creating DynamicalSystem from Atoms resets masses about quip

[noambernstein]

OK - I now understand where this is happening, but not why. For reasons that I don't understand, the second statement in the sequence

    ds = DynamicalSystem(at)
    print ds.atoms.mass

triggers a call to

    quippy/atoms.py:Atoms.__init__

where, around line 415,

    self.set_atoms(self.z)

is called. This call, I believe, is the one that overrides the mass property.

I don't think I understand the logic of atoms.py enough to figure out the right way to fix this, but maybe someone else does?

[jameskermode]

Should now be fixed. I've added a new test to catch any regressions.

If you are interested in why it was the print statement that triggered the change, this is because the Python Atoms object that wraps ds.atoms is only constructed when first accessed. This is what leads to the call to Atoms.__init__() which then calls set_atoms(). I've changed it to pass the current mass along, but it would be better to avoid reinitialising if all we are doing is construcing a wrapper for an existing Atoms.