From masoodyousaf1 at yahoo.com Tue Jul 2 03:26:27 2013 From: masoodyousaf1 at yahoo.com (Masood Yousaf) Date: Mon, 1 Jul 2013 18:26:27 -0700 (PDT) Subject: [xcrysden] Need guidance Message-ID: <1372728387.48508.YahooMailNeo@web121101.mail.ne1.yahoo.com> Respected XcrySden community members What is the interpretation of colours and their associated logarthimic scale values in 2D contour plots generated by xcrystalden ? Kindly also suggest some useful material for their explanation.? Best wishes Masood Universiti Tecknologi Malaysia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130701/711176f5/attachment.htm From member at linkedin.com Tue Jul 2 14:38:36 2013 From: member at linkedin.com (vishal jain jain) Date: Tue, 2 Jul 2013 12:38:36 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_vamos_nos_conectar_no_?= =?utf-8?q?LinkedIn=2E?= Message-ID: <599066352.43129610.1372768716148.JavaMail.app@ela4-app0130.prod> LinkedIn ------------ vishal jain jain solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de vishal jain jain http://www.linkedin.com/e/-fe5rcs-hin31scb-4t/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I418225353_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnPcRcPkOczwNd4ALknBztzpnjCkLe3sPc38OdzkSd34LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=0shqzSXZfS75Q1 Visualizar perfil de vishal jain jain http://www.linkedin.com/e/-fe5rcs-hin31scb-4t/rso/159669735/GE7f/name/128644874_I418225353_125/?hs=false&tok=1xCWx0oIrS75Q1 ------------------------------------------ Voc? est? recebendo e-mails de convites. Este e-mail era para Andr? Pereira XCrysden. Saiba por que isto est? inclu?do: http://www.linkedin.com/e/-fe5rcs-hin31scb-4t/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=1BJaCvUa_S75Q1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043 - EUA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130702/66a4a188/attachment.htm From tone.kokalj at ijs.si Wed Jul 10 13:27:52 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 10 Jul 2013 13:27:52 +0200 Subject: [xcrysden] Fwd: Fermi surface question In-Reply-To: References: Message-ID: <1373455672.4699.7.camel@catalyst.ijs.si> On Thu, 2013-06-27 at 11:46 +0800, Sidiq Khidzir wrote: > > Hi, > > > I'm trying to plot the Fermi surface but I can't seem to be able to do > so. I have used ABINIT to obtain the bxsf file. I've attached the > bxsf file with this email. Of course you cannot see it. The two bands you provided in your BXSF file are well below the Fermi energy (this is why the band-widths plot is provided prior to FS visualization window,i.e., to realize which bands cross the Fermi energy). But if you change the isovalue to something like -0.727, you will see some surfaces (but they ain't FS). Regards, -- 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 Wed Jul 10 13:32:57 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 10 Jul 2013 13:32:57 +0200 Subject: [xcrysden] Need guidance In-Reply-To: <1372728387.48508.YahooMailNeo@web121101.mail.ne1.yahoo.com> References: <1372728387.48508.YahooMailNeo@web121101.mail.ne1.yahoo.com> Message-ID: <1373455977.4699.11.camel@catalyst.ijs.si> On Mon, 2013-07-01 at 18:26 -0700, Masood Yousaf wrote: > Respected XcrySden community members > > What is the interpretation of colours and their associated logarthimic > scale values in 2D contour plots generated by xcrystalden ? Kindly > also suggest some useful material for their explanation. Here you can see some possible color-bases: http://www.xcrysden.org/doc/plane1control.html#__toc__4 The interpretation is that these colors run from minimun to maximum values specified in "Ranges" in a given selected scale (linear, log, ...). You may plot the thermometer (click the "display thermometer" checkbutton) to have some better idea of which color represents which values. 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 masoodyousaf1 at yahoo.com Wed Jul 10 15:24:26 2013 From: masoodyousaf1 at yahoo.com (Masood Yousaf) Date: Wed, 10 Jul 2013 06:24:26 -0700 (PDT) Subject: [xcrysden] Problem in printing/saving the structure and contour plots of electron density Message-ID: <1373462666.85615.YahooMailNeo@web121101.mail.ne1.yahoo.com> Respected Xcrystalden community and Sir Anton Kokalj I am working on xcrystalden embeded in WIEN2k code. I have completed my calculations successfully on xcrystalden but whenever I try to save the structure and contour plots of electron density fallowing error appears. Error: while executing exec /usr/bin/convert/home/wien2k/xcrys_tmp/xc_24560/tmp.ppm Kindly guide how to remove this error in order to save the structure and contour plots. Best wishes Masood -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130710/a7bc6603/attachment.htm From