how to get the initial configuration in dimer method?

kxshan · Post by **kxshan** » Mon Oct 29, 2007 12:20 pm

I read your paper about the dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives. I have built a cluster, would you like to tell me how to generate 1000 random configurations around the minimum.
thanks

Post by **graeme** » Mon Oct 29, 2007 2:04 pm

I would recommend using Lijun Xu's akmc.pl script for generating initial positions for dimer searches. It will also submit and check running jobs for you, abort bad jobs, minimize from saddles that you find, and step forward in time using KMC.

Information about this script is at:
http://theory.cm.utexas.edu/vtsttools/akmc/

This does, however, require quite a bit of computational time, and only makes sense if you can run on many processors. With your new cluster, though, it sounds like you are all set.

kxshan · Post by **kxshan** » Tue Oct 30, 2007 1:09 am

thank you for your help

kxshan · Post by **kxshan** » Thu Dec 27, 2007 6:46 am

dear sir
i can not understand the usage of akmc . Could you give me details of akmc?
my email: kxshan@mail.ustc.edu.cn

Post by **graeme** » Sat Dec 29, 2007 3:47 pm

The adaptive kinetic Monte Carlo script is more complicated than our other scripts. A brief description is available at:
http://theory.cm.utexas.edu/vtsttools/akmc/

Lijun Xu, who wrote the script, has been working on a manual (which may be available). He can also answer specific question.

kxshan · Post by **kxshan** » Mon Dec 31, 2007 1:31 am

thank you very much