Re: [Jmol-developers] Error reading UHF GAMESS output...
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 Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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
Re: [Jmol-developers] GAMESS reader/ bug report
Should be fixed. On Wed, Aug 18, 2010 at 7:46 PM, Jonathan Gutow gu...@uwosh.edu wrote: I got the latest version up and running. There definitely has been a change in file format...It may just be for UHF on linear molecules. I'll generate an additional set of test files to check this. Jonathan On Aug 18, 2010, at 4:48 PM, Jonathan Gutow wrote: We'll figure it out. I need to get my copy up and running again an verify that that is now the consistent output format. On Aug 18, 2010, at 3:17 PM, Whitwell, George wrote: I can't imagine that it is. The input file is about as simple as it could be. The same line and row of hyphens appears in the acceptable file, although preceded by different info: UHF=== OUTPUT - DENSITY CONVERGED - FINAL UHF ENERGY IS -107.5006542361 AFTER 6 ITERATIONS SPIN SZ =0.000 S-SQUARED =0.000 LZ VALUE ANALYSIS FOR THE MOS RHF===OUTPUT - DENSITY CONVERGED - TIME TO FORM FOCK OPERATORS= 0.0 SECONDS ( 0.0 SEC/ITER) TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ITER) FINAL RHF ENERGY IS -107.5006542361 AFTER 6 ITERATIONS LZ VALUE ANALYSIS FOR THE MOS Could the intervening stuff be offending your reader? -Original Message- From: Jonathan Gutow [mailto:gu...@uwosh.edu] Sent: Wednesday, August 18, 2010 4:05 PM To: jmol-developers@lists.sourceforge.net Cc: Whitwell, George Subject: Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report It seems to be coughing on the following line... LZ VALUE ANALYSIS FOR THE MOS I'm not sure what this is. It relates to something called the LZ degeneracy tolerance. I don't see it in UHF calculation I've done using GAMESS-US. George is this a special setting? Jonathan On Aug 18, 2010, at 2:40 PM, Jonathan Gutow wrote: It definitely doesn't work...This will take a little tracing...I've certainly loaded unrestricted calculations before. Thanks for spotting this. Jonathan On Aug 18, 2010, at 1:52 PM, Whitwell, George wrote: Bob et al, I greatly enjoyed the workshop and am on my way to including Jmol in my teaching materials. I'll let you know if anything special pops out. I mentioned to Jonathan a problem I found reading GAMESS output files. If I use SCFTYP=UHF, Jmol chokes on the output. I've attached example files. Thanks, George Dr. George E. Whitwell Assistant Professor - Chemistry North Carolina Wesleyan College Rocky Mount, NC (252) 985-5159 gwhitw...@ncwc.edu WGoutput.zip Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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 Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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 Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office:
Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report
done. I think this got included in 12.0.7 and 12.1.5 On Wed, Aug 18, 2010 at 4:48 PM, Jonathan Gutow gu...@uwosh.edu wrote: We'll figure it out. I need to get my copy up and running again an verify that that is now the consistent output format. On Aug 18, 2010, at 3:17 PM, Whitwell, George wrote: I can't imagine that it is. The input file is about as simple as it could be. The same line and row of hyphens appears in the acceptable file, although preceded by different info: UHF=== OUTPUT - DENSITY CONVERGED - FINAL UHF ENERGY IS -107.5006542361 AFTER 6 ITERATIONS SPIN SZ =0.000 S-SQUARED =0.000 LZ VALUE ANALYSIS FOR THE MOS RHF===OUTPUT - DENSITY CONVERGED - TIME TO FORM FOCK OPERATORS= 0.0 SECONDS ( 0.0 SEC/ITER) TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ITER) FINAL RHF ENERGY IS -107.5006542361 AFTER 6 ITERATIONS LZ VALUE ANALYSIS FOR THE MOS Could the intervening stuff be offending your reader? -Original Message- From: Jonathan Gutow [mailto:gu...@uwosh.edu] Sent: Wednesday, August 18, 2010 4:05 PM To: jmol-developers@lists.sourceforge.net Cc: Whitwell, George Subject: Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report It seems to be coughing on the following line... LZ VALUE ANALYSIS FOR THE MOS I'm not sure what this is. It relates to something called the LZ degeneracy tolerance. I don't see it in UHF calculation I've done using GAMESS-US. George is this a special setting? Jonathan On Aug 18, 2010, at 2:40 PM, Jonathan Gutow wrote: It definitely doesn't work...This will take a little tracing...I've certainly loaded unrestricted calculations before. Thanks for spotting this. Jonathan On Aug 18, 2010, at 1:52 PM, Whitwell, George wrote: Bob et al, I greatly enjoyed the workshop and am on my way to including Jmol in my teaching materials. I'll let you know if anything special pops out. I mentioned to Jonathan a problem I found reading GAMESS output files. If I use SCFTYP=UHF, Jmol chokes on the output. I've attached example files. Thanks, George Dr. George E. Whitwell Assistant Professor - Chemistry North Carolina Wesleyan College Rocky Mount, NC (252) 985-5159 gwhitw...@ncwc.edu WGoutput.zip Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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 Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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 -- This SF.net email is
Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report
