[Xplor-nih] Questions about tensor calculation and C++ vs Fortran code

[Charles at Schwieters.org]

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Hello Jie-rong--

> I have some questions about tensor calculation and C++/Fortran code.
> 
> Is there any difference between "calcTensor" in varTensorTools.py and
> "TENSOr" (Sass, 2001) in conventional Xplor-NIH? Are they the same thing?
> 

They are not the same.

> Does the potential energy terms in python modules e.g. NOEPot, RDCPot, still
> call the Fortran code of old X-plor to calculate the structure and penalty
> function?  or these new potential functions are only coded in C++ (e.g.
> NOEPot.cc) and nothing to do with the original Fortran?
> 

They have nothing to do with the Fortran code.

> If the calTensor is called at every cooling cycle to update the alignment
> tensor during simulated annealing, would it be computationally expensive? 
> Since it calculates the tensor "outside" the core and put result back to the
> core to do the structure calculation.  Will it be more efficient if the
> function of calcTensor is in the source code and recompiled, or it doesn't
> matter?

Probably too slow, and also not necessary. It suffices to periodically
recalculate the tensor (not every timestep).

> (I am writing a python helper, which is similar to calcTensor.  Steric
> alignment tensor can be obtained by sampling the structure over an
> isotropically distributed space (The result is the same as PALES multiplied
> by a constant).  The method is computationally expensive, so I am wondering
> if it can be improved.)

Most likely, it can be improved. The first task is to locate
bottlenecks- you might use a Python profiler for this. Once the
bottlenecks are identified, I might be able to give further advice.

best regards--
Charles
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