Analysis tools

This is a repository (under construction) of information with pointers on how to analyze and plot particular items of data generated by Siesta.

Note

Some of the tools mentioned in this how-to are covered in this excellent slide presentation by Andrei Postnikov.

Electronic Structure

  • Band structures

    Use the gnubands program (with the modern options), plus gnuplot. See examples here.

  • Fermi surfaces

    For this, the eig2bxsf tool can be used.

  • Charge density

    There are three (or more, with sisl) options to plot magnitudes that reside on the real-space grid (densities, potentials, LDOS, etc):

    • .RHO file with g2c_ng (former grid2cube)

    • Denchar

    • .RHO file with rho2xsf (or rho2vesta)

    • sisl

  • Wavefunctions

    Using denchar (See the manual here.)

  • Mulliken charges

    There is no standard way to plot these. Suggestions are welcome for visualization tools.

  • (p)DOS

    Two ways:

    • Using the standard block in the fdf file and post-processing the .PDOS file.

    • Generating ‘COOP’ output and using the mprop program in PDOS mode. (More options, more file space needed (but filters in the fdf can be used to output only interesting bands). Re-use docs and examples there.

  • fat-bands

    Using the ‘fat’ program in the COOP suite. See this tutorial`

  • COOP/COHP

    Using the ‘mprop’ program in the COOP suite. See this tutorial`

  • Spin texture

    Using the ‘spin_texture’ program in the COOP suite. See this tutorial`

  • Spins on atoms (e.g., with xsf files with coordinates plus vectors)

    Getting the spins on the atoms can be done by post-processing the Mulliken charges, and maybe by special output sections generated by specific options.

Forces on atoms, normal modes, etc

  • Forces on atoms