Bob, Thanks. You understand those readers better than I do. I'll take a peek and see if my solution was anything like yours. Jonathan On Aug 19, 2010, at 8:33 AM, Robert Hanson wrote: done. I think this got included in 12.0.7 and 12.1.5 On Wed, Aug 18, 2010 at 4:48 PM, Jonathan Gutow gu...@uwosh.edu wrote: We'll figure it out. I need to get my copy up and running again an verify that that is now the consistent output format. On Aug 18, 2010, at 3:17 PM, Whitwell, George wrote: I can't imagine that it is. The input file is about as simple as it could be. The same line and row of hyphens appears in the acceptable file, although preceded by different info: UHF=== OUTPUT - DENSITY CONVERGED - FINAL UHF ENERGY IS -107.5006542361 AFTER 6 ITERATIONS SPIN SZ =0.000 S-SQUARED =0.000 LZ VALUE ANALYSIS FOR THE MOS RHF===OUTPUT - DENSITY CONVERGED - TIME TO FORM FOCK OPERATORS= 0.0 SECONDS ( 0.0 SEC/ ITER) TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ ITER) FINAL RHF ENERGY IS -107.5006542361 AFTER 6 ITERATIONS LZ VALUE ANALYSIS FOR THE MOS Could the intervening stuff be offending your reader? -Original Message- From: Jonathan Gutow [mailto:gu...@uwosh.edu] Sent: Wednesday, August 18, 2010 4:05 PM To: jmol-developers@lists.sourceforge.net Cc: Whitwell, George Subject: Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report It seems to be coughing on the following line... LZ VALUE ANALYSIS FOR THE MOS I'm not sure what this is. It relates to something called the LZ degeneracy tolerance. I don't see it in UHF calculation I've done using GAMESS-US. George is this a special setting? Jonathan On Aug 18, 2010, at 2:40 PM, Jonathan Gutow wrote: It definitely doesn't work...This will take a little tracing...I've certainly loaded unrestricted calculations before. Thanks for spotting this. Jonathan On Aug 18, 2010, at 1:52 PM, Whitwell, George wrote: Bob et al, I greatly enjoyed the workshop and am on my way to including Jmol in my teaching materials. I'll let you know if anything special pops out. I mentioned to Jonathan a problem I found reading GAMESS output files. If I use SCFTYP=UHF, Jmol chokes on the output. I've attached example files. Thanks, George Dr. George E. Whitwell Assistant Professor - Chemistry North Carolina Wesleyan College Rocky Mount, NC (252) 985-5159 gwhitw...@ncwc.edu WGoutput.zip Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: 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 Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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
Re: [Jmol-developers] Error reading UHF GAMESS output...
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 x.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 Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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 ATT1..txtATT2..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
Re: [Jmol-developers] Error reading UHF GAMESS output...
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 exchangeB3LYP basis 6-31G* unrestrictedFALSE 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 9101112 eigenvalues: -0.846-0.740-0.740-0.597-0.597 -0.519 131415161718 eigenvalues: -0.459-0.438-0.417-0.417-0.359 -0.340 192021222324 eigenvalues: -0.340-0.246-0.246 0.004 0.004 0.091 2526 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 x.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 Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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
[Jmol-developers] 12.1.5 color alert
Jmol developers -- be on the look-out for problems with Jmol color schemes. I did a rather intense rewrite of ColorManager and ColorEncoder classes to get rid of some static classes there that could cause undesired inter-applet problems. It mostly has to do with when you set up custom color schemes, but it might also be with Jmol/Rasmol coloring or element coloring, which also use color schemes. Bob ps: The new color() function, by the way, is very powerful. See http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=5 Who want to be the first to write us a mapped isosurface color key? -- 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 -- 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
Re: [Jmol-developers] Error reading UHF GAMESS output...
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. 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 exchangeB3LYP basis 6-31G* unrestrictedFALSE 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 8 910 1112 eigenvalues: -0.846-0.740-0.740-0.597 -0.597-0.519 13141516 1718 eigenvalues: -0.459-0.438-0.417-0.417 -0.359-0.340 19202122 2324 eigenvalues: -0.340-0.246-0.246 0.004 0.004 0.091 2526 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 x.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
Re: [Jmol-developers] Error reading UHF GAMESS output...
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 exchangeB3LYP basis 6-31G* unrestrictedFALSE 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 91011 12 eigenvalues: -0.846-0.740-0.740-0.597-0.597 -0.519 1314151617 18 eigenvalues: -0.459-0.438-0.417-0.417-0.359 -0.340 1920212223 24 eigenvalues: -0.340-0.246-0.246 0.004 0.004 0.091 2526 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 x.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
Re: [Jmol-developers] Error reading UHF GAMESS output...
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 exchangeB3LYP basis 6-31G* unrestrictedFALSE 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 8 910 1112 eigenvalues: -0.846-0.740-0.740-0.597 -0.597-0.519 13141516 1718 eigenvalues: -0.459-0.438-0.417-0.417 -0.359-0.340 19202122 2324 eigenvalues: -0.340-0.246-0.246 0.004 0.004 0.091 2526 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
Re: [Jmol-developers] Error reading UHF GAMESS output...
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 rkant...@richmond.edu 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 exchangeB3LYP basis 6-31G* unrestrictedFALSE 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 91011 12 eigenvalues: -0.846-0.740-0.740-0.597-0.597 -0.519 1314151617 18 eigenvalues: -0.459-0.438-0.417-0.417-0.359 -0.340 1920212223 24 eigenvalues: -0.340-0.246-0.246 0.004 0.004 0.091 2526 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
