Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Friese Daniel Henrik]

And another question on this topic: Is it possible to select orbitals by 
symmetry? In the version I am using now (14.2.15) I can adress the orbitals by 
their order in energy.


$ mo 35


gives me the 35th orbital in the enery order. Is there also a possiblity to 
e.g. get the 35th orbital in pointgroup b?



Best regards,

Daniel


__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency

Von: Robert Hanson 
Gesendet: Dienstag, 8. September 2015 21:27
An: jmol-users@lists.sourceforge.net
Betreff: Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden 
input file: Problem with symmetry

Daniel, two suggestions:

1) Try 14.2
2) Send me the offending file so I can try that myself.


On Tue, Sep 8, 2015 at 4:46 AM, Friese Daniel Henrik 
> wrote:
Dear jmol users and developers,

Yesterday I was really happy when I found out that I can plot molecular 
orbitals in JMOL by just loading a molden input file which is generated 
automatically by the Dalton program. Today I tried this for another molecule 
and it turned out to be that it did not work. The major difference between the 
molecules is that the one I tried yesterday had no point group symmetry while 
the one I tried today has it. If I request plotting for e.g. orbital 80 by 
typing "mo 80" in the console nothing happens. There is neither an error 
message nor a result. Do I do anything wrong there or is it a bug? I am using 
version 13.2.7

Thanks to everybody who takes the time to answer.

Best regards,
Daniel



__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency

--

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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

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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Robert Hanson]

There is not a way to detect the point group of an MO.
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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Kubasik, Matthew A.]

Daniel,

Could it be the MO settings in your second file?   The MO’s may be there, just 
hard to see.   You may need to adjust the Jmol’s MO parameters in your second 
model that isn’t showing MO’s.

MO documentation is here:
http://chemapps.stolaf.edu/jmol/docs/index.htm?command=mo=14.3.16_2015.08.21

Specifically, try the CUTOFF parameter:

mo CUTOFF (decimal)
Sets the cutoff value for the isosurface that defines the orbital. This number 
may be dependent upon the computational package used to generate the orbitals. 
Values in the range 0.005 - 0.05 may need to be experimented with in order to 
get the best display. Values closer to zero lead to surfaces further from the 
atoms (larger orbitals). Both positive and negative cutoffs are allowed. A 
positive number indicates to use both positive and negative cutoffs. Adding an 
explicit "+" sign before the number indicates that only the positive part of 
the surface is desired.


Matt



On Sep 8, 2015, at 5:47 AM, Friese Daniel Henrik 
> wrote:

Dear jmol users and developers,

Yesterday I was really happy when I found out that I can plot molecular 
orbitals in JMOL by just loading a molden input file which is generated 
automatically by the Dalton program. Today I tried this for another molecule 
and it turned out to be that it did not work. The major difference between the 
molecules is that the one I tried yesterday had no point group symmetry while 
the one I tried today has it. If I request plotting for e.g. orbital 80 by 
typing "mo 80" in the console nothing happens. There is neither an error 
message nor a result. Do I do anything wrong there or is it a bug? I am using 
version 13.2.7

Thanks to everybody who takes the time to answer.

Best regards,
Daniel



__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency
--
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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Friese Daniel Henrik]

Dear Matthew,

Thank you for your reply. I do not use a second file. The command I am typing is

$ jmol jmol ecd_camb3lyp_6hel.molden

Then I get a jmol window with the structure. For a file for a molecule with 
similar size but without symmetry I can easily get the mos by typing e.g.

$ mo 80

in the jmol console. Then it takes some time to render the orbital. What 
happens in this case is that the calculation time is way shorter (although the 
molecule is of the same size) and nothing happens after it is through 
(indicated by a movement of the mouse indicator in the jmol window). I have 
also already compared the entries in the molden input files for the different 
molecules and the only difference I found is that for certain orbitals there is 
another indicator for the point group. Without point group symmetry the 
indicator is always A, in my case (C2 symmetry) it is either A or B. Also 
playing around with the cutoff values does not have any influence. When I open 
the console the number of orbitals is recognized properly, however I should 
mention that the order is not in energy order but in in energy order within the 
irreducible representation. The molden input file has been generated by the 
Dalton program by the way. 

I already had a look at the manual page but I did not find any solution for the 
problem. Do I maybe have to tell jmol that the orbitals contain symmetry?


