I can answer that. All measurements are assumed to be in bohr. As Miguel mentions, there is this original document that SUGGESTED that cube files might be in Angstroms sometimes and Bohrs other times. However, as I was developing from Miguel's code I noticed that his code ignored that and just used Bohrs. I followed up by looking at some files from Gaussian and found that website to not represent the files that Gaussian produces.
For example: http://educ.gaussian.com/visual/Diff/html/DiffGaussView.htm and http://educ.gaussian.com/visual/Diff/Files/acrolein1_gs.cube Acrolein SCF Total Density 8 -6.512752 -6.512752 -4.970736 77 0.190777 0.000000 0.000000 69 0.000000 0.190777 0.000000 96 0.000000 0.000000 0.190777 8 8.000000 0.000000 0.000000 0.000000 6 6.000000 0.000000 0.000000 4.587499 6 6.000000 1.406901 0.000000 6.727236 6 6.000000 1.306368 0.000000 1.987047 1 1.000000 -2.018605 0.000000 4.704662 1 1.000000 3.324973 0.000000 1.869695 1 1.000000 0.499266 0.000000 8.534192 1 1.000000 3.425507 0.000000 6.610073 These coordinates are all in Bohr, even without the supposedly necessary negative sign. So taking Gaussian.inc as the authority on Gaussian cube files, I went with Miguel's original plan. The simple solution is that since you obviously know fo cube files that are in Angstroms, we can add a system-wide flag that indicates that we should read cube files in Angstroms when necessary. Something like: set cubeFileUnitsAngstrom set cubeFileUnitsBohr or such. Bob Jonathan Gutow wrote: >Dear jmol experts, > I've encountered a scaling issue while converting surface >grid files from one program format to another. It appears to be the >difference between units of Bohr and Angstroms. Which does Jmol >expect, or does it check some how? > > Thanks for your help. > >Jonathan > > Miguel wrote: >>Dear jmol experts, >> I've encountered a scaling issue while converting surface >>grid files from one program format to another. It appears to be the >>difference between units of Bohr and Angstroms. Which does Jmol >>expect, or does it check some how? >> >> > >Jmol's isosurface support was for Gaussian .cube files. > >URL is at http://astronomy.swin.edu.au/~pbourke/dataformats/cube/index.html > >It says: > >"If the sign of the number of voxels in a dimension is positive then the >units are Angstroms, if negative then Bohr." > >** 2 minutes later ** > >This is certainly the document that I looked at when I implemented the >isosurface code, but a quick review of the code seems to indicated that I >may not have implemented this properly. In particular, the current >implementation looks like it is always converting scaling by >ANGSTROMS_PER_BOHR, rather than doing so only when the count is negative. > >So, this may be a bug. > >Sorry, I can't look into this any deeper at this time. > > >Miguel > > > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
