On 08. 04. 15 19:46, Robert Hanson wrote: > All the orbital coefficients are read, but then in creating the surfaces, > only s-f are used. >
Thanks a lot for the explanations, Bob. All the best, Max > On Wed, Apr 8, 2015 at 11:03 AM, Latévi Max LAWSON DAKU <max.law...@unige.ch >> wrote: > >> Dear Bob, >> >> I have been able to use jmol-14.3.13_2015.04.07 to view MOs in molden >> format; they were obtained from different calculations using up to g >> basis functions. Jmol does run nicely and fast :-) >> >> I also give a try to MOs for which spherical h basis functions are being >> used. The number of MOs is correctly detected. Unfortunately, the MOs >> are not rendered in this case. I added a [11H] line to the molden file. >> This line is read and the orbital types is reported as not being >> supported, as expected: >> >> Unsupported orbital type ignored: [9G] >> Unsupported orbital type ignored: [11H] >> >> 539 molecular orbitals in model 1.1 >> >> But the presence of this line does not change the behavior of jmol. >> I went into the sources >> >> ..../jsmol/j2s/J/adapter/readers/quantumMoldenReader.js >> >> to try to understand how this works. But, I'm really lost here. >> I guess the job is done with the "readMolecularOrbitals" method >> (line 196), but I cannot figure out how you implement skipping the >> unsupported basis functions. >> >> >> In case you have time for investigating this, I've made an archive >> "viz.tar.gz" containing the molden files. It is available for download >> at >> >> http://www.filedropper.com/viztar >> >> It contains >> >> - viz/molden.inp_ORIG >> - viz/molden.inp >> >> which only differs by the presence of the [11H] line in the latter. >> >> >> Thanks a lot for your help. >> >> All the best, >> Max >> >> >> On 08. 04. 15 01:25, Latévi Max LAWSON DAKU wrote: >>> Thanks a lot, Bob! This is great! it is running nicely and fast. >>> I'll also try it also on other files I don't have at hand. >>> >>> Thanks again. >>> >>> All the best, >>> Max >>> >>> >>> >>> On 07. 04. 15 19:49, Robert Hanson wrote: >>>> see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.04.07.zip >>>> >>>> On Tue, Apr 7, 2015 at 11:29 AM, Robert Hanson <hans...@stolaf.edu> >> wrote: >>>> >>>>> OK, the new Molden format skips entries with coef 0: >>>>> >>>>> Columbus: >>>>> >>>>> 43 3.393160933753838E-002 >>>>> 44 -4.598253748351849E-003 >>>>> 45 0.000000000000000E+000 >>>>> 46 0.000000000000000E+000 >>>>> 47 2.594945043892112E-002 >>>>> 48 -1.534056772906609E-002 >>>>> >>>>> >>>>> Dalton2015: >>>>> >>>>> 329 0.000001 >>>>> 331 -0.000001 >>>>> 334 -0.000001 >>>>> 343 -0.000002 >>>>> >>>>> We can work around that. >>>>> >>>>> On Tue, Apr 7, 2015 at 11:25 AM, Robert Hanson <hans...@stolaf.edu> >> wrote: >>>>> >>>>>> Unsupported basis type for atomno=1: 9G >>>>>> >>>>>> It should be able to just skip those. >>>>>> Also, there's a normalization problem.... >>>>>> >>>>>> will get back to you >>>>>> >>>>>> Bob >>>>>> >>>>>> >>>>>> On Tue, Apr 7, 2015 at 10:37 AM, Latévi Max LAWSON DAKU < >>>>>> max.law...@unige.ch> wrote: >>>>>> >>>>>>> Dear Bob, >>>>>>> >>>>>>> Using Jmol 13.2.0 or 14.2.13_2015.03.23, I'm not able to view >> molecular >>>>>>> orbitals output in molden format by the program package dalton2015. >> I'm >>>>>>> however able to see them with gmolden version 5.2.2. >>>>>>> >>>>>>> The number of available orbitals is correctly detected and printed by >>>>>>> jmol. But it is not possible to view them using the "mo" command or >> the >>>>>>> "surfaces" menu. You improved the support of the molden format for >> the >>>>>>> 13.x. release, enabling the support of g-i basis functions, which are >>>>>>> actually ignored. But I haven't used jmol for visualizing MOs for >> long >>>>>>> and I cannot tell what can go wrong. >>>>>>> >>>>>>> I used jmol 3.2.0 or 14.2.13_2015.03.23 to view the MOs in the >>>>>>> "columbus.molden" file: this worked great! The "columbus.molden" file >>>>>>> can be found in the archive "molden_test.tar.gz" which is available >>>>>>> online, for 30 days, at the address >>>>>>> >>>>>>> http://dl.free.fr/f6KsenkB8 >>>>>>> >>>>>>> In this archive, there is also the problematic molden file >>>>>>> "dalton2015.molden". The main difference I see between the formats >> used >>>>>>> for describing the MOs in "columbus.molden" and in >> "dalton2015.molden" >>>>>>> is that in the latter only the non-vanishing coefficients are given. >>>>>>> >>>>>>> >>>>>>> Please do not hesitate to contact me for any further information you >> may >>>>>>> need. I thank you in advance for your help. >>>>>>> >>>>>>> All the best, >>>>>>> Max >>>>>>> >>>>>>> >>>>>>> >> ------------------------------------------------------------------------------ >>>>>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >>>>>>> Develop your own process in accordance with the BPMN 2 standard >>>>>>> Learn Process modeling best practices with Bonita BPM through live >>>>>>> exercises >>>>>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- >>>>>>> event?utm_ >>>>>>> >> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >>>>>>> _______________________________________________ >>>>>>> Jmol-users mailing list >>>>>>> Jmol-users@lists.sourceforge.net >>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Robert M. Hanson >>>>>> Larson-Anderson Professor of Chemistry >>>>>> Chair, Department of Chemistry >>>>>> St. Olaf College >>>>>> Northfield, MN >>>>>> http://www.stolaf.edu/people/hansonr >>>>>> >>>>>> >>>>>> 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 >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Robert M. Hanson >>>>> Larson-Anderson Professor of Chemistry >>>>> Chair, Department of Chemistry >>>>> St. Olaf College >>>>> Northfield, MN >>>>> http://www.stolaf.edu/people/hansonr >>>>> >>>>> >>>>> 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 >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> >> ------------------------------------------------------------------------------ >>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >>>> Develop your own process in accordance with the BPMN 2 standard >>>> Learn Process modeling best practices with Bonita BPM through live >> exercises >>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- >> event?utm_ >>>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >>>> >>>> >>>> >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmol-users@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >> >> >> ------------------------------------------------------------------------------ >> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >> Develop your own process in accordance with the BPMN 2 standard >> Learn Process modeling best practices with Bonita BPM through live >> exercises >> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- >> event?utm_ >> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > > > ------------------------------------------------------------------------------ > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > Develop your own process in accordance with the BPMN 2 standard > Learn Process modeling best practices with Bonita BPM through live exercises > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
