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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> Jmol-users@lists.sourceforge.net
>>> 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
------------------------------------------------------------------------------
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
