VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 24 2013 - 04:59:00 CDT

On Tue, Sep 24, 2013 at 10:23 AM, Ari Turpeinen <ari.turpeinen_at_oulu.fi> wrote:

[...]

>> there is obviously a difference in the header segment of the cube
>> files that throws the parser off. can you just post the first 10 or so
>> lines from both of your files?
>
> Thank you for the quick response. There's an added 1 in the fifth column on
> the third row.

thanks. please take the attached updated plugin. uncompress it and
copy it into your directory with the existing molfile plugins (
$libdir/plugins/LINUXAMD64/molfile ) and try to load both cubefiles
again and let me know if that solves the issue.

axel.

>
> ariturpe_at_spin:~/Desktop/cubet$ head -n 10 g09C_dens.cube
> cb7_new density
> Electron density from Total SCF Density
> 126 -17.756981 -17.182058 -10.717971
> 95 0.376223 0.000000 0.000000
> 93 0.000000 0.376223 0.000000
> 58 0.000000 0.000000 0.376223
> 8 8.000000 -7.276515 -0.161584 5.411098
> 8 8.000000 -5.021790 -6.490272 5.802173
> 8 8.000000 1.884070 -8.013025 5.773882
> 8 8.000000 7.197353 -3.577459 5.716781
> ariturpe_at_spin:~/Desktop/cubet$ head -n 10 g09D_dens.cube
> cb7_new density
> Electron density from Total SCF Density
> 126 -17.756981 -17.182058 -10.717971 1
> 95 0.376223 0.000000 0.000000
> 93 0.000000 0.376223 0.000000
> 58 0.000000 0.000000 0.376223
> 8 8.000000 -7.276515 -0.161584 5.411098
> 8 8.000000 -5.021790 -6.490272 5.802173
> 8 8.000000 1.884070 -8.013025 5.773882
> 8 8.000000 7.197353 -3.577459 5.716781
>
> -Ari
>
>> > The release notes for Gaussian 09 rev D.01 contain the following
>> > regarding
>> > cubegen: "The cubegen utility now correctly produces Laplacian and ROHF
>> > density. It also now correctly computes the current density from jobs
>> > with
>> > basis sets with pure functions (5d 7f)." (In section bugfixes between
>> > G09
>> > revisions D.01 and C.01)
>>
>> this is irrelevant, but in the process some change in the file format
>> seems to have slipped in as well.
>>
>> axel.
>>
>> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.