a: I am not talking about just the number in the upper left corner
a: {atomno=3}.fxyz should have the fractionalcorrdinates respect to the new
cell
a: {atomno=3}.uxyz should be exactly as {atomno=3}.fxyz since the new cell is
the supercell
a: What should draw intersection unitcell hkl {2 2 2} do? it should behave as
in the unitcell
a: What should isosurface slab unitcell do? I think the unitcell now is the
uspercell.
a: What would we do with all the symmetry operators? They are defined in terms
of the simple unit cell. : For sake of semplicity could we force the supercell
to be P1. Then we will introduce the simmetry operator?
a: What would we do about the additional symmetry operators that would be
created? see above
My idea is that the user has two commands which act differentely:
1) expand the cell as now Jmol already does
2) force the expansion to be the new cell!
P.S. In principle when you apply the transformation the symmetry of the
supercell has to decrease or at least be the same not for certain increase !
thanks, Piero
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: [email protected]
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson [[email protected]]
Sent: Tuesday, September 21, 2010 1:47 PM
To: [email protected]
Subject: Re: [Jmol-developers] supercell option
Well, the point is that that's a huge problem. Because Jmol already uses the
symmetry elements found in the file to construct the model. I guess we could
add additional screw axes, but that would break the relationship between the
model and the file. So a general solution is not easy to see.
Tell me more exactly what you would like this "supercell" business to do.
Q: Are we just talking about the numbers in the upper left corner and the
outline of the unit cell?
Q: What should {atomno=3}.fxyz to report?
Q: What should {atomno=3}.uxyz to report?
Q: What should draw intersection unitcell hkl {2 2 2} do?
Q: What should isosurface slab unitcell do?
Q: What would we do with all the symmetry operators? They are defined in terms
of the simple unit cell.
Q: What would we do about the additional symmetry operators that would be
created?
All these need to be answered in order to understand the implications of
changing the unit cell dimensions.
Bob
On Tue, Sep 21, 2010 at 7:04 AM, P.Canepa
<[email protected]<mailto:[email protected]>> wrote:
Yes there is a screw axis!
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: [email protected]<mailto:[email protected]>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson [[email protected]<mailto:[email protected]>]
Sent: Tuesday, September 21, 2010 12:52 PM
To:
[email protected]<mailto:[email protected]>
Subject: Re: [Jmol-developers] supercell option
Let's not guess. I don't think that's correct, because in going from one unit
cell to another there is a translation, which, if you combine unit cells still
has to be represented. I guess technically it's a C-1 screw axis.
On Tue, Sep 21, 2010 at 2:01 AM, P.Canepa
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
wrote:
As long as you don't change the structure the symmetry is maintained. That's my
guess!
To be honest I am also looking for the cell expansion.
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail:
[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson
[[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>]
Sent: Tuesday, September 21, 2010 2:42 AM
To:
[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>
Subject: Re: [Jmol-developers] supercell option
Also, what about the symmetry operations? Wouldn't they have to have totally
different values? I'm not certain you can just multiply the unit cell in
general and have the same number of symmetry operations.
On Mon, Sep 20, 2010 at 8:41 PM, Robert Hanson
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>>
wrote:
Oh, you mean somehow tell it to display multiples of the unit cell instead of
the unit cell itself. Yes, I see how that could be useful especially in the
case of primitive unit cells.
Are we talking just about the display of the unit cell itself, or about the
coordinates and all? In other words, do you really want it to display different
values for a, b, and c? Do you want {atomno=3}.fxyz and/or {atomno=3}.uxyz to
change?
Bob
On Mon, Sep 20, 2010 at 1:56 PM, P.Canepa
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>>
wrote:
It doesn't the cell parameters are always the same as in the {1 1 1}!for
instance if my a in the 1 1 1 is 5 in the 2 1 1 has to become 10.
I thinks it should be an extra option as user may just want to expand the cell
without making the supercell, keeping the original cell parameters.
Thanks, Piero
--
Please consider the environment before printing this e-mail
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail:
[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson
[[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>]
Sent: Friday, September 17, 2010 5:01 PM
To:
[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
Subject: Re: [Jmol-developers] supercell option
load "" {2 2 2}
works just fine, right?
Bob
On Fri, Sep 17, 2010 at 2:04 AM, P.Canepa
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>>>
wrote:
Dear all,
could be possible to add an option to re-set the dimensions of the cell once
you the original cell is manipulated?
For instance load "" { 2 2 2} ; the command could be setSupercell ?
So then when the structure is esported both the coordinate and the cell
parameters are correctely exported.
Thanks, Piero
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail:
[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>>
mobile: +44 (0) 7772-9756456
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
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Jmol-developers mailing list
[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Jmol-developers mailing list
[email protected]<mailto:[email protected]>
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
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