Dear Lammps_users
I have dumped the stress into output file by
"dump 1 all custom 1000 drag.stress sxx syy szz".
But how can I integrate the stress with the atoms' coordinates
and draw the stress distribution on the model directly.
Can VMD do this?
I would appreciate for you suggestions.
Best Regards
Zhenyu Yang
State Key Laboratory of Nonlinear Mechanics (LNM)
Institute of Mechanics, Chinese Academy of Sciences
No.15 Beisihuanxi Road
Beijing 100080, P. R. China
FAX: 010-62579511
[email protected]...
2006-06-28
Yang,
If you mean coloring atoms based on their stress, you can use any
atomistic viewer (like VMD) to do it. Atomeye produces nice output of
property based coloring. A tutorial can be found here:
http://164.107.79.177/Archive/Graphics/A/
Hope this helps,
Arun
Zhenyu Yang wrote:
You probably want to add the x,y,z of the atoms in the dump
custom file so each line has coords and stress. The Pizza.py
tool associated with LAMMPS will let you color atoms
based on other attributes, in this case stress. I presume VMD
can do that as well, but I don't know how you would read
those attributes into VMD ...
Steve
Hi,
I am using VMD as atomic viewer and from my experience I do not think, that you can use it for displaying dynamic atomic properties, such as stress or velocity.
The reason lies in its actual purpose to work on biological molecules, especially proteins.
It only stores the structure of the molecular system, i e. atom type, bonds, .., once for all time steps. For each time step, there are only the atomic positions, that are kept, nothing else. If someone, wanted to display further dynamic data, he had to change quite a lot of the vmd-code itself.
This is for version 1.8.2, but I do not think that things have changed substantially for subsequent versions.
cheers,
Marco
Steve Plimpton wrote:
The way people usually use VMD to overlay additional data on simulation
visualizations is the use the crystalographic temperature column (which
corresponds to the tempFactor column in a PDB file. also known as the B
factor). I'm pretty sure it's not possible with the lammps trajectory
format, so you probably have to convert each frame into a PDB file and
then put the stress information in the Beta column (here's a guide to the
format:
http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html.
You want to use the tempFactor column - columns 61-66) and then in VMD set
it to color by Beta).