OK, the QChem reader should be working now -- default for UHF is all orbitals, alpha and beta; filter "BETA" or filter "ALPHA" works now; code better integrated into MOReader subclass. There were a few other minor problems there with labels as well.
Bob 2010/8/19 René Kanters <[email protected]> > 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 <[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 > <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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