Subprogram outputs

Several SIESTA subprograms produce output files that SiestaStudio can parse and display. You run the subprograms on your cluster; SiestaStudio handles the visualization.

Supported subprograms

tbtrans — transport calculations; SiestaStudio displays the transmission spectrum and related quantities.
vibra — phonon and vibrational modes; frequency-vs-wavevector plots.
denchar — charge density and orbital plots on a real-space grid.
macroave — macroscopic averages of the potential or charge density.
fat — fatband (orbital-projected band structure) analysis.
mprop — material properties extracted from the SIESTA run.

tbtrans transmission

Open <label>.TBT.AVTRANS_<elec1>-<elec2> for the k-averaged transmission, with the conductance and current at a chosen bias and temperature. With k-sampling (more than one TBT.k point) tbtrans also writes the k-resolved <label>.TBT.TRANS_<elec1>-<elec2>. The studio reads it block by block, shows the weighted sum as T(E), and Show each k-point adds the curve of every k-point with its weight.

denchar and STM images

denchar in 3D mode writes .cube files (<label>.RHO.cube, .DRHO.cube, <label>.K<k>.WF.<n>.REAL|IMAG|MOD|PHASE.cube), which open in the volumetric viewer. In 2D mode it writes plane tables, <label>.CON.SCF (charge), .CON.DEL (deformation charge) and <label>.CON.K<k>.WF.<n>.* (wave functions); these open as a 2D map. denchar needs the .PLD and .DIM files that WriteDenchar T writes, the .DM and the species' .ion files. Wave functions also need WriteWaveFunctions T, a WaveFuncKPoints block and WaveFuncKPointsScale in the SIESTA run (without the scale SIESTA writes an empty <label>.selected.WFSX); denchar reads that file as <label>.WFSX. In a workflow, a denchar step adds these flags to the SIESTA step before it and copies the files over, with the wave functions at Γ for the bands you choose in the Denchar panel (1 to 10 by default). Each band gives four files (real, imaginary, modulus, phase), so keep the range small for a large system.

For STM, a SIESTA run with a LocalDensityOfStates block writes <label>.LDOS, which opens like any other grid. plstm turns it into an image: plstm -z <height in bohr> <label>.LDOS writes the constant-height image <label>.LDOS.q.CH.STM (LDOS at the tip), and plstm -i <value> the constant-current image .CC.STM (tip height). Both open as a 2D map, with the value under the pointer shown below the image.

plstm needs an orthogonal cell with c along z, and it scans down from the top of the cell. Keep the slab away from z = 0 (for example, shift it up with an AtomicCoordinatesOrigin block) so that clean vacuum reaches the cell top; otherwise the periodic image of the slab sits at the top and plstm stops with "Surface above box boundary". plstm -H -I <label>.LDOS prints the height and value ranges to choose -z and -i from.

Fat bands

Open a fat <mpr>.<set>.EIGFAT file to see the bands with the weight of that orbital set as the marker size. The file has no Fermi level and no k-point labels, so the first plot uses absolute energies. Two buttons above the plot add more:

Align with .bands file — load the <label>.bands file of the same band calculation. The plot then shows E − E_F, with Γ, X and the other path labels on the k axis. The studio checks that both files have the same k-path and the same eigenvalues, and refuses a .bands file from another run. Clear Relative to E_F to go back to absolute energies.
Add orbital set (.EIGFAT) — add the other sets from the same fat run (for example the Mg and the O 2p sets) to compare them on one plot, one colour per set.

mprop curves

mprop curves open in one plot with a toggle per curve: <mpr>.<curve>.pdos, .coop and .cohp, and the system-wide <label>.alldos, .ados and .intdos. In .intdos the two curves are the integrated DOS (number of electrons up to E) and the integrated band energy.

Importing results

Pull the subprogram output files from the cluster just as you would for main SIESTA output. The studio detects the file type and opens the appropriate viewer automatically.

Running subprograms

SiestaStudio does not run the subprograms for you. You need to run them on your cluster (typically after the main SIESTA run finishes) and then pull the output back.