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#609 Bug with MOPAC orbital visualization for gold atoms
I think I found a bug in visualizing s and p orbitals for gold atoms that are generated by the MOPAC program (.mgf files). I've attached the file for a single gold atom as an example. As far as I can tell, d orbitals show fine. but p and s orbitals don't show.
The issues seems to be unique to gold. If you change gold to silver (i.e. 79 --> 47), the orbitals display properly.
the cutoff needs to be smaller for those very tight S and P orbitals.
Try
mo cutoff 0.005
On Tue, Dec 3, 2019 at 1:58 PM John jmhimara@users.sourceforge.net wrote:
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Related
Bugs: #609
Hmm, that's interesting. Normally I get an error from MOPAC telling me
But it's fixed ince I decrease the cutoff, as you suggest. Why is that not an issue if I change the gold atom to a silver one (same exact file, just manually changing the gold atoms to silver ones in the file)? The orbitals display fine in that one. Does the orbital plotting of Jmol take into account WdW radii ?
Unfortunately, decreasing the cuttoff is not ideal, because that messes up the rest of the orbital. I'm looking at gold clusters where the HOMOs are a linear combination of s, p, and d orbitals. If I decrease the cuttoff, the d portion becomes too diffuse and cover up the core portion which are dominated by s and p orbitals. Nevertheless I'll mess with the options to see if I can get an optimal view.
You can't just change the atomic number in a MOPAC calculation result. All
the numbers you see there are calculated for a specific element. (Remember,
MOPAC is an empirical calculation.) This is the MOPAC calculation for
gold, not silver. If you want the calculation for gold, run that in MOPAC.
[this is the MOPAC calculation result for silver not gold, that is]
On Thu, Dec 5, 2019 at 4:20 PM Robert Hanson hansonr@stolaf.edu wrote:
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Sorry, you misunderstood me. I'm not talking about changing anything in MOPAC. Rather, I was refering to changing the atoms in the output file (the .mgf file) after the calculation. I can edit the file manually after the calculation is done -- I leave everything else as is and only change the atomic numbers from gold to silver. As far as I can tell, that tricks Jmol into thinking they are silver atoms, whereas the underlying MOPAC calculation is done with gold.
If I do that, then I have no trouble visualizing the orbitals at the default cutoff value.
It seems to be the other way around. The numbers in the file are for
silver, not gold.
On Thu, Dec 5, 2019 at 7:04 PM John jmhimara@users.sourceforge.net wrote:
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Related
Bugs: #609
(send me the file for silver, perhaps, if that is not the case)
Oh I see. I think I have uploaded the wrong file (I did single calculation with silver for testing purposes), but otherwise what I said holds true. I'll upload the correct file as an example.
Sorry about that.
revitalizing this, as the bug in Jmol has been found, and an issue with MOPAC's Slater normalization is being addressed.