ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
Writing files
$ ag -n -1 a*.traj -o new.traj
Possible formats are: traj, xyz, cube, pdb, eps, png, and pov. For details, see the io module documentation.
Interactive use
The ag program can also be launched directly from a Python script or interactive session:
>>> from ase import *
>>> atoms = ...
>>> view(atoms)
or
>>> view(atoms, repeat=(3, 3, 2))
or, to keep changes to your atoms:
>>> atoms.edit()
NEB calculations
Use Tools → NEB to plot energy barrier.
$ ag --interpolate 3 initial.xyz final.xyz -o interpolated_path.traj
Plotting data from the command line
Plot the energy relative to the energy of the first image as a function of the distance between atom 0 and 5:
$ ag -g "d(0,5),e-E[0]" x.traj
$ ag -t -g "d(0,5),e-E[0]" x.traj > x.dat # No GUI, write data to stdout
The symbols are the same as used in the plotting data function.
Defaults for ag
Using a file ~/.ase/gui.py, certain defaults can be set. If it exists, this file is executed after initializing the
variables and colours normally used in ag. One can change the default graphs that are plotted, and the default radii
for displaying specific atoms. This example will display the energy evolution and the maximal force in a graph
and also display Cu atoms (Z=29) with a radius of 1.6 Angstrom.
gui_default_settings[’gui_graphs_string’] = "i, e - min(E), fmax"
gui_default_settings[’covalent_radii’] = [[29,1.6]]
High contrast settings for ag
In revision 2600 or later, it is possible to change the foreground and background colors used to draw the atoms,
for instance to draw white graphics on a black background. This can be done in ~/.ase/gui.py.
gui_default_settings[’gui_foreground_color’] = ’#ffffff’ #white
gui_default_settings[’gui_background_color’] = ’#000000’ #black
74 Chapter 7. Documentation for modules in ASE