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
