Bugs item #1598349, was opened at 2006-11-17 13:22 Message generated for change (Comment added) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1598349&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: v10.9 Status: Closed Resolution: Invalid Priority: 5 Private: No Submitted By: Noel O\'Boyle (baoilleach) Assigned to: Bob Hanson (hansonr) Summary: Gaussian Cube File incorrect units Initial Comment: Hello Miguel, Bob, I am trying to visualise isosurfaces of cube files which I have generated myself. Jmol's cube file reader assumes that the cube file units are in Bohrs. However, this is only true if the 'number of points' is a negative value. Otherwise, the units are Angstroms (this applies to the units of the origin, as well as the units of the spacing). This is described briefly at http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/: """ If the sign of the number of voxels in a dimension is positive then the units are Angstroms, if negative then Bohr. """ I think the behavior is undefined if some of the signs of the 'number of voxels' are positive and some are negative (i.e. what units should be used for the origin in that case?). I would very much appreciate if you could fix this. Regards, Noel ---------------------------------------------------------------------- >Comment By: Noel O\'Boyle (baoilleach) Date: 2006-12-06 09:03 Message: Logged In: YES user_id=850620 Originator: YES You're absolutely right - apologies for the inconvenience. It was this input system that I used in the past, and I got mixed up due to reading different web pages. Noel ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-12-05 17:33 Message: Logged In: YES user_id=1082841 Originator: NO Noel, I know what the problem is. There seems to be confusion (generally) between "Gaussian Input" and "Gaussian Output" files. Rene Canters just sent me this link, which I recommend: http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm Careful reading indicates that the N<0 business for Bohr/Angstroms is for the input cards. Later on it says: Output File Formats .... All values in the cube file are in atomic units, regardless of the input units. That's the key -- all units in a cube OUTPUT file are atomic units -- Bohr. A lot of people have been confused by this. Bob ---------------------------------------------------------------------- Comment By: Noel O\'Boyle (baoilleach) Date: 2006-12-05 10:29 Message: Logged In: YES user_id=850620 Originator: YES I cannot say I'm 100% convinced. The problem of course is that Gaussian haven't published a specification for cube files themselves. I think I figured out the format (some years ago) by looking at the contents of a cube file, rather than looking at web pages. I cannot remember however, whether I was able to make an Angstrom-type cube file using Gaussian's cubegen itself. In short, if I get my hands on cubegen and am able to generate an Angstrom-type cube file, I will report back to this bug. In the meanwhile, since it's only the surface I'm interested in, I will use the "angstroms" option, or generate my data in bohr, as you suggest. The code you reference behaves as you describe. However, if you look at the comments at the start of the code, it describes the specification as I have described it. :-) """ If N1<O the input cube coordinates are assumed to be in Bohr, otherwise, they are interpreted as Angstroms (|N1| is used as the number of X-direction points in any case) """ Thanks, Noel ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-11-30 20:37 Message: Logged In: YES user_id=1082841 Originator: NO Noel, Ah, yes. Quite a long history this issue has. I'm sorry, but that page you reference has an error. Somehow, somewhere along the way this specification was changed, and Gaussian Cube files -- despite the clear indication that only a negative count should indicate Bohr -- are all in Bohr, even with the count positive. Evidence of this is given in the code at http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c which reads the files as Bohr even with N > 0. I understand your pain. If you are trying to read the file just for its atom coordinates, you are out of luck; if you are reading the file specifically for its surface and you can get the coordinates from another file, try the "angstroms" isosurface option. Bob Hanson Bob ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1598349&group_id=23629 ------------------------------------------------------------------------- Take Surveys. Earn Cash. 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