Best way to read forces and positions and energies into Atomic Simulation Environment (ASE)?

Question

My current procedure is to create a .xyz file out of my MD run for a crystal structure. I can read the energy and also each atomic position. But I want to add forces. If I add forces as the additional three columns for each atom, ASE seems to ignore this. ASE considers only the first three columns per atom which are the positions.

What's the best way to read positions and forces into ASE?

I'm working with FHI aims and I've just done an MD run. I don't think this is as important because the object to read FHI aims with ASE seems to be deprecated.

Answer 1

ASE should be able to read forces from the additional columns. Here is an example of an .xyz file which contains forces.

2
Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3:forces:R:3:magmoms:R:1 energy=-6.801137982077364 dipole="-1.3543798178593251e-15 -1.5609399349163789e-15 6.566746345129899e-16" magmom=0.0 pbc="F F F"
H        3.00000000       3.00000000       2.62674398      -0.00000000      -0.00000000      -0.00053835       0.00000000
H        3.00000000       3.00000000       3.37325602      -0.00000000      -0.00000000       0.00053835       0.00000000

For ASE to read it with forces, you can do

>>> import ase.io
>>> atoms = ase.io.read('h2.xyz')
>>> atoms.get_forces()
array([[-0.        , -0.        , -0.00053835],
       [-0.        , -0.        ,  0.00053835]])
>>> from ase import __version__
>>> __version__
'3.22.0b1'

I hope it helps. If not, then I suggest to post a sample of your xyz file to see if there is a way to make it compatible.