Hello,
How can I visualize LAMMPS results showing the bond between chains of polymers.
Regards,
Leyla
Hello, Layla:
This has to be done with an external package, such as pizza.py (available from the LAMMPS website), VMD, or PyMol.
hi,
another possibility is to write a custom converter to crunch dumps and data files to the vtk format. with paraview you then have all the possibilites for visualization and other post processing.
best,
nikita
You can also use the dump image command to produce
JPG snapshots of your system, which can include bonds.
Steve
Dear Nikita
These two programs I know about which are popular for visualizing
LAMMPS trajectories:
-VMD (& topotools)
-atomeye
---------- VMD+topotools --------
I attached some instructions for using topotools and VMD to
visualize LAMMPS data files and trajectories. It works fine as long
as the number of particles is a constant, and as long as you don't
need to show bonds breaking and forming during the simulation.
(A longer version of this explanation is located in section 4.3 and
appendix C of the moltemplate manual downloadable at
http://www.moltemplate.org/doc/)
The official topotools documentation is located here:
https://sites.google.com/site/akohlmey/software/topotools/topotools---documentation
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---introduction
---------- AtomEye --------
Some instructions and links for AtomEye are below:
https://icme.hpc.msstate.edu/mediawiki/index.php/Making_Atomistic_Movies_using_AtomEye
http://li.mit.edu/Archive/Graphics/A/
AtomEye was used to make this movie:
https://icme.hpc.msstate.edu/mediawiki/index.php/File:Al_comp_108k2.gif
Cheers!
Andrew
README_visualize.txt (2.85 KB)