[gpaw-users] GPAW versions

[Poul Georg Moses]

  On 11/12/10 6:55 AM, Jens Jørgen Mortensen wrote:
> On Fri, 2010-11-12 at 15:42 +0100, Christian Glinsvad wrote:
>> Jens Jørgen Mortensen wrote:
>>>> On Wed, 2010-11-10 at 19:34 -0800, Monica Garcia Mota wrote:
>>>> Hi,
>>>>
>>>> I have calculated oxygen adsorption energy on TiO2 using two
>>>> different GPAW versions: 0.7.6383 and 0.7.2.6974. The absolute
>>>> energy values for TiO2 surface and O-TiO2 are shifted up 0.37 eV
>>>> with the new GPAW version.
>>>>
>>>> I’m using Dipole correction in my calculations. Does it work in
>>>> both GPAW versions in the same way?
>>>>
>>>> Thanks,
>>>>
>>>> Monica Garcia
>> There's no difference in the way the dipole correction is implemented
>> between revision 6383 and 6974, as far as I can tell, nor did we fix any
>> major bugs. We did however do a bit of restructuring:
>> 6383:6974 diff:
>> https://trac.fysik.dtu.dk/projects/gpaw/changeset?new=trunk%406974&old=trunk%406383
>> 6383:6974 timeline:
>> https://trac.fysik.dtu.dk/projects/gpaw/timeline?from=08%2F13%2F10&daysback=112
>>
>>> On Thu, 2010-11-11 at 09:02 +0100, Jens Jørgen Mortensen wrote:
>>>
>>> Thanks, I got your text files and it does look very strange. I'll see
>>> if I can figure out what the problem is.
>>>
>>> The text files didn't make it to the mailing list because they were
>>> too big, but I have them on casimir in /tmp, so those of you in
>>> Lyngby can find them there.
>>>
>>> Jens Jørgen
>> I looked through them and did a side-by-side comparison (jens: there are
>> 4 files matching /tmp/O*.txt so I assume you meant the two largest?).
> No.  You should compare the last configuration of O-TiO2v072-DP.txt with
> the configuration in O-TiO2v076-DP.txt.  The configurations are
> identical, but give different energies.
>
> JJ
>
I think there must be some link to the dipole correction. I did a test 
for a different system not using the dipole correction and find no 
difference in energy. Monica also finds no difference in total energies 
when not using the dipole correction (Correct me if I am wrong Monica).

I have noticed that the poisson solver changes settings when the dipole 
correction is included. Could it be that something has been changed in 
the  Poisson solver between versions?

Cheers,

Poul Georg


>>   It
>> appears to me that you're getting slightly different geometries during
>> the QN relaxation and you probably just need to tighten your convergence
>> criteria as 'density' and 'energy' have influence on force evaluation.
>>
>> Additionally, it strikes me that you've run these with quite different
>> parallelization options, which may explain the difference in "entropy"
>> that led to the two calculations to diverge a bit.
In my world 0.5 eV does not fall within the range of "a bit". To me this 
is quite puzzling.

>> It's also curious to me that the forces at the end of the relaxation are
>> quite large for the atoms I assume are fixed, and there are quite many
>> of them. Just be warned that atom fixation can lead to an oblong minima
>> in the potential energy landscape and therefor also convergence issues.
>>
>> Regards
>> Christian Glinsvad
>>
>>>> Here is my script:
>>>>
>>>> import os,sys
>>>> import numpy as np
>>>> from math import *
>>>> from gpaw import GPAW
>>>> from ase import Atoms
>>>> from ase import Atom
>>>> from ase.constraints import FixAtoms
>>>> from ase.optimize import QuasiNewton
>>>> from ase.visualize import *
>>>> from ase.io import *
>>>> from ase.data import reference_states as _refstate
>>>> from ase.lattice.tetragonal import SimpleTetragonalFactory
>>>> from gpaw.mixer import Mixer
>>>> from gpaw.poisson import PoissonSolver
>>>> from gpaw.dipole_correction import DipoleCorrectionPoissonSolver
>>>>
>>>>
>>>> slab=read('OonCUS-TiO2-2.gpw')
>>>>
>>>> name = 'OonCUS-TiO2-pru'
>>>>
>>>> calc_name=name + '.txt'
>>>> traj_name=name + '.traj'
>>>> log_name=name + '.log'
>>>> gpwdat = name + '.gpw'
>>>>
>>>>
>>>> mask=[atom.tag<1 for atom in slab]
>>>> slab.set_constraint(FixAtoms(mask=mask))
>>>>
>>>>
>>>> p = PoissonSolver()
>>>> mixer=Mixer(0.1, 5, weight=50.0)
>>>> calc = GPAW(h=0.2,
>>>>              kpts=(4, 4, 1),     # k-points
>>>> 	    xc = 'RPBE',
>>>>              #eigensolver='cg',
>>>>              txt=calc_name,
>>>>              convergence = { 'energy' : 0.001,  #default is 0.0005?
>>>>                              'density' : 1.0e-3, # default is 1.0e-4
>>>>                              'eigenstates' : 1.0e-9}, #default
>>>>              nbands=-20,
>>>>              width=0.10,
>>>>              verbose=True,
>>>>              mixer=mixer,
>>>>              poissonsolver=DipoleCorrectionPoissonSolver(p,2))
>>>>
>>>> calc.attach(calc.write, 1,gpwdat)
>>>>
>>>> slab.set_calculator(calc)
>>>> traj = PickleTrajectory(traj_name,'w',slab)
>>>> qn = QuasiNewton(slab,logfile = log_name)
>>>> qn.attach(traj)
>>>> qn.run(fmax=0.05)
>>>> calc.write(gpwdat)
>>>>
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