On Fri, Mar 21, 2008 at 6:47 PM, Louis Ricard
louis.ricard@polytechnique.edu wrote:
Hi.
This may not be the correct list.
First:
I discovered avogadro about two months ago and I am impressed by its
improvements
over this short period.
Second:
I had a close look at the recent multiple gausscube support in
openbabel.
The format of files generated by the cubegen utility is, as far as I
know, not documented.
There is a reference (1) in the source file. This is only a summary of
the file format and we are don’t have more details. Is there a
specific issue that we handle incorrect? For example, we’ve only seen
cube files in bohr, so we assume that cube files are always in bohr.
From another reference (2):
“If the sign of the number of voxels in a dimension is positive then
the units are Angstroms, if negative then Bohr.”
This isn’t the case for our test files…
(1) http://www.gaussian.com/g_ur/u_cubegen.htm
(2) http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/
Attempts to visualize such files in avogadro lead to funny results,
so I tried modifying the openbabel
gausscubeformat.cpp. I am not a fluent C++ user, but after fiddling
for a while, I think
I untangled some issues. And I would like to submit the enclosed patch
to your attention.
At this point, reading the file is quite slow, but …
Do you mean that the isosurface has a funny form? I also had the
problem with additional empty lines between cubes in the file (I fixed
this but forgot to commit, your also patch solves this problem), but
in this case you don’t see any surface…
One problem I have is submitting a new test file: my test file is
quite large, even zipped.
I do not want to clutter the list with it, so to whom or how do I
submit it?
You can mail it to me and I can commit it to the repository.
Thank you for the patch, I’ll test it and commit if it works…
Kind regards,
Tim