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
-- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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