From ndimakis at gmail.com Wed Aug 5 00:49:06 2009 From: ndimakis at gmail.com (Nicholas Dimakis) Date: Tue, 4 Aug 2009 17:49:06 -0500 Subject: [xcrysden] Problem with 2D charge density maps Message-ID: Hello I have the following systems, Pt-CO and PtOs-CO (I replaced 2 Pt atoms with Os). My calculations are using CRYSTAL06. I was able to plot the 3D maps (charge differences) with no problems. However I cannot get the 2D maps in a way that shows blue and red regions similar to the ones shown at http://www.xcrysden.org/Pictures.html. Any ideas ? Thank you -- Nikolaos Dimakis Assistant Professor Department of Physics and Geology University of Texas-Pan American 1201 W. University Drive Edinburg, TX 78539-2999 Phone: (956) 380-8761 Fax:(956) 381-2423 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090804/952d29d4/attachment.htm From tone.kokalj at ijs.si Thu Aug 6 18:57:19 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 06 Aug 2009 18:57:19 +0200 Subject: [xcrysden] Problem with 2D charge density maps In-Reply-To: References: Message-ID: <1249577839.10668.5.camel@walk.ijs.si> On Tue, 2009-08-04 at 17:49 -0500, Nicholas Dimakis wrote: > > Hello > > I have the following systems, Pt-CO and PtOs-CO (I replaced 2 Pt > atoms with Os). My calculations are using CRYSTAL06. I was able to > plot the 3D maps (charge differences) with no problems. However I > cannot get the 2D maps in a way that shows blue and red regions > similar to the ones shown at http://www.xcrysden.org/Pictures.html. > > Any ideas ? Dear Nikolaos, You will have to be more specific what is the problem with "not getting the 2D maps". At this moment I can only give you some links, where this kind of plotting is described. The xcrysden --> crystal interface is described here: http://www.xcrysden.org/doc/crystal.html (in particular: http://www.xcrysden.org/doc/crystal.html#__toc__30 and http://www.xcrysden.org/doc/crystal.html#__toc__34 ) As for general help about 3D-isosurface/2D-contour, see this: http://www.xcrysden.org/doc/density.html http://www.xcrysden.org/doc/plane1control.html http://www.xcrysden.org/doc/isocontrol.html Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Thu Aug 6 19:14:55 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 06 Aug 2009 19:14:55 +0200 Subject: [xcrysden] LIBRARY-RELATED ERROR In-Reply-To: <794492.78471.qm@web51510.mail.re2.yahoo.com> References: <794492.78471.qm@web51510.mail.re2.yahoo.com> Message-ID: <1249578895.10668.19.camel@walk.ijs.si> On Thu, 2009-07-16 at 18:01 -0700, Vahid Askarpour wrote: > TCL_LIBRARY=/Users/Vahid/XCrySDen-1.5.17-bin/external/lib/tcl8.5 > XCRYSDEN_TOPDIR=/Users/Vahid/XCrySDen-1.5.17-bin > XCRYSDEN_SCRATCH=/Users/Vahid/xcrys_tmp > > dyld: Library not loaded: /usr/X11/lib/libXmu.6.dylib > Referenced from: /Users/Vahid/XCrySDen-1.5.17-bin/bin/xcrys > Reason: Incompatible library version: xcrys requires version 9.0.0 or later, b > ut libXmu.6.dylib provides version 6.2.0 I believe the message says that your mac software is too old: xcrysden has been compiled on a higher version of X libraries, which are not backward compatible with the one on your computer. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From ndimakis at gmail.com Fri Aug 7 00:10:31 2009 From: ndimakis at gmail.com (Nicholas Dimakis) Date: Thu, 6 Aug 2009 17:10:31 -0500 Subject: [xcrysden] Problem with 2D charge density maps In-Reply-To: <1249577839.10668.5.camel@walk.ijs.si> References: <1249577839.10668.5.camel@walk.ijs.si> Message-ID: Hello Thanks for your email. I am trying t get graphs like the one shown on http://www.xcrysden.org/Pictures.html and especially the ones at "Charge density difference of ethylene adsorbed on perfect Ag(001) surface (left), above mono-atomic step of Ag(410) surface (middle), and on-top of Ag ad-atom (right). Ref: