It'does not work when you replicated the isosurface for crystals. I tried with a slab. -- 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: P.Canepa [[email protected]] Sent: Tuesday, October 26, 2010 3:17 PM To: [email protected] Subject: Re: [Jmol-users] Several questions I am sorry the structure beneath the map but not the map. I mean I don't get the superimposed map -- 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, October 26, 2010 3:11 PM To: [email protected] Subject: Re: [Jmol-users] Several questions "structure below"? PovRay export of isosurfaces works for me. On Tue, Oct 26, 2010 at 8:43 AM, P.Canepa <[email protected]<mailto:[email protected]>> wrote: Does the povray export work for isosurface. Because when I try to export them I get just the structure below. Is any thing in particular I should enter ? Thanks -- 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, October 26, 2010 1:34 PM To: [email protected]<mailto:[email protected]> Subject: Re: [Jmol-users] Several questions The atom in the plane is returned by within(0, ....) I believe. On Tue, Oct 26, 2010 at 3:57 AM, P.Canepa <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: I am sorry, it just works great! I was wondering if I want to leave atom in the plane and remove only the atom above or below. it's there any way to exclude them ? Secondly, I have also introduce in J-ICE an option to remove atoms around an atom, something like: select within( distance, { x y z}); remove selected or hide selected. I'd like to draw a sphere of radius distance around the point. Is it possible ? draw sphere1 width 3.5 {0 0 0} translucent draws a sphere with id $sphere1 of diameter 3.5 Angstroms centered at {0 0 0} don't forget to exclude the point itself. Note that an atom's xyz coordinates or the atom itself can be used: draw sphere1 width 3.5 {atomno=30} translucent and same goes for WITHIN: select within(3.5, {atomno=30}) and not atomno=30 for example. I know there is an option for isosurface, can I use it ? Can also the user decide to remove outside the distance? It would be nice! 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]>> mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________________ From: Robert Hanson [[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>] Sent: Monday, October 25, 2010 5:36 PM To: [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> Subject: Re: [Jmol-users] Several questions I tried: isosurface plane {0.5, 0, 0, -0.5} select within(2.0, plane, {0.5, 0, 0, -0.5}) selectionhalos on select within(-2.0, plane, {0.5, 0, 0, -0.5}) isosurface hkl {2 0 0} select within(-2.0, hkl, {2 0 0}) select within(2.0, hkl, {2 0 0}) with a polymer example (polymer.out), and it worked just fine. Can you show me a concrete example that doesn't work for you, Piero? On Mon, Oct 25, 2010 at 10:58 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: I tried select WITHIN(distance,planeType, planeDesignation) with slab and polymer. This doesn't make difference between negative and positive numbers in slab and polymer once defined the plane. 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: Monday, October 25, 2010 12:02 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-users] Several questions On Sun, Oct 24, 2010 at 7:05 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]>>><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, I got several questions to ask 1) I was wondering whether is possible or not to re-set the origin of the unitcell. The command set unitcell {1/2 1/2 1/2 } do that. Apparently is just a graphical nice feature.In fact, I noticed that whenever I operate an expansion of the cell with the command load '' { 2 1 1 } the cell origin is always set to 0 0 0. How come ? Is it possible to fix the origin of the cell. This becomes particularly useful when user want to change periodical properties of crystals. Because the symmetry operators are based on the unit cell having a specific origin. Obviously if you have P1 symmetry it doesn't matter, but that's a special case. Changing the unit cell using the UNITCELL command is not just for looks. It changes the calculation of atom properties uxyz, ux, uy, and uz. 2) I also noticed a possible bug when I use PACKED on 2D slab periodic structure, the structure becomes flat loosing all the Z coordinates. I didn't try the case od polymer but I suspect is the same. ok, I'll get that fixed. 3) Is in Jmol any way to select many atoms in one shot ! It would be nice having a sort of 2D, 3D graphic selectors. The possibility of drawing line, circle and sphere into Jmol to select many atoms contemporaneously would be rather useful. This is especially true when the user want for instance remove atoms located in the same area or refine a structure before creating a snapshot. Secondly the numerical selection available in Jmol is only useful when atom are grouped forming sequence. This is not always the case. all this is possible. Check the documentation. 4) Bob the Z-matrix functions you kindly sent me doesn't work for crystals and surfaces. To be precise it works but loosing entirely the structure periodicity.Have a try Are you saying you want to add an atom in every unit cell using internal coordinates? Then I think that's up to you to write a specialized set of functions that does that. It should be possible. Just increment the final atom position by whatever unit cell coordinates you have, and it should work. Thanks a lot, 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 ----------------------------------------------------------- ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Jmol-users mailing list [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]>>>> 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 ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Jmol-users mailing list [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[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 ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Jmol-users mailing list [email protected]<mailto:[email protected]><mailto:[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 ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ 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 ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
