ase/quippy interoperability I/O issue

[jameskermode]

Reported by Noam Bernstein:

If you convert from ase to quippy and back, the info field is not written in the extxyz:

cat t.py

import ase, ase.io, sys, quippy

at1 = ase.io.read("t.extxyz", 0)

at1.info['test'] = "bob"

print "print ase.Atoms with ase.io.write"
ase.io.write(sys.stdout, at1, format='extxyz')

at1q = quippy.Atoms(at1)
print "convert ase.Atoms to quippy.Atoms, print with ase.io.write"
ase.io.write(sys.stdout, at1q, format='extxyz')

at1 = ase.Atoms(at1q)

print "convert ase.Atoms to quippy.Atoms, convert back, print with ase.io.write"
ase.io.write(sys.stdout, at1, format='extxyz')

python t.py

ase.Atoms with ase.io.write
2
Lattice="2.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 2.0" Properties=species:S:1:pos:R:3:Z:I:1 test=bob pbc="T T T"
Si      0.00000000       0.00000000       9.00000000       14 
Si      1.00000000       1.00000000       1.00000000       14 
convert ase.Atoms to quippy.Atoms, print with ase.io.write
2
Lattice="2.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 2.0" Properties=species:S:1:pos:R:3:Z:I:1 test=bob pbc="T T T"
Si      0.00000000       0.00000000       9.00000000       14 
Si      1.00000000       1.00000000       1.00000000       14 
convert ase.Atoms to quippy.Atoms, convert back, print with ase.io.write
2
Lattice="2.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 2.0" Properties=species:S:1:pos:R:3:Z:I:1 pbc="T T T"
Si      0.00000000       0.00000000       9.00000000       14 
Si      1.00000000       1.00000000       1.00000000       14```

[jameskermode]

This turns out to be a bug in the ase.Atoms constructor which ignores the info attribute when copying from an existing Atoms object. Patch submitted to ASE developers.

[jameskermode]

Fixed in ASE in commit 4470:
https://trac.fysik.dtu.dk/projects/ase/changeset/4470/trunk/ase