[gpaw-users] Van der Waals correction
Michael Walter
Michael.Walter at fmf.uni-freiburg.de
Thu May 10 09:06:12 CEST 2012
The problem was the missing van der Waals radius of Radon (not in Bondi)
needed for the estimate of the van der Waals radius of gold after TS09.
I've added that in the latest version of trunk.
You'll have to create also the Rn setup for which we do not have parameters
yet. Maybe someone familiar with setup peculiarities could help here.
Best,
Michael
2012/5/10 Rico Friedrich <friedrir at mailserver.tu-freiberg.de>
> Dear GPAW users,
>
> for instance if I do a calculation with the following input-file:
>
> from ase import io
> from ase.parallel import parprint
> from gpaw import GPAW, MixerSum, MixerDif, FermiDirac, PoissonSolver
> from ase.lattice.surface import *
> from ase.optimize import QuasiNewton, MDMin
> from ase.data.s22 import data, s22
> from ase.calculators.vdwcorrection import vdWTkatchenko09prl
> from gpaw.analyse.hirshfeld import HirshfeldDensity, HirshfeldPartitioning
> from gpaw.analyse.vdwradii import vdWradii
>
> au=fcc111('Au', size=(3,3,5))
>
> au.center(vacuum=6.0)
>
> c = GPAW(
> #h=0.22,
> gpts=(160, 160, 160),
> kpts=(1,1,1),
> mode='lcao',
> spinpol=True,
> basis='dzp',
> xc='PBE',
> mixer=MixerSum(),
> occupations=FermiDirac(5e-3),
> maxiter=300,
> poissonsolver=PoissonSolver(**relax='GS', eps=1e-10),
> )
>
> au.set_calculator(c)
> epot = au.get_potential_energy()
>
> ## add vdw correction
> cc = vdWTkatchenko09prl(**HirshfeldPartitioning(c),
> vdWradii(au.get_chemical_**symbols(), 'PBE'))
> au.set_calculator(cc)
> epot_vdw = au.get_potential_energy()
>
> relax = QuasiNewton(au, trajectory='Au_TS09.traj',
> logfile='Au_TS09.rel.log')
> relax.run(fmax=0.05)
>
> parprint('Epot: {0}'.format(epot_vdw))
>
> c.write('au_TS09.gpw', mode='all')
> c.attach(c.write, n, 'Au_TS09.gpw', mode='gpw:wfs_tmp/psit_Gs%dk%**dn%d')
> io.write('Au_relTS09.xyz', au)
>
> parprint('>>> DONE <<<')
>
>
> the run aborts after writing the "Local Magnetic Moments" and I get an
> error including:
>
> cc = vdWTkatchenko09prl(**HirshfeldPartitioning(c),
> vdWradii(au.get_chemical_**symbols(), 'PBE'))
>
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 54, in
> vdWradii
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 54, in
> vdWradii
> n_g, r_g = get_density(Zrg)
> n_g, r_g = get_density(Zrg)
>
> n_g, r_g = get_density(Zrg)
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> n_g, r_g = get_density(Zrg)
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> n_g, r_g = get_density(Zrg)
> n_g, r_g = get_density(Zrg)
>
> n_g, r_g = get_density(Zrg)
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> n_g, r_g = get_density(Zrg)
> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35, in
> get_density
> xc, world)
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> xc, world)
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> xc, world)
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> xc, world)
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> xc, world)
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> xc, world)
> xc, world)
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> xc, world)
> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in __init__
> symbols = [chemical_symbols[Z] for Z in Z_a]
> symbols = [chemical_symbols[Z] for Z in Z_a]
> symbols = [chemical_symbols[Z] for Z in Z_a]
> symbols = [chemical_symbols[Z] for Z in Z_a]
> TypeError: TypeError: TypeError: TypeError: list indices must be integers,
> not NoneType
>
> Could anyone help? Thanks in advance.
>
> Best,
>
> Rico
>
>
>
>
> Zitat von Michael Walter <Michael.Walter at fmf.uni-**freiburg.de<Michael.Walter at fmf.uni-freiburg.de>
> >:
>
>
> Hi,
>>
>> 2012/5/9 Rico Friedrich <friedrir at mailserver.tu-**freiberg.de<friedrir at mailserver.tu-freiberg.de>
>> >
>>
>> Dear GPAW users,
>>>
>>> I try to do a calculation with a molecule adsorbed on an Au-surface
>>> and want to use the Van der Waals correction of Tkatchenko and
>>> Scheffler for geometry optimization. Calculations on the pure
>>> molecular structure without the gold atoms work fine. Then I obtained
>>> the values for the C6 coefficient and the other parameters in the
>>> vdwcorrection.py file for gold Ruiz et al. PRL 108 (2012). However
>>> when I include the gold atoms in the relaxation I still get an
>>> error-message including the following lines:
>>>
>>> cc = vdWTkatchenko09prl(**HirshfeldPartitioning(c),
>>> vdWradii(aupc.get_chemical_**symbols(), 'PBE'))
>>> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 54,
>>> in vdWradii
>>> cc = vdWTkatchenko09prl(**HirshfeldPartitioning(c),
>>> vdWradii(aupc.get_chemical_**symbols(), 'PBE'))
>>> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 54,
>>> in vdWradii
>>> n_g, r_g = get_density(Zrg)
>>> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35,
>>> in get_density
>>> n_g, r_g = get_density(Zrg)
>>> File "/home/friedrir/lib/python/**gpaw/analyse/vdwradii.py", line 35,
>>> in get_density
>>> xc, world)
>>> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in
>>> __init__
>>> xc, world)
>>> File "/home/friedrir/lib/python/**gpaw/setup.py", line 1018, in
>>> __init__
>>> symbols = [chemical_symbols[Z] for Z in Z_a]
>>> TypeError: list indices must be integers, not NoneType
>>> GPAW CLEANUP (node 3): <type 'exceptions.TypeError'> occurred.
>>> Calling MPI_Abort!
>>> symbols = [chemical_symbols[Z] for Z in Z_a]
>>>
>>>
>>> Is there any idea how to overcome the problem. Thanks in advance.
>>>
>>>
>> could you provide an example that shows the problem, please ?
>>
>> Best,
>> Michael
>>
>>
>> Best regards,
>>>
>>> Rico Friedrich
>>>
>>> ______________________________**_________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.**dk <gpaw-users at listserv.fysik.dtu.dk>
>>> https://listserv.fysik.dtu.dk/**mailman/listinfo/gpaw-users<https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users>
>>>
>>>
>>
>>
>> --
>> ------------------------------**------------
>> PD Dr Michael Walter
>> Address: Freiburger Materialforschungszentrum
>> Stefan-Meier-Straße 21
>> D-79104 Freiburg i. Br.
>> Germany
>> Tel.: +49 761 203 4758 and +49 761 203 7695
>> Fax: +49 761 203 4701
>> email: Michael.Walter at fmf.uni-**freiburg.de<Michael.Walter at fmf.uni-freiburg.de>
>> www: http://omnibus.uni-freiburg.**de/~mw767<http://omnibus.uni-freiburg.de/~mw767>
>>
>>
>
>
>
--
------------------------------------------
PD Dr Michael Walter
Address: Freiburger Materialforschungszentrum
Stefan-Meier-Straße 21
D-79104 Freiburg i. Br.
Germany
Tel.: +49 761 203 4758 and +49 761 203 7695
Fax: +49 761 203 4701
email: Michael.Walter at fmf.uni-freiburg.de
www: http://omnibus.uni-freiburg.de/~mw767
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