[ase-users] Resort atoms object by atom number

[Eric Hermes]

On Fri, 2017-12-08 at 19:47 +0100, fabian via ase-users wrote:
> Dear all,
> I read a POSCAR file into an atoms object via
> atoms = read("POSCAR")
> now i want to resort the atoms object such that the atom with the
> Number n_atom is moved from its postion to the index 0 
> (1 if not counted the pythonic way), such that it is later writen as
> the first entry  into the atoms object. 
> later i want to write the object via:
> write('POSCAR', atoms, vasp5=True, sort=False,
> direct=True,long_format=True, format='vasp')
> and have the entry corresponding to n_atom as the first Atom in the
> POSCAR file. I found a dirty workaround with temp files but
> this means i have to convert each initial structure to the right
> format . Else i create wrong files.
> Is this possible within ASE?
> On a side not if i pop an atom via:
> atoms.pop( n_atom)
> 
> is n_atom defined the pythonic way and starting at 0?

To start by answering your last question: yes, everything in ASE is 0-
indexed. Note that this is not only the Pythonic way, it is a common
standard used by most languages with some notable exceptions (Fortran,
Julia, and R probably being the most relevant).

In fact, you should be able to use Atoms.pop() to do exactly what you
want. Try the following:

atoms = atoms.pop(n_atom) + atoms

One other thing is that when ASE sorts VASP POSCAR files, the first
atom will never change place, so sort=False is not completely necessary
(you can still use it if you want to though).

Eric

> 
> Al the best
> fabian
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