Hello Gary--
>
> 1.how do you ?write mixed python c /fortran based potentials using pypot?
> Specifically?I wanted to use c for calculating energies and derivatives but
> python for all other?set-up?house keeping etc
Probably the closest example to what you want to do is
python/h3JNCPot.py in recent distributions. Depending on the nature of
the numerical calculations, builtin Xplor-NIH or numpy code might be
fast enough. If not, you'll have to go through swig.
> 2. how can I access the non bonded list from c or fortran and from
> python?
There is no easy way to do this. Our experience is that all nonbond
lists are different- different update frequency, distance cutoff,
etc. We just roll our own when necessary. An example can be found in
xplor/nmrPot/nbTargetPot.cc
> 3. in PyPot based potentials is calcEnergy guaranteed to be called before
> calcEnergyAndDerivs as shown in the example you give in the documentation
>
No. calcEnergy *can* be called separately (for instance, in Monte
Carlo algorithms) so that expensive gradient calculations aren't made,
calcEnergyAndDerivs must return an energy. One option is for
calcEnergyAndDerivs to call calcEnergy.
I hope this helps--
Charles
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Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
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