This is fixed for Jmol 13.0.9 and 13.1.9. When mapping CASTEP cube data,
Jmol was not resetting the origin to (0,0,0) at the start of mapping. So it
was pulling mapped data from the wrong place in the cube file.
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
Thank you very much, Otello, for spotting this.
Bob
On Thu, Nov 15, 2012 at 8:29 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> I'll investigate this further later today.
>
>
>
> On Thu, Nov 15, 2012 at 8:09 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> wait, I see. If I do
>>
>> isosurface "m.pot"
>>
>> then I see that the CASTEP output surface overflows into the bottom of
>> the unit cell. Yes, that's a problem. You need the PERIODIC keyword after
>> the MAP keyword in the isosurface command. Still, I'm seeing the top not
>> the same as the bottom. So there is still something odd there.
>>
>>
>>
>>
>> On Thu, Nov 15, 2012 at 7:55 AM, Robert Hanson <hans...@stolaf.edu>wrote:
>>
>>> When I try those files, this looks better to me:
>>>
>>> load "m.castep" {3 3 1}
>>> isosurface s1 resolution 10 sasurface 1.4 map "m.pot" translucent
>>>
>>> Isn't that more what you are looking for?
>>>
>>> Not sure of the additional parameters you are adding there.
>>>
>>> Bob
>>>
>>>
>>>
>>> On Thu, Nov 15, 2012 at 5:52 AM, Otello Maria Roscioni <
>>> otellomaria.rosci...@unibo.it> wrote:
>>>
>>>> I would like to visualize the electrostatic potential above a
>>>> crystalline surface. I have carried out a single-point calculation at
>>>> the plane-wave/DFT level of theory with the program CASTEP, asking to
>>>> save the formatted electrostatic potential in a separate file (with the
>>>> option "write_formatted_potential true").
>>>>
>>>> In order to map the electrostatic potential on the solvent accessible
>>>> surface -with periodic boundary conditions applied- I use the following
>>>> commands:
>>>>
>>>> $ load "molybdenite_001_01.castep" {3 3 1}; restrict cell=665; unitcell
>>>> {1 1 1/2}
>>>> $ isosurface 1 resolution 10 sasurface 1.4 map
>>>> "molybdenite_001_01.pot_fmt"
>>>>
>>>> However, the resulting top and bottom surfaces are not symmetrical as I
>>>> would expect. Furthermore, the electrostatic potential does not seem to
>>>> have been computed with the correct PBC. Is there something I miss in
>>>> the syntax?
>>>>
>>>> Thank you very much for the help!
>>>> Otello
>>>>
>>>> PS files to reproduce my test are here:
>>>> http://dl.dropbox.com/u/4235054/surf_example.zip
>>>>
>>>> --
>>>> Otello M. Roscioni
>>>> Dipartimento di Chimica Industriale "Toso Montanari"
>>>> Università di Bologna
>>>> Viale Risorgimento 4
>>>> 40136 Bologna, Italy
>>>>
>>>>
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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
>>>
>>>
>>>
>>
>>
>> --
>> 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
------------------------------------------------------------------------------
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SAP, cloud infrastructure, etc. Download 30-day Free Trial.
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