[gmx-developers] lookup table in invsqrt algorithm

David van der Spoel spoel at xray.bmc.uu.se
Wed May 18 14:12:21 CEST 2011

On 2011-05-18 07.43, Haiqing Zhao wrote:
> Hi,
> Yes, I have studied that part for several days, and understand the skills Gromacs use in designing the two tables. But how to produce the Lookup table. I still did not get any idea.
> Thanks.
> Haiqing
I'm glad to see that there are people who want to understand the gory 
details as well! The program to generate the table seems to have 
disappeared from the gromacs distribution, in older distro's, e.g. 3.0.5 
there was a program src/gmxlib/mlinl_invsqrt.c. The original author of 
this program, Alfons Sijbers, left the project in 1992. I guess there is 
a more modern version of this though.

Maybe Erik or Berk has a version?

> On May 17, 2011, at 11:51 PM, Mark Abraham wrote:
>> On 18/05/2011 1:30 PM, Haiqing Zhao wrote:
>>> Hello, all,
>>> Does anybody know gmx_software_invsqrt work? I mean the algorithm. I found the code is in "vec.h" in "include" folder. But I have no idea of how lookup table is produced. There are two: exptab, and fracttab. It uses the space very well.
>>> I hope you could give me some hint.
>> See manual appendix B.3
>> Mark
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-request at gromacs.org.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

More information about the gromacs.org_gmx-developers mailing list