Best regards,
Daniel


__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency


Von: Kubasik, Matthew A. 
Gesendet: Dienstag, 8. September 2015 13:22
An: jmol-users@lists.sourceforge.net
Betreff: Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden 
input file: Problem with symmetry

Daniel,

Could it be the MO settings in your second file?   The MO’s may be there, just 
hard to see.   You may need to adjust the Jmol’s MO parameters in your second 
model that isn’t showing MO’s.

MO documentation is here:
http://chemapps.stolaf.edu/jmol/docs/index.htm?command=mo=14.3.16_2015.08.21

Specifically, try the CUTOFF parameter:

mo CUTOFF (decimal)
Sets the cutoff value for the isosurface that defines the orbital. This number 
may be dependent upon the computational package used to generate the orbitals. 
Values in the range 0.005 - 0.05 may need to be experimented with in order to 
get the best display. Values closer to zero lead to surfaces further from the 
atoms (larger orbitals). Both positive and negative cutoffs are allowed. A 
positive number indicates to use both positive and negative cutoffs. Adding an 
explicit "+" sign before the number indicates that only the positive part of 
the surface is desired.


Matt



On Sep 8, 2015, at 5:47 AM, Friese Daniel Henrik 
> wrote:

Dear jmol users and developers,

Yesterday I was really happy when I found out that I can plot molecular 
orbitals in JMOL by just loading a molden input file which is generated 
automatically by the Dalton program. Today I tried this for another molecule 
and it turned out to be that it did not work. The major difference between the 
molecules is that the one I tried yesterday had no point group symmetry while 
the one I tried today has it. If I request plotting for e.g. orbital 80 by 
typing "mo 80" in the console nothing happens. There is neither an error 
message nor a result. Do I do anything wrong there or is it a bug? I am using 
version 13.2.7

Thanks to everybody who takes the time to answer.

Best regards,
Daniel



__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency
--
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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Robert Hanson]

Daniel, two suggestions:

1) Try 14.2
2) Send me the offending file so I can try that myself.


On Tue, Sep 8, 2015 at 4:46 AM, Friese Daniel Henrik  wrote:

> Dear jmol users and developers,
>
> Yesterday I was really happy when I found out that I can plot molecular
> orbitals in JMOL by just loading a molden input file which is generated
> automatically by the Dalton program. Today I tried this for another
> molecule and it turned out to be that it did not work. The major difference
> between the molecules is that the one I tried yesterday had no point group
> symmetry while the one I tried today has it. If I request plotting for e.g.
> orbital 80 by typing "mo 80" in the console nothing happens. There is
> neither an error message nor a result. Do I do anything wrong there or is
> it a bug? I am using version 13.2.7
>
> Thanks to everybody who takes the time to answer.
>
> Best regards,
> Daniel
>
>
>
>
> __
> Dr. Daniel Friese
> Centre for Theoretical and Computational Chemistry
> Universitetet i Tromsø - Norges Arktiske Universitet
> Norway
>
> Best regards also to the secret reader from the National Security Agency
>
>
> --
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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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
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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Friese Daniel Henrik]

Dear Robert,


Thanks for your mail. I now changed to version 14.2.15 and everything is 
working fine. Are you interested in the input file anyway to fix some bugs?


Best regards,

Daniel


__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency

Von: Robert Hanson 
Gesendet: Dienstag, 8. September 2015 21:27
An: jmol-users@lists.sourceforge.net
Betreff: Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden 
input file: Problem with symmetry

Daniel, two suggestions:

1) Try 14.2
2) Send me the offending file so I can try that myself.


On Tue, Sep 8, 2015 at 4:46 AM, Friese Daniel Henrik 
> wrote:
Dear jmol users and developers,

Yesterday I was really happy when I found out that I can plot molecular 
orbitals in JMOL by just loading a molden input file which is generated 
automatically by the Dalton program. Today I tried this for another molecule 
and it turned out to be that it did not work. The major difference between the 
molecules is that the one I tried yesterday had no point group symmetry while 
the one I tried today has it. If I request plotting for e.g. orbital 80 by 
typing "mo 80" in the console nothing happens. There is neither an error 
message nor a result. Do I do anything wrong there or is it a bug? I am using 
version 13.2.7

Thanks to everybody who takes the time to answer.

