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Quick introduction


AG can read the following types of files:

  • ASE trajectory files
  • XYZ files
  • GPAW text files and restart files
  • Dacapo text and nc-files
  • CUBE files
  • VNL files
$ ag N2Fe110-path.traj

Selecting part of a trajectory

A Python-like syntax for selecting a subset of configurations can be used. Instead of the Python syntax list[start:stop:step], you use filaname@start:stop:step

$ ag x.traj@0:10:1  # first 10 images
$ ag x.traj@0:10    # first 10 images
$ ag x.traj@:10     # first 10 images
$ ag x.traj@-10:    # last 10 images
$ ag x.traj@0       # first image
$ ag x.traj@-1      # last image
$ ag x.traj@::2     # every second image

If you want to select the same range from many files, the you can use the -n or --image-number option:

$ ag -n -1 *.traj   # last image from all files
$ ag -n 0 *.traj    # first image from all files


Type ag -h for a description of all command line options.

Writing files

$ ag -n -1 a*.traj -o new.traj

Possible formats are: traj, xyz, eps and png.

Plotting data

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 -p "d(0,5),e-E[0]" x.traj > x.dat  # No GUI, write data to stdout

Interactive use

AG can also be launched directly from a Python script or interactive session:

>>> from ase import *
>>> view(atoms)

NEB and ANEB calculations

Use Tools -> NEB to plot energy barrier.

$ ag --aneb *.traj
$ ag --interpolate 3 initial.xyz final.xyz -o interpolated_path.traj

ase2: GUI (last edited 2010-10-20 09:11:15 by localhost)