OK, then that's a bug in Jmol -- it is expecting the orbitals in
energy-order and needs to have that for displaying homo and lumo. If it's
all right with you, I would like to add a sort to those so that they are in
the proper energy order and not symmetry order. Is there any real reason to
keep them in symmetry order? You can always only load just a given symmetry
if you want.
On Mon, May 13, 2013 at 7:13 AM, Latévi Max LAWSON DAKU <max.law...@unige.ch
> wrote:
>
>
> On 13. 05. 13 12:38, Robert Hanson wrote:
>
> My pleasure. It's a fix for 13.0 and 13.1.
>
>
> :-)
>
> It so comfortable to use the MO command from the console ;-)
>
> A couple of chemistry questions:
>
> Q: Why in this Fe(NCH)6 complex are there only 19 occupied orbitals? They
> look great, but aren't there far more valence electrons? Many of them look
> like core orbitals. I count at least 60 valence electrons just in HCN. So
> where are they? (Only 38 electrons accounted for?)
>
>
> There are 107 electrons. The MOs are in fact displayed by blocks,
> according to
> their symmetry: Ag orbitals come first, then those of B3u, B2u, B1g, B1u,
> B2g,
> B3g and finally Au symmetry (grep Sym molden.inp). This in ok in that the
> number
> of MOs of a given symmetry can be read in the main Dalton2011 output.
>
>
> Q: Why are the doubly-occupied orbitals labeled "Alpha"? Aren't
> "alpha/beta" orbitals singly occupied?
>
>
> These MOs are obtained from a restricted-open-shell (actually, ROHF)
> calculation calculations,
> and the spin-up and spin-down spinorbitals have the same spatial parts. In
> this case, as you
> noticed, the molden driver in Dalton2011 simply outputs the MOs only once,
> with the right
> occupation numbers and labeling them "Alpha". The "Spin= (Alpha|Beta)"
> entry seems required
> by molden when specifying MOs.
>
> Please do not hesitate for any other question you may have.
>
> Best,
> Max
>
>
>
>
> Bob
>
>
> On Mon, May 13, 2013 at 2:59 AM, Latévi Max LAWSON DAKU <
> max.law...@unige.ch> wrote:
>
>> Thanks a lot, Bob !
>>
>> This is working nicely :-)
>>
>> Best,
>> Max
>>
>> On 13. 05. 13 00:13, Robert Hanson wrote:
>>
>> OK, the Molden reader should work up to orbital type i. (Untested past
>> g.) Anything past f will be ignored. Assumptions here:
>>
>> type spherical/cartesian: G 9/15, H 11/21, I 13/28 (all ignored)
>>
>> http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.12a.zip
>>
>>
>> Bob
>>
>>
>>
>>
>> On Sun, May 12, 2013 at 12:41 PM, Latévi Max LAWSON DAKU <
>> max.law...@unige.ch> wrote:
>>
>>> Dear Bob,
>>>
>>> I have been able to generate an input file, in molden format, which
>>> can be viewed with molden/gmolden-5.0 (geometry and MOs). Trying
>>> to open it with Jmol-13.0.14 fails with the following error message
>>>
>>> script ERROR: Error reading file at line 442:
>>> g 2 1.00
>>> 8
>>> for file /tmp/molden.inp
>>> type Molden
>>> ----
>>> load >> "molden.inp" <<
>>>
>>> which may correspond to the fact that "g" functions are not supported.
>>>
>>> Do you have time to look at this ? If so, the file, compressed,
>>> (molden.inp.gz)
>>> can be downloaded at the following address
>>>
>>> This file (molden.inp.gz) can be found at the a
>>> http://dl.free.fr/muBvAUeyr
>>>
>>> All the best,
>>> Max
>>>
>>>
>>>
>>>
>>> On 03. 05. 13 14:47, Robert Hanson wrote:
>>>
>>>
>>>
>>>
>>> On Thu, May 2, 2013 at 2:40 PM, Latévi Max LAWSON DAKU <
>>> max.law...@unige.ch> wrote:
>>>
>>>>
>>>>
>>>> On 02. 05. 13 19:34, Robert Hanson wrote:
>>>>
>>>> Max,
>>>>
>>>>
>>>>
>>>> Dear Bob,
>>>>
>>>> I thank you a lot for your kind reply.
>>>>
>>>>
>>>> Well, there are a couple problems with the Malden reader -- requiring
>>>> no blank line after [GTO] is an easy fix; g orbitals not implemented
>>>> (easily fixed). Maybe a bigger issue (not solvable, probably).
>>>>
>>>> Q: Are you OK with ignoring the g orbitals?
>>>>
>>>>
>>>> Yes. They should contribute little to the molecular orbitals, which
>>>> I am interested in. Actually, if proceeding so, would it possible to
>>>> ignore 'h' and 'i' functions as well ?
>>>>
>>>
>>> sure. What are the number of orbitals in h/i cartesian/spherical sets?
>>>
>>>
>>>>
>>>>
>>>> There seems to be something I'm missing. There are only 492 listed MO
>>>> coefficients, but there are 711 listed atomic orbitals.
>>>>
>>>> 711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)
>>>>
>>>> Those numbers should match. (NEED to match.)
>>>>
>>>> Q: So what is 492?
>>>>
>>>>
>>>> This really is the number of basis functions: the basis set is made
>>>> of 492 contracted Gaussian functions, consisting each in a linear
>>>> combination of some of the 711 primitive Gaussian functions.
>>>> I guess that the manner in which the MOs are listen takes the
>>>> contractions into account.
>>>>
>>>
>>> I don't see it. Please explain this particular file set in detail.
>>> There 301 Gaussian sets listed, not 492.
>>>
>>> 301 = 166 s + 84 p + 34 d + 15 f + 2 g
>>>
>>> For example:
>>>
>>> s 22 1.00
>>> 4316265.0000000 1.0000000000
>>> 646342.4000000 0.0000000000
>>> 147089.7000000 0.0000000000
>>> 41661.5200000 0.0000000000
>>> 13590.7700000 0.0000000000
>>> 4905.7500000 0.0000000000
>>> 1912.7460000 0.0000000000
>>> 792.6043000 0.0000000000
>>> 344.8065000 0.0000000000
>>> 155.8999000 0.0000000000
>>> 72.2309100 0.0000000000
>>> 32.7250600 0.0000000000
>>> 15.6676200 0.0000000000
>>> 7.5034830 0.0000000000
>>> 4.6844000 0.0000000000
>>> 3.3122230 0.0000000000
>>> 1.5584710 0.0000000000
>>> 1.2204000 0.0000000000
>>> 0.6839140 0.0000000000
>>> 0.1467570 0.0000000000
>>> 0.0705830 0.0000000000
>>> 0.0314490 0.0000000000
>>>
>>> Each set may have more than one directional component, thus we have
>>> total number of independent coefficients:
>>>
>>> 711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)
>>>
>>> How do you figure that there are only 492 MO coefficients?
>>>
>>>
>>>
>>>
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>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> 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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and
>> their applications. This 200-page book is written by three acclaimed
>> leaders in the field. The early access version is available now.
>> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
>>
>>
>>
>> _______________________________________________
>> Jmol-users mailing
>> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
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>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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
>
>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and
> their applications. This 200-page book is written by three acclaimed
> leaders in the field. The early access version is available now.
> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
>
>
>
> _______________________________________________
> Jmol-users mailing
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> ------------------------------------------------------------------------------
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> their applications. This 200-page book is written by three acclaimed
> leaders in the field. The early access version is available now.
> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
> _______________________________________________
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>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
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