[ase-users] Error in Bader tutorial

[Jens Jørgen Mortensen]

On 02/25/2015 02:22 PM, Peter Bjerre Jensen wrote:
> Hi again
>
> I did not finish it.. Also the Bohr unit should be imported "from 
> ase.units import Bohr", and also from ase.io import write (or 
> atoms.write, which I think is the standard?)

Thanks for reporting this.  I have updated the GPAW and ASE web-pages:

     https://wiki.fysik.dtu.dk/gpaw/tutorials/bader/bader.html
     https://wiki.fysik.dtu.dk/ase/ase/dft/bader.html

And, now the Bader analysis will run every weekend so that we should 
find out if it starts going bad again!

Jens Jørgen

>
> This script will work:
>
>     from gpaw import GPAW
>     from ase.structure import molecule
>     from ase.units import Bohr
>
>     atoms = molecule('H2O', cell=[7.5, 9, 9], calculator=GPAW(h=.17,
>     xc='PBE'))
>     atoms.center()
>     atoms.get_potential_energy()
>
>     density = atoms.calc.get_all_electron_density(gridrefinement=4) *
>     Bohr**3
>     atoms.write('water_density.cube', data=density)
>
> Furthermore the output using GPAW 0.10.0.11364, ASE 3.8.1.3440 and 
> bader 0.28a is slightly different:
>
>         #         X           Y           Z CHARGE     MIN DIST   
>     ATOMIC VOL
>      --------------------------------------------------------------------------------
>         1      7.0865      8.5038      9.0672      9.0927 1.3250  
>     2670.4802
>         2      7.0865      9.9461      7.9403      0.4536 0.3159   
>     719.8122
>         3      7.0865      7.0615      7.9403      0.4536 0.3159   
>     709.3161
>      --------------------------------------------------------------------------------
>         VACUUM CHARGE:               0.0000
>         VACUUM VOLUME:               0.0000
>         NUMBER OF ELECTRONS:    10.0000
>
>
> Best regards
> Peter
>
> Peter Bjerre Jensen
> Postdoc
> DTU Energy
>
> Technical University of Denmark
>
> 	
> Department of Energy Conversion and Storage
> Fysikvej, Building 307
> 2800 Kgs. Lyngby
> Direct +45 45253204
> pbjen at dtu.dk <mailto:pbjen at dtu.dk>
> www.ecs.dtu.dk <http://www.ecs.dtu.dk>
>
>
>
>
> -------- Videresendt meddelelse --------
> Subject: 	Error in Bader tutorial
> Date: 	Wed, 25 Feb 2015 14:01:23 +0100
> From: 	Peter Bjerre Jensen <pbjen at dtu.dk>
> To: 	ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
>
>
>
> Hi
>
> The script example at https://wiki.fysik.dtu.dk/ase/ase/dft/bader.html 
> does not work - molecule is not loaded with "from ase import *"; 
> however "from ase.structure import molecule" would fix it.
>
> Best regards
> Peter
>
> Peter Bjerre Jensen
> Postdoc
> DTU Energy
>
> Technical University of Denmark
>
> 	
> Department of Energy Conversion and Storage
> Fysikvej, Building 307
> 2800 Kgs. Lyngby
> Direct +45 45253204
> pbjen at dtu.dk <mailto:pbjen at dtu.dk>
> www.ecs.dtu.dk <http://www.ecs.dtu.dk>
>
>
>
>
>
>
>
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