A. Kokalj et al., J. Phys. Chem. B 106, 9839--9846 (2002)." [blue and red regions] What I do is to read the f.9 files from CRYSTAL06 and do a 2d map difference calculation using xcrysden. I use resolution 0.1 in the first card The "second" screen pops-up (i.e., CRYSTAL06 properties have been calculated and then I do the following Select color basis :RGB Scale function Linear (or anything else it same results as long as I adjust the range) Ranges: the default is -7.12 to +39.86 and I get nothing !. If i go to -0.001 +0.001 then I get something, which are the isolines that I was looking for. If I pick display color plane then I get blue, red areas in green (or other color) backbground. Is it possible to have a white plane so red, blue and the isolines also to be visible ? Thank you On Thu, Aug 6, 2009 at 11:57 AM, Tone Kokalj wrote: > On Tue, 2009-08-04 at 17:49 -0500, Nicholas Dimakis wrote: > > > > Hello > > > > I have the following systems, Pt-CO and PtOs-CO (I replaced 2 Pt > > atoms with Os). My calculations are using CRYSTAL06. I was able to > > plot the 3D maps (charge differences) with no problems. However I > > cannot get the 2D maps in a way that shows blue and red regions > > similar to the ones shown at http://www.xcrysden.org/Pictures.html. > > > > Any ideas ? > > Dear Nikolaos, > > You will have to be more specific what is the problem with "not getting > the 2D maps". > > At this moment I can only give you some links, where this kind of > plotting is described. The xcrysden --> crystal interface is described > here: > > http://www.xcrysden.org/doc/crystal.html > > (in particular: http://www.xcrysden.org/doc/crystal.html#__toc__30 > and http://www.xcrysden.org/doc/crystal.html#__toc__34 ) > > As for general help about 3D-isosurface/2D-contour, see this: > > http://www.xcrysden.org/doc/density.html > http://www.xcrysden.org/doc/plane1control.html > http://www.xcrysden.org/doc/isocontrol.html > > > Regards, Tone > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Nikolaos Dimakis Assistant Professor Department of Physics and Geology University of Texas-Pan American 1201 W. University Drive Edinburg, TX 78539-2999 Phone: (956) 380-8761 Fax:(956) 381-2423 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090806/e7dbf440/attachment.htm From tone.kokalj at ijs.si Mon Aug 10 13:24:46 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 10 Aug 2009 13:24:46 +0200 Subject: [xcrysden] Problem with 2D charge density maps In-Reply-To: References: <1249577839.10668.5.camel@walk.ijs.si> Message-ID: <1249903486.31888.72.camel@walk.ijs.si> On Thu, 2009-08-06 at 17:10 -0500, Nicholas Dimakis wrote: > What I do is to read the f.9 files from CRYSTAL06 and do a 2d map > difference calculation using xcrysden. > > I use resolution 0.1 in the first card > > The "second" screen pops-up (i.e., CRYSTAL06 properties have been > calculated and then I do the following > > Select color basis :RGB > Scale function Linear (or anything else it same results as long as I > adjust the range) > Ranges: the default is -7.12 to +39.86 and I get nothing !. The default range is from minimum to maximum value that appears in the data-grid. > If i go to -0.001 +0.001 then I get something, which are the isolines > that I was looking for. Which is what you are supposed to set! > If I pick display color plane then I get blue, red areas in green (or > other color) backbground. Is it possible to have a white plane so red, > blue and the isolines also to be visible ? You get green because you selected RGB color-basis (RGB=Red-Green-Blue). To get the blue-white-red colors of colorplane, you sould select the BLUE-WHITE-RED color-basis. Then you may also change the color of isolines to black to make them more apparent. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html