VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jun 28 2006 - 05:46:21 CDT

On Wed, 28 Jun 2006, Zhenyu Yang wrote:

ZY> Dear VMD users
ZY>
ZY> If I have the atom coordinate file and the stress file
ZY> how to color the atoms according to stress.
ZY> All the output files are dumped in LAMMPS.

the general procedure to color atoms by a property that is not
directly supported by VMD, is to read the data yourself and
store it in the 'user' field and then use the 'User' coloring
method. please see:

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3
and
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect4

in the first case the user data is directly calculated from the
trajectory and stored in the user field. in the second it is read
from a file but used to dynamically change a non per-frame property.
now if you would implement a reader as in the second example
and then store the data into the user field as in the first example,
should get what you desire.

happy VMDing,
    axel.

ZY>
ZY> Would you please help me out on this problem.
ZY>
ZY>
ZY> 　　　　　　　
ZY> 　Best Regards
ZY>
ZY> 　Zhenyu Yang
ZY> State Key Laboratory of Nonlinear Mechanics (LNM)
ZY> Institute of Mechanics, Chinese Academy of Sciences
ZY> No.15 Beisihuanxi Road
ZY> Beijing 100080, P. R. China
ZY> FAX: 010-62579511
ZY> 　yangzy_at_lnm.imech.ac.cn
ZY> 　2006-06-28
ZY> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.