VMD-L Mailing List

From: Ari Turpeinen (ari.turpeinen_at_oulu.fi)
Date: Tue Sep 24 2013 - 06:57:21 CDT

On Tue, Sep 24, 2013 at 12:59 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>

The updated plugin works. Both cubefiles are now parsed correctly.
Thanks again.

-Ari

>
> 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.
>