[gpaw-users] Van der Waals correction
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Thu May 10 14:17:09 CEST 2012
On 05/10/12 09:06, Michael Walter wrote:
> 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.
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2010-December/000583.html
Still from the old generator.py
Marcin
>
> Best,
> Michael
>
> 2012/5/10 Rico Friedrich <friedrir at mailserver.tu-freiberg.de
> <mailto: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
> <mailto:Michael.Walter at fmf.uni-freiburg.de>>:
>
>
> Hi,
>
> 2012/5/9 Rico Friedrich <friedrir at mailserver.tu-freiberg.de
> <mailto: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
> <mailto:gpaw-users at listserv.fysik.dtu.dk>
> 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 <tel:%2B49%20761%20203%204758> and +49
> 761 203 7695 <tel:%2B49%20761%20203%207695>
> Fax: +49 761 203 4701 <tel:%2B49%20761%20203%204701>
> email: Michael.Walter at fmf.uni-freiburg.de
> <mailto:Michael.Walter at fmf.uni-freiburg.de>
> www: http://omnibus.uni-freiburg.de/~mw767
> <http://omnibus.uni-freiburg.de/%7Emw767>
>
>
>
>
>
>
>
> --
> ------------------------------------------
> 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
> <mailto:Michael.Walter at fmf.uni-freiburg.de>
> www: http://omnibus.uni-freiburg.de/~mw767
> <http://omnibus.uni-freiburg.de/%7Emw767>
>
--
***********************************
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk
***********************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20120510/a97a0ca8/attachment.html
More information about the gpaw-users
mailing list