA.nc file read_grid
(name[, idx])Reads a grid in the current SIESTA.nc file read_sc
()Returns a SuperCell object from a SIESTA.nc file write
(*args, **kwargs)Generic write method which should be overloaded in child-classes write_es
(ham, **kwargs)Writes Hamiltonian model to file write_geom
(geom)Creates the NetCDF file and writes the geometry information Creates/Opens a SileCDF
Opens a SileCDF with
mode
and compression levellvl
. Ifmode
is in read-mode (r) the compression level is ignored.The final
access
parameter sets how the file should be open and subsequently accessed.- means direct file access for every variable read
- means stores certain variables in the object.
Attributes
file
Filename of the current Sile
Methods
ArgumentParser
(*args, **kwargs)Returns the arguments that is available for this Sile ArgumentParser_out
([parser])Appends additional arguments based on the output of the file grids
()Return a list of available grids in this file. isDataset
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisDimension
(obj)Return true if obj
is an instance of the NetCDF4Dimension
typeisGroup
(obj)Return true if obj
is an instance of the NetCDF4Group
typeisRoot
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisVariable
(obj)Return true if obj
is an instance of the NetCDF4Variable
typeiter
([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_es
(**kwargs)Returns a tight-binding model from the underlying NetCDF file read_geom
()Returns Geometry object from a SIESTA.nc file read_grid
(name[, idx])Reads a grid in the current SIESTA.nc file read_sc
()Returns a SuperCell object from a SIESTA.nc file write
(*args, **kwargs)Generic write method which should be overloaded in child-classes write_es
(ham, **kwargs)Writes Hamiltonian model to file write_geom
(geom)Creates the NetCDF file and writes the geometry information -
read_geom
()[source]¶ Returns Geometry object from a SIESTA.nc file
NOTE: Interaction range of the Atoms are currently not read.
-
read_grid
(name, idx=0)[source]¶ Reads a grid in the current SIESTA.nc file
Enables the reading and processing of the grids created by SIESTA
-
write_es
(ham, **kwargs)[source]¶ Writes Hamiltonian model to file
Parameters: ham :
Hamiltonian
modelthe model to be saved in the NC file
Ef : double=0
the Fermi level of the electronic structure (in eV)