[ase-users] relaxation problem in the cluster model

[Tao Jiang]

Dear Hayat,



On Mar 2, 2011, at 11:24 PM, hayat hocine wrote:

> Dear ESA users mailing list
> I want to fix three gold atoms and relax the copper atom (Cu) in the
> CuAu3 cluster.
> ------------ the script
> 
> #!/usr/bin/env python
> from ase import *
> from ase.calculators.jacapo import *
> from ase.lattice.surface import *
> from ase.constraints import FixAtoms
> 
> import numpy as np
> 
> CuAu3 = Atoms([Atom('Au',[2.259749,3.880966,1.845724]),
>             Atom('Au',[3.508997,1.692649,1.878040]),
>             Atom('Au',[0.989053,1.704892,1.866603]),
>             Atom('Cu',[2.087748,2.462808,3.699057])],
>            cell=(8,8,8))
> CuAu3.center()
> 
> mask = FixAtoms ([True,True,True,False])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mask=FixAtoms(mask=[True,True,True,False])

This should work.

> CuAu3.set_constraint(mask)
> 
> calc = Jacapo('CuAu3-relax.nc',
>               pw = 350,
>               ft = 0.01,
>               atoms = CuAu3)
> qn = QuasiNewton (CuAu3, trajectory='CuAu3-relax.traj')
> qn.run()
> 
> view(CuAu3)
> 
> E3 = CuAu3.get_potential_energy()
> print E3
> ---------------------
> 
> Cordially
> 
> Hocine hayat
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