Aniekan.Ukpong at up.ac.za Fri Jul 12 10:12:13 2013 From: Aniekan.Ukpong at up.ac.za (Aniekan Ukpong) Date: Fri, 12 Jul 2013 10:12:13 +0200 Subject: [xcrysden] How can one move a selection (or fragment) of atoms with xcrysden? Message-ID: <51DFD67D0200007600284D29@gwise.up.ac.za> Dear all, My sincere apologies if this issue has already been treated here ('So far, I just can't find it through my archives query). I would like to know if there is some funtionality within xcrysden that allows a selection (or fragment) of atoms to be moved, withing the GUI? Sincerely, Aniekan -- Dr A. M. Ukpong, PhD (UCT) Department of Physics, University of Pretoria, Pretoria 0002, South Africa. Cell (1): +27 72 096 3302 Cell (2): +27 73 092 0896 Office: +27 12 420 3502 Fax: +27 86 546 7130 E-mail: aniekan.ukpong at up.ac.za From masoodyousaf1 at yahoo.com Fri Jul 12 17:49:27 2013 From: masoodyousaf1 at yahoo.com (Masood Yousaf) Date: Fri, 12 Jul 2013 08:49:27 -0700 (PDT) Subject: [xcrysden] Error: grab failed: another application has grub Message-ID: <1373644167.75736.YahooMailNeo@web121101.mail.ne1.yahoo.com> Dear Xcrytalden community members. I got this error while Xcrytalden was calculating electron density for contour plots. Error: grab failed: another application has grub I have two queries. what is the effect of this error on calculation ? How to remove this error ? Thanks in advance. Best wishes Masood -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130712/497ce051/attachment.html From peramsreenivas at gmail.com Sat Jul 13 14:02:56 2013 From: peramsreenivas at gmail.com (Peram sreenivasa reddy) Date: Sat, 13 Jul 2013 17:32:56 +0530 Subject: [xcrysden] Difference charge density Message-ID: Dear Xcrysden, Recently I am trying to analyze the Difference charge density plots. I got 2D plot. But i am troubling to analyze the plots. By using color thermo meter what can we conformed?. i.e if the value is negative means what? and positive means means what?. Is it indicate flow of charge from one atom to another atom from low electro negativity to high electro negativity?. Thank you in advance...... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130713/f1144836/attachment.htm From morganteng at gmail.com Mon Jul 15 21:28:43 2013 From: morganteng at gmail.com (Ao Teng) Date: Mon, 15 Jul 2013 15:28:43 -0400 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) Message-ID: Hello, Could anybody give me a clear instruction on how to install xCrysden? I'm using Ubuntu 12.04. I searched quite a bit on INTERNET, but all the instructions I found led to failure. Thank you in advance! Morgan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130715/e30c1ea4/attachment.htm From 1272370076 at qq.com Mon Jul 15 22:16:31 2013 From: 1272370076 at qq.com (=?gb18030?B?ZGFkYW5pdQ==?=) Date: Tue, 16 Jul 2013 04:16:31 +0800 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) Message-ID: there is an file named "INSTALL" or ?README? which will tell you in the package you downloaded. ------------------ Original ------------------ From: "Ao Teng"; Date: Tue, Jul 16, 2013 03:28 AM To: "xcrysden"; Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) Hello, Could anybody give me a clear instruction on how to install xCrysden? I'm using Ubuntu 12.04. I searched quite a bit on INTERNET, but all the instructions I found led to failure. Thank you in advance! Morgan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130716/635d31d5/attachment.htm From 1272370076 at qq.com Mon Jul 15 22:28:14 2013 From: 1272370076 at qq.com (=?ISO-8859-1?B?ZGFkYW5pdQ==?=) Date: Tue, 16 Jul 2013 04:28:14 +0800 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) Message-ID: try to add " >log 2>err" to every install instruction .and read the err file to find the problem every step ,you can search the problem . this is an general way to install a sofware with linux : 1: read the install file with the package 2:recod the step by append " >log 2>err" to every instruction 3:cat the recod file to see whether this step is successful and solve every error message or some warnings. 