Here are the links to the articles:
1. Improving Goldschmidt Division, Square Root...
2. High Speed inverse square root
3. Pseudo Division and Pseudo Mult...
4. digit-recurrent arithmatic
Yeah, its is kindof a grab-bag topically speaking.
The following information is taken from /include/types/nrnb.h:
The four numbers following an inner loop (inl) tell a good deal of information about that loop. The first number (as in inl(1st)(2nd)(3rd)(4th)) tell the Coulomb Type, the second tells the Van der Waals type, the third tells the solvent optimizations being used, and the forth tells the free energy option. The number 0 (zero) in any of these positions stands for no, none, or turned off.
position meaning 1 2 3 4
1st coulomb type normal Reaction field Table
2nd Van der Waals Lennard-Jones Buckingham Table Bham-Table
3rd solvent optimiz. general water water-water
4th free energy Lambda Softcore
here are some educational links (I hope):
1. http://numericalmethods.eng.usf.edu/siteindex.html
2. http://www.amara.com/papers/nbody.html
3. http://www.ap.univie.ac.at/users/ves/cp0102/dx/node107.html
The first is a link to Univ. Southern Florida's engineering page, which contains a good explaination of how to do division, without doing division. The explaination is listed as an example of a "Physical Problem" for CS Engineers in (nonlinear?) Differential Equations (the first topic, not interpolation). The third link is attached to the university of Wien in Germany, so it is probably reliable.
The second is an individual's webpage, and it contains brief explainations for different ways of doing molecular dynamics. Probably not directly useful, but informative.
A short list of key phrases: vectorization, vector implementation, vector extension.
Places to start from:
Craig Hunter's (of NASA) paper on evaluation of PowerMac G4 systems
the FFTW papers
the GROMACS manual
the GROMACS papers
the documentation for the gcc complier concerning vector capabilities
related topic/information:
hpc.sourceforge.net has information about memory and cache useage.
I have posted most of my notes on the GROMACS source that I have been grep'ing around in, in the CVS directory for numerical methods.
Here, hopefully, is a link to it: /cluster/project/numerical-methods/doc/schaejo_gromacs_notes.txt