Yes that's great for the time being! Any how have a look there. -- 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: Friday, September 24, 2010 8:54 PM To: [email protected] Subject: Re: [Jmol-users] supercells OK, I have that in now; reducing to P1 exclusively. On Fri, Sep 24, 2010 at 2:36 PM, P.Canepa <[email protected]<mailto:[email protected]>> wrote: yes I think it is! This is how the supercell works in CRYSTAL A supercell is obtained by defining the new unit cell vectors as linear combinations of the primitive cell unit vectors (See SUPERCON for crystallographic cell vectors reference). The point symmetry is defined by the number of symmetry operators in the new cell. It may be reduced, not increased. The new translation vectors b01, b02, b03 are defined in terms of the old vectors b1, b2, b3 and of the matrix E, read in input by rows, as follows: b01 = e11 · b1 + e12 · b2 + e13 · b3 b02 = e21 · b1 + e22 · b2 + e23 · b3 b03 = e31 · b1 + e32 · b2 + e33 · b3 The symmetry is automatically reduced to the point symmetry operators without translational components and a further reduction of the symmetry is also possible. 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]> mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________________ From: Robert Hanson [[email protected]<mailto:[email protected]>] Sent: Friday, September 24, 2010 5:53 PM To: [email protected]<mailto:[email protected]> Subject: [Jmol-users] supercells OK, I've had a little lesson just now in supercells. (Thank you, Stephen Todd!) I think the command is going to be: load "myfile.xxx" {2 2 2} supercell "2x, x+y, z" Now, that will load 8 SUPERCELLS, each which will be constructed based on the defined unit cell of the file. (An added UNITCELL parameter would let you set that as well.) --The cell parameters will be changed --The symmetry will be set to P1. --The same "packed" and other load options will apply here, but to the supercell instead of the unit cell itself. Is it safe to say that the numbers there have to be positive integers? I.E. not "-2x, x-y, -z" ? Bob On Fri, Sep 24, 2010 at 10:33 AM, P.Canepa <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: Dear Bob OK I would like to have both visualize the supercell construction on the screen and export it with the right cell parameter! We should have also on right corner the parameters and the space group updated otherwise the user might be confused! What do you think ? However XCRYSDEN works out the supercell simply graphically as it's only acting on the input for cRYSTAL. Is then crystal which carries out the supercell recalculating the internal symmetry. Xcrysden simply write something like that into a input file suitable for crystal: SUPERCEL 2 0 0 0 2 0 0 0 2 I am sorry if I don answer at all your question. I am pretty busy this time but I am looking forward to develop the outcar reader for VASP. Thank, 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]>> mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________________ From: Robert Hanson [[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>] Sent: Friday, September 24, 2010 4:24 PM To: P.Canepa Subject: Re: xcrysden supercell So how can I help you get what you are interested in doing? On Fri, Sep 24, 2010 at 10:14 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]>>>> wrote: You are right. the fractional coordinates don't change you are right! Thank, Bob -- 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 24, 2010 2:42 PM To: P.Canepa Subject: xcrysden supercell Piero, I'm still trying to understand the supercell business. I see: http://www.xcrysden.org/doc/crystal.html#__toc__14 Is this what you are talking about? I can't implement xCrysDen here, but I think I get the general idea. This seems to me to be more than just a "supercell" -- it's a selection of atoms within a certain bounding box defined using unit cell axes vectors: {2a, (a+b), c} Certainly you could do that relatively easily in Jmol already, but it might not be obvious at first how to do that. Is that the sort of thing you are after? Really this should be very easy to do in Jmol right now, and if this is all you are after, we could certainly implement a new select WITHIN option for this. In xcrysden, surely, the fractional coordinates don't change, do they? How does this relate to your "export" idea. (Export to what, exactly, in what format?) Bob -- 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 -- 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-users mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
