[ase-users] help

[Niels Bendtsen Halck]

Hi again

Well you essentially have to do it one atom at a time if you want to construct it only with ase.

I would highly suggest to build the molecule in other software and then load the structure with any ase supported formats. You can see the list here https://wiki.fysik.dtu.dk/ase/ase/io/io.html#ase.io.read

If you insist on using ase you have to build an ATOMS object. 

Here is an example that I have used. You will have to update the atom types and positions.


from ase import Atoms
from ase.visualize import view

system = read('init.traj')

system = Atoms([Atom('Mn', position=(0, 0, 0)),
	            Atom('O', position=(2, 0, 0)),
	            Atom('O', position=(0, 2, 0)),
                Atom('Mn', position=(2, 0, 2)),
                Atom('Ca', position=(3, 2, 0)),
                Atom('O', position=(2, 2, 2)),
                Atom('Mn', position=(0, 2, 2)),
                Atom('O', position=(0, 0, 2)),
], cell=cell, pbc=(0,0,0))

system.center(vacuum=10)


view(system)

Sincerely
Niels Bendtsen Halck
Postdoc
DTU Energy
Bygning 309
2800 Kgs. Lyngby
ntben at dtu.dk
________________________________________
Fra: ase-users-bounces at listserv.fysik.dtu.dk [ase-users-bounces at listserv.fysik.dtu.dk] på vegne af Franck Olivier Ngassam Nyakam via ase-users [ase-users at listserv.fysik.dtu.dk]
Sendt: 8. marts 2017 10:17
Til: ase-users at listserv.fysik.dtu.dk
Emne: [ase-users] help

Hello sir

I would like to build a MnPc system on Ag (111) and have the positions how to construct the MnPc molecule (Mn = manganese; Pc = phthalocianine). How to do it on ase?