Best regards,
Daniel



__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency

--

___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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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

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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Angel Herráez]

Hi Daniel
I really have little experience with MO, but sometimes the file contains 
several "models" or "frames" and the info on MO are not in the first frame
Try advancing to other frames (either by command like frame 2 or using the 
button bar in Jmol app) and then invoke the MO


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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

[Kubasik, Matthew A.]

Daniel,

By “second file” I only meant the file that is not working.

Like Angel, I’m no expert on MO visualization, either.  In version 14.3.16 of 
the Jmol app, the console shows (when reading Gaussian files) which model has 
the mo’s.

For example, the console reads, upon loading a gaussian log file:

24 models
26 molecular orbitals in model 1.2
26 molecular orbitals in model 1.10
26 molecular orbitals in model 1.12

$ model 1.12
$ mo 1

So, you may want to download a more recent version to have a console confirm 
for you that mo’s exist in your file.

Gaussian performs a population analysis before and after geometry optimization, 
so you get MO’s in model 1.2 and model 1.10.  I must confess I do not know 
what, exactly, is the difference between mo’s in model 1.10 vs model 1.12.  
They look identical to me.  Subsequent models hold the normal mode information.)

(File read by Jmol was generated by g09,  using a route section of # HF/6-31G 
opt freq pop=full gfprint)

Matt

On Sep 8
, 2015, at 8:02 AM, Friese Daniel Henrik 
> wrote:

Dear Matthew,

Thank you for your reply. I do not use a second file. The command I am typing is

$ jmol jmol ecd_camb3lyp_6hel.molden

Then I get a jmol window with the structure. For a file for a molecule with 
similar size but without symmetry I can easily get the mos by typing e.g.

$ mo 80

in the jmol console. Then it takes some time to render the orbital. What 
happens in this case is that the calculation time is way shorter (although the 
molecule is of the same size) and nothing happens after it is through 
(indicated by a movement of the mouse indicator in the jmol window). I have 
also already compared the entries in the molden input files for the different 
molecules and the only difference I found is that for certain orbitals there is 
another indicator for the point group. Without point group symmetry the 
indicator is always A, in my case (C2 symmetry) it is either A or B. Also 
playing around with the cutoff values does not have any influence. When I open 
the console the number of orbitals is recognized properly, however I should 
mention that the order is not in energy order but in in energy order within the 
irreducible representation. The molden input file has been generated by the 
Dalton program by the way.

I already had a look at the manual page but I did not find any solution for the 
problem. Do I maybe have to tell jmol that the orbitals contain symmetry?


Best regards,
Daniel


__
Dr. Daniel Friese
Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency


Von: Kubasik, Matthew A. >
Gesendet: Dienstag, 8. September 2015 13:22
An: jmol-users@lists.sourceforge.net
Betreff: Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden 
input file: Problem with symmetry

Daniel,

Could it be the MO settings in your second file?   The MO’s may be there, just 
hard to see.   You may need to adjust the Jmol’s MO parameters in your second 
model that isn’t showing MO’s.

MO documentation is here:
http://chemapps.stolaf.edu/jmol/docs/index.htm?command=mo=14.3.16_2015.08.21

Specifically, try the CUTOFF parameter:

mo CUTOFF (decimal)
Sets the cutoff value for the isosurface that defines the orbital. This number 
may be dependent upon the computational package used to generate the orbitals. 
Values in the range 0.005 - 0.05 may need to be experimented with in order to 
get the best display. Values closer to zero lead to surfaces further from the 
atoms (larger orbitals). Both positive and negative cutoffs are allowed. A 
positive number indicates to use both positive and negative cutoffs. Adding an 
explicit "+" sign before the number indicates that only the positive part of 
the surface is desired.


Matt



On Sep 8, 2015, at 5:47 AM, Friese Daniel Henrik 
> wrote:

Dear jmol users and developers,

Yesterday I was really happy when I found out that I can plot molecular 
orbitals in JMOL by just loading a molden input file which is generated 
automatically by the Dalton program. Today I tried this for another molecule 
and it turned out to be that it did not work. The major difference between the 
molecules is that the one I tried yesterday had no point group symmetry while 
the one I tried today has it. If I request plotting for e.g. orbital 80 by 
typing "mo 80" in the console nothing happens. There is neither an error 
message nor a result. Do I do anything wrong there or is it a bug? I am using 
version 13.2.7

Thanks to everybody who takes the time to answer.

Best regards,
Daniel