Oh - and if all you want is the visualization of a G orbital, you
can always use something like
ISOSURFACE phase atomicOrbital 5 4 3
:)
On Sat, Jun 19, 2010 at 11:01 AM, SourceForge.net <nore...@sourceforge.net
> wrote:
Feature Requests item #3017994, was opened at 2010-06-18 06:33
Message generated for change (Comment added) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3017994&group_id=23629
Please note that this message will contain a full copy of the
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including the initial issue submission, for this request,
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Category: Interface Improvements
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Rene Kanters (rkanters)
Assigned to: Nobody/Anonymous (nobody)
Summary: higher than d orbitals in MOs
Initial Comment:
I was wondering whether it would be possible to have Jmol display
MOs from quantum programs that are higher than the d orbitals.
I understand that currently Jmol ignores those oribitals so as long
as an orbital one looks at doesn't have much f (g, h, i)
contributions it should not affect the visual part much, but I
wonder whether that is something that could be added without too
much trouble...
----------------------------------------------------------------------
>Comment By: Bob Hanson (hansonr)
Date: 2010-06-19 11:01
Message:
Sure - and I'm not suggesting what I implemented is the best solution,
either. The basic idea is this (just modified yesterday). Originally
the
readers read the basis functions, saving either slater parameters or
gaussian shells, depending upon the type of calculation. Then, in
addition
to that, the readers read the MO coefficients. You had managed to
get the
QChem reader to re-order its MO coefficients and basis shells, but
that
turned out to be way too complicated in terms of generalizing, so I
decided
instead to opt for just reading the file data as is, but also
providing a
set of int[] arrays that particularly for D and F shells indicates the
mapping of MO coefficients to Jmol-expected (Gaussian) order.
While each reader in principle could just provide this array, I saw
that
as being error-prone from a maintenance point of view.
So instead I have the readers simply producing the list of D and F
labels
as found in the file and then also provide lists (DC_LIST, DS_LIST,
FC_LIST, FS_LIST) that also list these in Jmol/Gaussian order.
(Realize
that when reading NBO output within Gaussian files, even there the
orbitals
need re-ordering.) That way I don't have to remember how the mapping
works;
I just have to make sure that any reader is making that list. Then
BasisFunctionReader has a method getDFMap that creates the needed
dfCoefMaps[][] array elements.
For readers such as PSI, which don't provide any label information in
their MO coefficient lists, I guess we would just have to find out
what
that ordering is and create the dfCoefMaps[][] arrays ourselves. But
others
are simpler -- just get the list of D and F orbitals found in the
file and
pass them on.
The added complication that some files, such as Gaussian with NBO
included, have two DIFFERENT orders. This was causing the problem with
those Gaussian files you sent. I caught on to that yesterday, and
now the
way it works is that the dfCoefMaps[][] array is stored in the
individual
MO Hashtable, not the overall one for the model. This seems to work
well.
In addition, I had a mistake in how Jmol found the orbital label,
and that
was causing the first/last atom Sn problem that you observed.
I'm pretty sure that is going to work now. All the NBO bond orbitals I
looked at looked fine.
Like you say, except for the very high virtual orbitals, I don't think
having the G orbitals in there could make much of a difference in
visualization -- at least that's what I'm told. The coefficients are
just
too small.
Bob
----------------------------------------------------------------------
Comment By: Rene Kanters (rkanters)
Date: 2010-06-18 16:13
Message:
I just checked out the new version and am a bit surprised now that
there
are a bunch of NBOs that do not show anything, e.g., from tm_sna.tgz
(filter "NBO" loaded) in the last model if you do MO 82 you won't see
anything, all the way up to 99. At 100 it starts showing orbitals
again. Is
this because of the large g contributions? If so, maybe at least the
mo
label should show up with some kind of visual warning?
----------------------------------------------------------------------
Comment By: Rene Kanters (rkanters)
Date: 2010-06-18 16:00
Message:
I'll check it out.
By the way, I wasn't disagreeing with you on your approach of not
having
each reader do the orbital reshuffling (which I may have started
when I
believe the qchem reader was the first one to have the orbital
ordering
different than gaussian). I was just having a hard time following
all the
intricacies of what you set up :-).
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2010-06-18 14:20
Message:
ok, that's taken care of. There was an additional bug in the NBO
reader
that was not checking for orbital type when the atom number was <
10. While
this is tricky, I still contend it's way easier than having each
reader
re-organize it's MO coefficients on the fly. Especially for large
numbers
of orbitals like this. Just have to be careful! Please check it out,
Rene.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2010-06-18 12:35
Message:
ah, SO tricky... OK, so if you have two different sequences in the
reader
-- in this case Gaussian and NBO, then the sequence has to be tied
to the
orbital, not the collection of orbitals. Ah, so tricky!....
----------------------------------------------------------------------
Comment By: Rene Kanters (rkanters)
Date: 2010-06-18 11:13
Message:
I think I just lost my long message I was typing here.. Sigh... So
here I
go again.
I just ran two calculations for Sn(CH3)4 (tm_sna.log with Sn as the
first
atom and tm_snb.log with Sn as the last atom) with NBO analysis.
tm_sna.log has for NBO 82 a Rydberg state with 1.1239 AO
contribution to
the NBO. tm_snb.log has the same one as NBO 130 both for the last
model in
the structure). Loading these with filter "NBO" and doing a 'model
last'
then allows for
tm_sna.log: MO 82 : see the Ry*(53)Sn, which looks like just an s
orbital
on a carbon, because no g-orbital contribution shown. That is
misleading
:-)
tm_snb.log: MO 130 : shows no orbital whatsoever! Not even a label (I
think that this is a bug?) MO 129 shows nicely the f-orbital, though.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2010-06-18 11:05
Message:
I think you just have to run the calculation with and without G
orbitals to
see what difference it makes. It's not a huge amount of code, but I
don't
know what the functions are, so it would definitely take some effort
-- If
you want to implement it, you certainly are welcome to. Good student
project!
----------------------------------------------------------------------
Comment By: Rene Kanters (rkanters)
Date: 2010-06-18 08:11
Message:
Sorry about the mistake. I knew it does f's :-).
Without being able to visualize the orbitals with and without the g
(and
higher) AO contributions it is hard to say whether the effect is
large or
not. You may be right indeed that it will not, but it would be nice
to be
able to see g orbitals even if they only contribute to virtual
orbitals
(like the Sn example I provided for the spherical/cartesian tests.
I was wondering whether it may be (for you :-) and easy extension to
what
is already available. If it is then forget that I asked, if you
would like
to consider I think it would be a nice feature (that is why I posted
it
with feature requests).
I'll talk to one of the students here who does some Sn calculations
that
involve g orbitals in the basis set to set up a calculation to get a
g03
ouput file for that.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2010-06-18 06:42
Message:
Jmol handles up through F orbitals. Hard to believe there's a
significant
visual contribution from G,H,I. Examples?
----------------------------------------------------------------------
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St. Olaf College
1520 St. Olaf Ave.
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