There's a demo of this now up at
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm (middle column, half way
down)
Files are in http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip
On Fri, Nov 23, 2012 at 7:25 PM, Robert Hanson <[email protected]> wrote:
> so the image shows up in the email, if we are under the message limit...
>
>
>
> On Fri, Nov 23, 2012 at 5:22 PM, Robert Hanson <[email protected]> wrote:
>
>> Here is
>>
>> load co2.smol
>> mo homo squared
>>
>>
>>
>> On Fri, Nov 23, 2012 at 5:15 PM, Robert Hanson <[email protected]>wrote:
>>
>>> I'm pretty sure the squares of the orbitals are perfectly cylindrical.
>>> Why do you say they are not?
>>>
>>> sin^2(theta) + cos^2(theta) = 1
>>>
>>>
>>>
>>> On Fri, Nov 23, 2012 at 2:33 PM, Shore, Jay <[email protected]>wrote:
>>>
>>>>
>>>> This brings up a very interesting point – the electron density is not
>>>> just the sum of the squares of the orbitals. Think about carbon monoxide –
>>>> the electron density is perfectly cylindrical while the square of the
>>>> orbitals is not.
>>>>
>>>>
>>>> From: Robert Hanson <[email protected]>
>>>> Reply-To: "[email protected]" <
>>>> [email protected]>
>>>> Date: Friday, November 23, 2012 8:05 AM
>>>> To: "[email protected]" <
>>>> [email protected]>
>>>>
>>>> Subject: Re: [Jmol-users] Molecular Orbitals squaring
>>>>
>>>> This is great! Your idea will be used by many, I am sure. Organic
>>>> chemists like to talk about electron density, and we often calculate it
>>>> from charge density, but this sets the stage for doing this from MOs. For
>>>> now, it's just specific sets of orbitals, but I can make that work for all
>>>> occupied orbitals based on occupancy. Very nice!
>>>>
>>>> OK, I'll check out the Molden file reading. Jmol reads MOs up through
>>>> F.
>>>>
>>>> Bob
>>>>
>>>>
>>>> On Thu, Nov 22, 2012 at 6:02 PM, Leonardo Matheus <[email protected]>wrote:
>>>>
>>>>> Dear Bob,
>>>>>
>>>>> Thank you very very much! That is exactly what I wanted, and indeed
>>>>> the benzene example is great!
>>>>>
>>>>> But unfortunately I had two problems, for which I have posted examples
>>>>> at my webpage at http://romeo.if.usp.br/~leommj (I'm new here at the
>>>>> mailing list, and don't know if I could send attachments instead).
>>>>>
>>>>> 1) For long molecules, the squared orbitals are cut in the middle of
>>>>> the molecule. As this happens with different orbital combinations, and the
>>>>> (non-squared) MOs extend through all the molecule, I think this should be
>>>>> a
>>>>> bug. An example for this bug is on the file OC8H10.molden at the website
>>>>> above.
>>>>>
>>>>> 2) I can't plot the orbital of thiophene (squared or not). Does Jmol
>>>>> have a problem with d orbitals (I hope not, as I intended to use molecules
>>>>> with other third row elemets)? Or is it just a compatibility problem with
>>>>> my .molden files? This file is named SC4H4.molden at the same webpage.
>>>>>
>>>>> PS: I already had one such compatibility problem between my files and
>>>>> Jmol; I had to manually add a space between "[Atoms]" and "(Angs)" on the
>>>>> second line of the file for Jmol be able to read them.
>>>>>
>>>>> Many, many thanks for your help!
>>>>>
>>>>> Leonardo Jorge
>>>>> PhD Student at USP - Brazil
>>>>> Nanomol group
>>>>> http://nanomol.if.usp.br
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>>
>>>>> At Thu, 22 Nov 2012 10:40:14, Robert Hanson wrote:
>>>>>
>>>>> Leonardo,
>>>>>
>>>>> ___JmolVersion="13.1.9_dev"
>>>>>
>>>>> new feature: MO [0.5 21 0.5 20] SQUARED
>>>>> -- squares MO psi functions as it combines them.
>>>>>
>>>>> see http://chemapps.stolaf.edu/jmol/Jmol-13.zip
>>>>>
>>>>> Let me know if that is what you were talking about. I think it is.
>>>>>
>>>>> VERY interesting result with
>>>>>
>>>>> load c6h6.smol
>>>>> mo [0.5 20 0.5 21] squared
>>>>>
>>>>> This is the degenerate pair of HOMO orbitals. The result is a symmetric
>>>>> electron density equivalent at each carbon.
>>>>>
>>>>> Bob
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Monitor your physical, virtual and cloud infrastructure from a single
>>>>> web console. Get in-depth insight into apps, servers, databases,
>>>>> vmware,
>>>>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>>>>> Pricing starts from $795 for 25 servers or applications!
>>>>> http://p.sf.net/sfu/zoho_dev2dev_nov
>>>>> _______________________________________________
>>>>> Jmol-users mailing list
>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Monitor your physical, virtual and cloud infrastructure from a single
>>>> web console. Get in-depth insight into apps, servers, databases, vmware,
>>>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>>>> Pricing starts from $795 for 25 servers or applications!
>>>> http://p.sf.net/sfu/zoho_dev2dev_nov
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>>
>
>
> --
> 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
>
>
>
--
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
------------------------------------------------------------------------------
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
