Re: [Jmol-developers] supercell option

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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 
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Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@ke...
mobile: +44 (0) 7772-9756456
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________________________________________
From: Robert Hanson [ha...@st...]
Sent: Tuesday, September 21, 2010 1:47 PM
To: jmo...@li...
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 <pc...@ke...<mailto:pc...@ke...>> wrote:
Yes there is a screw axis!
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Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@ke...<mailto:pc...@ke...>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson [ha...@st...<mailto:ha...@st...>]
Sent: Tuesday, September 21, 2010 12:52 PM
To: jmo...@li...<mailto:jmo...@li...>
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 <pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>> 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.

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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: pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson [ha...@st...<mailto:ha...@st...><mailto:ha...@st...<mailto:ha...@st...>>]
Sent: Tuesday, September 21, 2010 2:42 AM
To: jmo...@li...<mailto:jmo...@li...><mailto:jmo...@li...<mailto:jmo...@li...>>
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 <ha...@st...<mailto:ha...@st...><mailto:ha...@st...<mailto:ha...@st...>><mailto:ha...@st...<mailto:ha...@st...><mailto:ha...@st...<mailto:ha...@st...>>>> 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 <pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>>> 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
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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: pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson [ha...@st...<mailto:ha...@st...><mailto:ha...@st...<mailto:ha...@st...>><mailto:ha...@st...<mailto:ha...@st...><mailto:ha...@st...<mailto:ha...@st...>>>]
Sent: Friday, September 17, 2010 5:01 PM
To: jmo...@li...<mailto:jmo...@li...><mailto:jmo...@li...<mailto:jmo...@li...>><mailto:jmo...@li...<mailto:jmo...@li...><mailto:jmo...@li...<mailto:jmo...@li...>>>
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 <pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>>>> 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
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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: pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>><mailto:pc...@ke...<mailto:pc...@ke...><mailto:pc...@ke...<mailto:pc...@ke...>>>>
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