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, base]) 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, base]) FDF-input file
outSileSiesta(filename[, mode, comment]) Output file
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
dmSileSiesta(filename[, mode]) Density matrix file
hsxSileSiesta(filename[, mode]) Hamiltonian and overlap matrix file
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])
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])
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

Additionally the PHtrans code also has these files

phtncSileTBtrans(filename[, mode, lvl, access]) PHtrans file object
phtsencSileTBtrans(filename[, mode, lvl, access]) PHtrans file object
phtavncSileTBtrans(filename[, mode, lvl, access]) PHtrans file object

VASP (vasp)

carSileVASP(filename[, mode, comment]) CAR file object This file-object handles both POSCAR and CONTCAR files
doscarSileVASP(filename[, mode, comment]) VASP DOS output
poscarSileVASP(filename[, mode, comment])
contcarSileVASP(filename[, mode, comment])
eigenvalSileVASP(filename[, mode, comment]) VASP eigenvalue output

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