ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

y doing:
$ ag -b si001+h2.traj -g i,e,e+ekin
ASE Manual, Release 3.6.1.2828
The -b option turns on plotting of bonds between the atoms. Check that the total energy is a conserved quantity
in this microcanonical simulation.
You can also use VMD to visualize the trajectory. To do this, you need a .xyz file that you can write using ag:
$ ag si001+h2.traj -o si.xyz -r 2,2,1
Then simply open the file using VMD:
$ vmd si.xyz
and set Graphics/Representations from the main menu in order to get a nice picture.
You can also try to repeat the simulation with a different dynamics. For instance you can model a canonical
ensemble with the Langevin dynamics, which couples the system to a heat bath:
dyn = Langevin(atoms, 1 * fs, kB * 300, 0.002, trajectory=traj)
6.5 Videos
The following video tutorials are available:
• Overview and installation of ASE, by Anthony Goodrow (duration: ~5min 30sec; size: 26 MB) - en:
6.5. Videos 51