From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 24 2013 - 02:37:55 CDT

On Tue, Sep 24, 2013 at 8:20 AM, Ari Turpeinen <Ari.Turpeinen_at_oulu.fi> wrote:
> Hi all,
>
> The cubegen utility included with Gaussian 09 rev D.01 creates cubefiles
> that do not seem to be compatible with the cubeplugin in VMD 1.9.1
> (LINUXAMD64 version). Cubes generated with rev C.01 work perfectly.
>
> I ran into the problem when trying to visualize electrostatic potential maps
> by following the steps in
> http://www.chem.gla.ac.uk/staff/granth/esp-map.html Opening the density cube
> results in the following console output (similar for the esp cube):
>
> Console output (cube generated w/ rev D.01 cubegen)
> ====================================================
> cubeplugin) Coordinates will be rotated to comply
> cubeplugin) with VMD's conventions for periodic display.
> cubeplugin) Calculation of unit cell size failed. Continuing anyways...
> cubeplugin) Coordinates will be rotated to comply
> cubeplugin) with VMD's conventions for periodic display.
> cubeplugin) Calculation of unit cell size failed. Continuing anyways...
> Info) Using plugin cube for structure file
> /home/ariturpe/Desktop/cubet/g09D_dens.cube
> cubeplugin) trying to read cube data set 0
> Info) Analyzing Volume...
> Info) Grid size: 1x0x0 (0 MB)
> Info) Total voxels: 0
> Info) Min: 0.000000 Max: 0.000000 Range: 0.000000
> Info) Computing volume gradient map for smooth shading
> Info) Added volume data, name=g09D_dens.cube : Gaussian Cube: cb7_new
> density
> Info) Using plugin cube for coordinates from file
> /home/ariturpe/Desktop/cubet/g09D_dens.cube
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 126
> Info) Bonds: 147
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 1
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 28 Nucleic: 0
> Info) Finished with coordinate file
> /home/ariturpe/Desktop/cubet/g09D_dens.cube.
> ====================================================
>
> For comparison, output from cube file generated with rev C.01 cubegen
> ====================================================
> Info) Using plugin cube for structure file
> /home/ariturpe/Desktop/cubet/g09C_dens.cube
> cubeplugin) trying to read cube data set 0
> Info) Analyzing Volume...
> Info) Grid size: 95x93x58 (7 MB)
> Info) Total voxels: 512430
> Info) Min: -0.000000 Max: 3.158510 Range: 3.158510
> Info) Computing volume gradient map for smooth shading
> Info) Added volume data, name=g09C_dens.cube : Gaussian Cube: cb7_new
> density
> Info) Using plugin cube for coordinates from file
> /home/ariturpe/Desktop/cubet/g09C_dens.cube
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 126
> Info) Bonds: 147
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 1
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 28 Nucleic: 0
> Info) Finished with coordinate file
> /home/ariturpe/Desktop/cubet/g09C_dens.cube.
> ====================================================
>
> The differences between the cubefiles generated by different cubegen
> versions are too large to be included here, but I can provide the cubefiles
> if there is interest.

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?

> 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.

>
> -Ari
>
>
>
>
>

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