Example basis optimization for the water molecule.
Global soft-confinement parameters.

TEMPLATE and VARS define the optimization problem. Be careful to match
the names that you use in the TEMPLATE (without leading '$') with
those in the VARS file. DO NOT leave any line blank in VARS (not even
at the end).

Look in PARAMS to set the appropriate values of the parameters which
influence the Simplex process (it uses a two-level approach, with
amoeba-like iterations followed by periodic restarts with new
simplex hyper-tetrahedra of progressively smaller sizes. The stopping
criteria are a fractional energy tolerance (compared to the differences
between the highest and lowest energies of the vertices) and a minimum
fractional size for the hyper-tetrahedron.

The run_script.sh script simply drives Siesta to perform the calculations.
You need at least siesta-2.1.46.

To run the optimization, simple execute ../../simplex from this
directory.

(You might want to put all this in a queuing-system script...)
