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 <[email protected]> > 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 <[email protected]> > >> 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 <[email protected]> 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 [email protected] >>> 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 >>> [email protected] >>> 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 >> [email protected] >> 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 > [email protected] > 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
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