Hi Bob,
There are unrestricted calculations (just not Hartree Fock, but B3LYP,
which provides the same reporting on orbitals) in benzene-plus-
UB3LYP-631Gd.out, benzene_plus-UB3LYP_nosym.out and enediyne.out.
There are also restricted open shell ones benzene_plus-
ROB3LYP_nosym.out and benzene-plus-ROB3LYP-631Gd.out and regular
restricted ones benzene-B3LYP-631Gd.out, benzene-RB3LYP_nosym.out, H2O-
B3LYP-631Gd.out, H2O-B3LYP-631Gd_pure.out and H2O.out.
I just committed a new benzene-RHF.out file in the qchem folder for
the Jmol-datafiles. (It took me a while to figure out how to do that
again :-).
Cheers,
René
On Aug 19, 2010, at 2:03 PM, Robert Hanson wrote:
Rene, if you can put some sample QChem UHF files in the data
directory that illustrate this, it would be helpful.
Bob
2010/8/19 René Kanters <rkant...@richmond.edu>
Hi Bob,
Since the calculation is restricted the alpha and beta orbitals are
exactly the same. Only for restricted open shell or unrestricted
calculations are their differences only in the singly occupied (and
virtual) orbitals for the former and for the latter all alphas and
betas can be (and usually are) different.
right, I see. I still don't see why the discrepency in number of
orbitals.
I haven't checked the code, but I think I am collecting in the
'Alpha MOs, Restricted' line the latter word to find out whether it
was really restricted, in which case I am not even looking for the
betas: therefor 1 set of only alpha orbitals.
I hope that helps.
René
On Aug 19, 2010, at 12:28 PM, Robert Hanson wrote:
I think part of the problem was that with some of the really high
level calculations there can be hundreds of alpha and beta
orbitals. The filterMO() method is in MOReader, so it is common to
any file implementing NBOs, Gamess, Gaussian, Jaguar, QChem,
GenNBO, and Psi. That's what picks up on the filter "BETA"
business. As for QChem, it's not set up to recognize alpha/beta
mixes yet.
Rene, in benzene-B3LYP-631Gd.out (data files) can you explain to me
how these sections match up?
--------------------------------------------------------------
User input:
--------------------------------------------------------------
$comment
benzene RB3LYP/6-31G*
$end
...
$rem
jobtype OPT
exchange B3LYP
basis 6-31G*
unrestricted FALSE
print_general_basis TRUE
print_orbitals TRUE
$end
...
Alpha MOs, Restricted
-- Occupied --
-10.188 -10.188 -10.188 -10.187 -10.187 -10.187 -0.846 -0.740
1 A1g 1 E1u 1 E1u 1 E2g 1 E2g 1 B1u 2 A1g 2 E1u
-0.740 -0.597 -0.597 -0.519 -0.459 -0.438 -0.417 -0.417
2 E1u 2 E2g 2 E2g 3 A1g 2 B1u 1 B2u 3 E1u 3 E1u
-0.359 -0.340 -0.340 -0.246 -0.246
1 A2u 3 E2g 3 E2g 1 E1g 1 E1g
-- Virtual --
0.004 0.004 0.091 0.145 0.145 0.164 0.182 0.182
1 E2u 1 E2u 4 A1g 4 E1u 4 E1u 1 B2g 4 E2g 4 E2g
....
Beta MOs, Restricted
-- Occupied --
-10.188 -10.188 -10.188 -10.187 -10.187 -10.187 -0.846 -0.740
1 A1g 1 E1u 1 E1u 1 E2g 1 E2g 1 B1u 2 A1g 2 E1u
-0.740 -0.597 -0.597 -0.519 -0.459 -0.438 -0.417 -0.417
2 E1u 2 E2g 2 E2g 3 A1g 2 B1u 1 B2u 3 E1u 3 E1u
-0.359 -0.340 -0.340 -0.246 -0.246
1 A2u 3 E2g 3 E2g 1 E1g 1 E1g
-- Virtual --
0.004 0.004 0.091 0.145 0.145 0.164 0.182 0.182
1 E2u 1 E2u 4 A1g 4 E1u 4 E1u 1 B2g 4 E2g 4 E2g
...
RESTRICTED (RHF) MOLECULAR ORBITAL
COEFFICIENTS
1 2 3 4
5 6
eigenvalues: -10.188 -10.188 -10.188 -10.187
-10.187 -10.187
7 8 9 10
11 12
eigenvalues: -0.846 -0.740 -0.740 -0.597
-0.597 -0.519
13 14 15 16
17 18
eigenvalues: -0.459 -0.438 -0.417 -0.417
-0.359 -0.340
19 20 21 22
23 24
eigenvalues: -0.340 -0.246 -0.246 0.004
0.004 0.091
25 26
eigenvalues: 0.145 0.145
Why just 26 orbitals? Are they "alpha" or "beta"?
2010/8/19 René Kanters <rkant...@richmond.edu>
I believe that that is different than what is done in the qchem
reader where both sets of orbitals are read by default. At least
that is the way I initially implemented it. The tricky part with
that is that the number of MOs is doubled and you have to know what
the number of the highest alpha one is to say which MO you want to
show for the betas (unless you use the popup where the energies may
help).
Would it make sense to have a separate list of beta MOs 'parallel'
to the alpha ones and use for the restricted cases (or cases where
the output only provides one set of orbitals) as the default set of
orbitals. That way you could ask for the 3rd beta MO using 3 is the
MO index?
Just a thought.
René
On Aug 19, 2010, at 9:31 AM, Robert Hanson wrote:
I just updated the GAMESS reader so that it would work with files
that include a line "LZ VALUES..." just after the alpha set, and I
noticed that as well. Yes, it was deliberately set that way ---
that beta orbitals are not read by default. To read the BETA
orbitals, use
load "xxxxx.out" filter "BETA"
probably needs documentation....
Will that do?
Bob
On Thu, Aug 19, 2010 at 7:41 AM, Jonathan Gutow <gu...@uwosh.edu>
wrote:
It appears we have more problems than just the slight change in
file format...At some point we changed things so that in UHF files
(even the old format) the beta set of orbitals is not read. I
guess I haven't checked this in about 6-8 months. Bob, I may need
you to help me on this.
Jonathan
Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh Office:
920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
------------------------------------------------------------------------------
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
<ATT00001..txt><ATT00002..txt>
------------------------------------------------------------------------------
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
<ATT00001..txt><ATT00002..txt>
------------------------------------------------------------------------------
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
<ATT00001..txt><ATT00002..txt>
------------------------------------------------------------------------------
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
