MO 24 in Co_ just has a very tight cutoff. So the default 0.05 is too
large. You can see a bit of it with 0.03.
I'm not seeing the problem with CuZ. Maybe the same. Also, since Jmol does
not include G orbitals, anything that is pure G will not show up. But then
you would see the integrated density far from 1.000. To see that issue
set debug
prior to the MO command, then inspect the Java console:
*Molecular orbital #196/980 Using surface reader
org.jmol.jvxl.readers.IsoMOReader@7a17a678 atoms will be used in the
surface calculationMaximum number of voxels for index=0 exceeded (197) --
set to 80isosurface resolution for axis 1 set to 4.0103846 points/Angstrom;
80 voxelsMaximum number of voxels for index=1 exceeded (168) -- set to
80isosurface resolution for axis 2 set to 4.7048836 points/Angstrom; 80
voxelsMaximum number of voxels for index=2 exceeded (134) -- set to
80isosurface resolution for axis 3 set to 5.9048047 points/Angstrom; 80
voxelsgenerating isosurface data for MO using cutoff 0.05Normalizing AOs:
true slaters:falseQuantumCalculation: origin = [-9.84943, -8.395532,
-6.689468] steps = [0.24935265, 0.21254511, 0.1693536] origin(Bohr)=
[-18.612627, -15.865171, -12.641195] steps(Bohr)= [0.47120574, 0.40164992,
0.32003024] counts= 80 80 80calculation type not identified --
continuing Unsupported basis type for atomno=1: 9G Unsupported basis type
for atomno=2: 9GIntegrated density = 0.9861017boundbox corners {-3.8674343
-2.2718866 -1.6450598} {3.8676503 2.2715719 1.6453059}*
On Mon, Jul 6, 2015 at 10:01 AM, Latévi Max LAWSON DAKU <max.law...@unige.ch
> wrote:
> Dear Bob,
>
> There is a bug which shows up when trying to view molecular
> orbitals with the "mo" command: some orbitals are displayed
> but other aren't, and even the information about the file
> (molden type), the model and the MO are not shown.
>
>
> I've made a compressed archive with two files ("Co_molden.inp"
> and "CuZ_molden.inp"), for which the bug is observed: the archive
> is named "cases.tar.gz", it can be downloaded at the following
> address
>
> http://dl.free.fr/eyxJUJHEa
>
> - For the file "Co_molden.inp", the MO number 24 cannot be shown.
> This happens with the versions 14.2.14_2015.06.11 and 14.3.15_2015.06.19b.
>
> - With a colleague who's using Jmol 14.2.13_2015.03.23, we were not
> able to view the MO 196 and others in the file "CuZ_molden.inp".
> But with the versions 14.2.14_2015.06.11 and 14.3.15_2015.06.19b,
> it seems we can view all MOs.
>
>
> I remain at your disposal for any further information you may need
> and I thank in advance for your help.
>
>
> Best regards,
> Max
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
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