All the orbital coefficients are read, but then in creating the surfaces,
only s-f are used.
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
> _______________________________________________
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>
--
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
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