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exercises:2017_ethz_mmm:pythonmd

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The instructions for loading the appropriate modules in .bashrc:
> cd
> nano .bashrc
module load new gcc/4.8.2 python/2.7.12 # include this line in the file
> . .bashrc

To visualize an xyz file:

> ipython

In [1]: from ase.io import read
In [2]: from ase.visualize import view
In [3]: s=read("file.xyz")
In [4]: view(s)

At this point you can rotate the structure, select an atom, then two (you get the distance) or three (you get the angle)…

 STAMI 
exercises/2017_ethz_mmm/pythonmd.1488471295.txt.gz · Last modified: 2017/03/02 16:14 by dpasserone