Input/Output (sisl.io)

Available files for reading/writing

sisl handles a large variety of input/output files from a large selection of DFT software and other post-processing tools.

Since sisl may be used with many other packages all files are name siles to distinguish them from files from other packages.

Basic IO methods/classes

add_sile(suffix, cls[, case, gzip])

Add files to the global lookup table

get_sile(file, *args, **kwargs)

Retrieve an object from the global lookup table via filename and the extension

SileError(value[, obj])

Define an error object related to the Sile objects

External code in/out put supported

List the relevant codes that sisl can interact with. If there are files you think are missing, please create an issue here.

Generic files

Files not specificly related to any code.

tableSile(filename[, mode, comment])

ASCII tabular formatted data

xyzSile(filename[, mode, comment])

XYZ file object

pdbSile(filename[, mode, comment])

PDB file object

cubeSile(filename[, mode, comment])

CUBE file object

moldenSile(filename[, mode, comment])

Molden file object

xsfSile(filename[, mode, comment])

XSF file for XCrySDen

BigDFT (bigdft)

asciiSileBigDFT(filename[, mode, comment])

ASCII file object for BigDFT

GULP (gulp)

gotSileGULP(filename[, mode, comment])

GULP output file object

fcSileGULP(filename[, mode, comment])

GULP output file object

OpenMX (openmx)

omxSileOpenMX(filename[, mode, comment])

OpenMX-input file

ScaleUp (scaleup)

orboccSileScaleUp(filename[, mode, comment])

orbocc file object for ScaleUp

refSileScaleUp(filename[, mode, comment])

REF file object for ScaleUp

rhamSileScaleUp(filename[, mode, comment])

rham file object for ScaleUp

Siesta (siesta)

fdfSileSiesta(filename[, mode, comment])

FDF-input file

outSileSiesta(filename[, mode, comment])

Output file from Siesta

xvSileSiesta(filename[, mode, comment])

Geometry file

bandsSileSiesta(filename[, mode, comment])

Bandstructure information

eigSileSiesta(filename[, mode, comment])

Eigenvalues as calculated in the SCF loop, easy plots using sdata

pdosSileSiesta(filename[, mode, comment])

Projected DOS file with orbital information

gridSileSiesta(filename[, mode])

Binary real-space grid file

gridncSileSiesta(filename[, mode, lvl, access])

NetCDF real-space grid file

onlysSileSiesta(filename[, mode])

Geometry and overlap matrix

dmSileSiesta(filename[, mode])

Density matrix file

hsxSileSiesta(filename[, mode])

Hamiltonian and overlap matrix file

wfsxSileSiesta(filename[, mode])

Binary WFSX file reader for Siesta

ncSileSiesta(filename[, mode, lvl, access])

Generic NetCDF output file containing a large variety of information

ionxmlSileSiesta(filename[, mode, comment])

Basis set information in xml format

ionncSileSiesta(filename[, mode, lvl, access])

Basis set information in NetCDF files

orbindxSileSiesta(filename[, mode, comment])

Orbital information file

faSileSiesta(filename[, mode, comment])

Forces file

fcSileSiesta(filename[, mode, comment])

Force constant file

kpSileSiesta(filename[, mode, comment])

k-points file in 1/Bohr units

rkpSileSiesta(filename[, mode, comment])

Special k-point file with units in reciprocal lattice vectors

TranSiesta (siesta)

tshsSileSiesta(filename[, mode])

Geometry, Hamiltonian and overlap matrix file

tsdeSileSiesta(filename[, mode])

Non-equilibrium density matrix and energy density matrix file

tsgfSileSiesta(filename[, mode])

Surface Green function file containing, Hamiltonian, overlap matrix and self-energies

tsvncSileSiesta(filename[, mode, lvl, access])

TranSiesta potential input Grid file object

TBtrans (tbtrans)

tbtncSileTBtrans(filename[, mode, lvl, access])

TBtrans output file object

deltancSileTBtrans(filename[, mode, lvl, access])

TBtrans \(\delta\) file object

tbtgfSileTBtrans(filename[, mode])

Surface Green function file containing, Hamiltonian, overlap matrix and self-energies

tbtsencSileTBtrans(filename[, mode, lvl, access])

TBtrans self-energy file object with downfolded self-energies to the device region

tbtavncSileTBtrans(filename[, mode, lvl, access])

TBtrans average file object

tbtprojncSileTBtrans(filename[, mode, lvl, …])

TBtrans projection file object

Additionally the PHtrans code also has these files

phtncSilePHtrans(filename[, mode, lvl, access])

PHtrans file object

phtsencSilePHtrans(filename[, mode, lvl, access])

PHtrans file object

phtavncSilePHtrans(filename[, mode, lvl, access])

PHtrans file object

phtprojncSilePHtrans(filename[, mode, lvl, …])

PHtrans projection file object

VASP (vasp)

carSileVASP(filename[, mode, comment])

*CAR VASP files for defining geomtries

doscarSileVASP(filename[, mode, comment])

Density of states output

eigenvalSileVASP(filename[, mode, comment])

Kohn-Sham eigenvalues

chgSileVASP(filename[, mode, comment])

Charge density plus geometry

locpotSileVASP(filename[, mode, comment])

Electrostatic (or total) potential plus geometry

Wannier90 (wannier90)

winSileWannier90(filename[, mode, comment])

Wannier seedname input file object

Low level methods/classes

Classes and methods generically only used internally. If you wish to create your own Sile you should inherit either of Sile (ASCII), SileCDF (NetCDF) or SileBin (binary), then subsequently add it using add_sile which enables its generic use in all routines etc.

get_siles([attrs])

Retrieve all files with specific attributes or methods

get_sile_class(filename, *args, **kwargs)

Retrieve a class from the global lookup table via filename and the extension

BaseSile()

Base class for all sisl files

Sile(filename[, mode, comment])

Base class for ASCII files

SileCDF(filename[, mode, lvl, access])

Creates/Opens a SileCDF

SileBin(filename[, mode])

Creates/Opens a SileBin