[ase-users] Structure Optimization

[Niels Theis Bendtsen]

Could you provide the traj file so we can see what happens?

Sincerely
Niels Theis Bendtsen
Ph.d.-studerende
FYS-CAMD
DTU Fysik
Bygning 307
2800 Kgs. Lyngby
Direkte telefon 45253177
ntben at fysik.dtu.dk
www.fysik.dtu.dk



________________________________________
Fra: ase-users-bounces at listserv.fysik.dtu.dk [ase-users-bounces at listserv.fysik.dtu.dk] på vegne af Sungsik Kim [sungsik312 at gmail.com]
Sendt: 10. april 2013 15:21
Til: ase-users
Emne: [ase-users] Structure Optimization

Hello,

I am Sungsik kim.

I am studying dissociative adsorption of methane on platinum.

I have a problem with structure optimization.

When I add CH4 on the slab, positions of four H atoms are changed after

optimization.

Is there any way to fix the positions of four hydrogen atoms in methane

on the slab?

Even though I used fixbondlength and fixinternals, hydrogens are not fixed in

methane.

#################################################################

from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.io<http://ase.io> import write
import numpy as np
from ase.io<http://ase.io> import read
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize import QuasiNewton
from ase.visualize import view
from ase.optimize import BFGS
from ase.lattice.surface import fcc100, add_adsorbate
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.data.molecules import molecule
from ase.io<http://ase.io> import read
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize import BFGS
import numpy as np
import matplotlib.pylab as plt
from ase.calculators.jacapo import *
from ase.vibrations import Vibrations
from ase.optimize import FIRE
from ase.constraints import FixBondLength
from ase.constraints import FixBondLengths
# Definition of Molecules
O2=molecule('O2')
CH3=molecule('CH3')
CH3.set_tags((1,2,2,2))
CH4=molecule('CH4')
CH4.set_tags((3,4,4,4,4))


# Initial State
slab = fcc100('Pt', size=(2, 2, 1))
add_adsorbate(slab, CH4, 3, (1.4,1.4))
mask = [atom.symbol ==  'Pt'  for atom in slab]
slab.set_constraint(FixAtoms(mask=mask))
view(slab)
calc1 = Jacapo('inita.nc<http://inita.nc>',
          xc='PBE',
          pw=350,
              kpts=(2,2,1),
              atoms=slab)
qn = QuasiNewton(slab, trajectory='inita.traj')
qn.run(fmax=0.05)
print slab.get_potential_energy()

##############################################################

Thank you for your time.

Sincerely

Sungsik