Menu
▾
▴
Re: [Jmol-developers] supercell option
|
From: Robert H. <ha...@st...> - 2010-09-21 15:58:07
|
OK, no time to work on this now, but it could be possible. Something like:
load quartz.cif {3 3 3} unitcell {2 2 2}
would say "create 27 cells, each consisting of 8 cells described in the
file" (or on this command line).
The tricky part will be that we will have to
-- generate all the atom positions as usual using the {2 2 2} lattice
-- adjust fractional coordinates
-- assign P1 symmetry and change a, b, and c distances
-- apply the symmetry business again using the {3 3 3} lattice
All this would be in AtomSetCollectionReader.
All symmetry operations would have to be removed.
Bob
On Tue, Sep 21, 2010 at 10:29 AM, P.Canepa <pc...@ke...> wrote:
> make sense the P1.
>
> I think I'm hearing you say that you would not be loading multiples of the
> supercell. Or do you also want to be able to do that? I think we would like
> to have multiples . because you build a new cell which of course could be
> expanded later for a better view
> 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: pc...@ke...
> mobile: +44 (0) 7772-9756456
> -----------------------------------------------------------
> ________________________________________
> From: Robert Hanson [ha...@st...]
> Sent: Tuesday, September 21, 2010 4:24 PM
> To: jmo...@li...
> Subject: Re: [Jmol-developers] supercell option
>
> OK, so then I think this is a LOAD command option, not something that would
> be applied after that. If you change the supercell, you have to reload the
> file.
>
> I think I'm hearing you say that you would not be loading multiples of the
> supercell. Or do you also want to be able to do that?
>
> It does seem like it would require setting the symmetry to P1 and removing
> all symmetry operations. Symmetry operations are all in terms of 1/12 unit
> cell dimensions, and obviously that is not possible with large supercells.
> So the resultant unit cell would have to be P1.
>
> All fractional coordinates would need to be recalculated based on the size
> of the supercell before the reader returns the model.
>
> Might be possible.
>
> Bob
>
> On Tue, Sep 21, 2010 at 9:44 AM, P.Canepa <pc...@ke...<mailto:
> pc...@ke...>> wrote:
> 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: pc...@ke...<mailto:pc...@ke...>
> mobile: +44 (0) 7772-9756456
> -----------------------------------------------------------
> ________________________________________
> From: Robert Hanson [ha...@st...<mailto:ha...@st...>]
> Sent: Tuesday, September 21, 2010 1:47 PM
> To: jmo...@li...<mailto:
> 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...><mailto:pc...@ke...<mailto:pc...@ke...>>>
> 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: 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 12:52 PM
> To: jmo...@li...<mailto:
> jmo...@li...><mailto:
> 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...
> >><mailto: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.
>
> --
> 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: Tuesday, September 21, 2010 2:42 AM
> 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
>
> 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...>>><mailto: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...>>><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:
> 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: 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
> -----------------------------------------------------------
> ________________________________________
> 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...>>><mailto: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...>>><mailto:
> 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...>>>><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...<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
> --
> 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...>>>><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...<mailto:pc...@ke...>>>>>
> mobile: +44 (0) 7772-9756456
> -----------------------------------------------------------
>
>
> ------------------------------------------------------------------------------
> 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
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>>>>
> 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
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>>>
> 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.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>>
> 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
> Jmo...@li...<mailto:
> Jmo...@li...><mailto:
> Jmo...@li...<mailto:
> Jmo...@li...>>
> 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
> Jmo...@li...<mailto:
> Jmo...@li...>
> 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
> Jmo...@li...
> 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
|
