This directory contains programs or scripts that can be helpful to
process SIESTA output, or to supplement the functionality of the
program.  Some of them are experimental. See the individual
directories for documentation.

Eig2DOS:   Estimation of the Density of States from the .EIG file.
           (by E. Artacho and A. Garcia)

Bands:     Tools for plotting band structures (including "fatbands")

COOP: Generation of COOP/COHP/PDOS curves for chemical analysis.
      Computation of data to generate "fatbands" plots.

Optimizer: General-purpose optimizer. Useful for basis-set and
	   pseudopotential optimization (by A. Garcia)

Projections: Compute projections of electronic structure of a system
	     over the orbitals of a subsystem.

MPI_test:    Tests to help diagonose the interface to MPI.

pseudo-xml:  Converts pseudopotential files in XML format to .psf form.
	     (by J. Junquera and A. Garcia)

test-xml:    Experimental tool to compare two CML files.

pseudo-xml: Conversion of pseudo files in XML format to formatted
	    form.	    

Plrho/plrho: Plots in 3D the electron density and other functions
             calculated by siesta (by Jose M. Soler)

Denchar: Produces 2D and 3D plots of charge and spin density, and of
         wave-functions. Uses the density matrix and basis orbital
         information (by J. Junquera and P. Ordejon).

DensityMatrix: Utilities to process and convert density-matrix files.

Gen-basis : Stand-alone program 'gen-basis' to generate basis sets and
            KB projectors, and 'ioncat' program for extraction of
            information from .ion files.

Contour: grid2d: As Denchar but for any function defined in the 3D
         grid.  grid1d: Extracts a 1D line of data out of the 3D grid.
         Based on the 3D grid (by E. Artacho)

Contrib: Code contributed by Siesta users (expanding collection). See
	 the individual documentation materials.

MD: Some sample scripts for the extraction of some MD information from
    the output file (by A. Garcia)

Vibra: Package to compute phonon frequencies and modes (by P. Ordejon)

Optical: Calculation of optical properties (by D. Sanchez-Portal)

PyAtom: Python scripts for plotting and data extraction (by A. Garcia)

pdosxml: Utility to process the PDOS file (in XML format). (by
	 A. Garcia)

WFS: Utilities for wavefunction-file manipulation

STM/plstm:   Simple program for STM simulations (by P. Ordejon)

STM/ol-stm:  Ordejon-Lorente STM image simulator

Grid: Utilities for the manipulation of grid files.

sies2arc: Converts output coordinates to the arc movie format (by
	  J. Gale)

CMLComp: Tools to use the information contained in the CML file
         produced by the program (by Toby White, Andrew Walker,
         and others)

Macroave: Macroscopic averaging for interfaces and surfaces (by
	  J. Junquera)

SiestaSubroutine: Code and examples of the driving of Siesta by an
                  external agent (by J. Soler and A. Garcia)

Scripting: Experimental scripting modules in Python (by A. Garcia)

VCA: Utilities to help in Virtual-Crystal calculations (by A. Garcia)

MM_Examples: Force-field examples

vpsa2bin: Converts formatted pseudopotential files to unformatted
	  form.

vpsb2asc: Converts unformatted pseudopotential files to formatted
	  form.

Other useful resources:

Directory Tutorials/Bases contains examples and scripts to help
in the generation of basis sets and KB projectors.