4:try every step until you finished. hope this will help you . ------------------ Original ------------------ From: "Ao Teng"; Date: Tue, Jul 16, 2013 03:28 AM To: "xcrysden"; Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) Hello, Could anybody give me a clear instruction on how to install xCrysden? I'm using Ubuntu 12.04. I searched quite a bit on INTERNET, but all the instructions I found led to failure. Thank you in advance! Morgan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130716/dde64bf0/attachment.htm From morganteng at gmail.com Mon Jul 15 23:18:18 2013 From: morganteng at gmail.com (Ao Teng) Date: Mon, 15 Jul 2013 23:18:18 +0200 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) In-Reply-To: References: Message-ID: <41536D32-9B19-4E2D-BE5B-32AF8D58FF5E@gmail.com> Thank you, I will give it a try. Ao On Jul 15, 2013, at 22:28, "dadaniu" <1272370076 at qq.com> wrote: > try to add " >log 2>err" to every install instruction .and read the err file to find the problem every step ,you can search the problem . > > this is an general way to install a sofware with linux : > 1: read the install file with the package > 2:recod the step by append " >log 2>err" to every instruction > 3:cat the recod file to see whether this step is successful and solve every error message or some warnings. > 4:try every step until you finished. > hope this will help you . > > > ------------------ Original ------------------ > From: "Ao Teng"; > Date: Tue, Jul 16, 2013 03:28 AM > To: "xcrysden"; > Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) > > Hello, > > Could anybody give me a clear instruction on how to install xCrysden? I'm using Ubuntu 12.04. I searched quite a bit on INTERNET, but all the instructions I found led to failure. Thank you in advance! > > Morgan > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130715/5cb3b00b/attachment.htm From tone.kokalj at ijs.si Thu Jul 18 10:34:09 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Jul 2013 10:34:09 +0200 Subject: [xcrysden] Problem in printing/saving the structure and contour plots of electron density In-Reply-To: <1373462666.85615.YahooMailNeo@web121101.mail.ne1.yahoo.com> References: <1373462666.85615.YahooMailNeo@web121101.mail.ne1.yahoo.com> Message-ID: <1374136449.11955.5.camel@catalyst.ijs.si> On Wed, 2013-07-10 at 06:24 -0700, Masood Yousaf wrote: > > Respected Xcrystalden community and Sir Anton Kokalj > > > I am working on xcrystalden embeded in WIEN2k code. I have completed > my calculations successfully on xcrystalden but whenever I try to save > the structure and contour plots of electron density fallowing error > appears. > > Error: while executing > exec /usr/bin/convert/home/wien2k/xcrys_tmp/xc_24560/tmp.ppm This is likely not the whole error message. It should be something like this: exec /usr/bin/convert /home/wien2k/xcrys_tmp/xc_24560/tmp.ppm output_filename where "output_filename" is the name of the file into which you intended to print. Try to execute this same command manually (prior to exiting xcrysden, as exit deletes the /home/wien2k/xcrys_tmp/xc_24560/ directory) . What happens? Regards, -- 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 Jul 18 10:38:18 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Jul 2013 10:38:18 +0200 Subject: [xcrysden] How can one move a selection (or fragment) of atoms with xcrysden? In-Reply-To: <51DFD67D0200007600284D29@gwise.up.ac.za> References: <51DFD67D0200007600284D29@gwise.up.ac.za> Message-ID: <1374136698.11955.9.camel@catalyst.ijs.si> On Fri, 2013-07-12 at 10:12 +0200, Aniekan Ukpong wrote: > Dear all, > My sincere apologies if this issue has already been treated here ('So far, I just can't find it through my archives query). > > I would like to know if there is some funtionality within xcrysden that allows a selection (or fragment) of atoms to be moved, withing the GUI? No there is not, unless you also have a CRYSTAL program and xcrysden configured properly (in this case the AdvGeom menu is active). Regards, -- 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 Jul 18 10:45:37 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Jul 2013 10:45:37 +0200 Subject: [xcrysden] Error: grab failed: another application has grub In-Reply-To: <1373644167.75736.YahooMailNeo@web121101.mail.ne1.yahoo.com> References: <1373644167.75736.YahooMailNeo@web121101.mail.ne1.yahoo.com> Message-ID: <1374137137.11955.16.camel@catalyst.ijs.si> On Fri, 2013-07-12 at 08:49 -0700, Masood Yousaf wrote: > Dear Xcrytalden community members. > > I got this error while Xcrytalden was calculating electron density for > contour plots. > > > Error: grab failed: another application has grub There are several ways (known to me) how this can happen: the displayed virtual desktop page has changed while the "Calculating" popup window exists (i.e. during the calculation) or you have closed that popup window. > what is the effect of this error on calculation ? Shouldn't cause any harm, unless it takes away the "focus", i.e., one can neither click the xcrysden's buttons nor type in the entries anymore ... Regards, -- 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 Jul 18 10:51:20 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Jul 2013 10:51:20 +0200 Subject: [xcrysden] Difference charge density In-Reply-To: References: Message-ID: <1374137480.11955.21.camel@catalyst.ijs.si> On Sat, 2013-07-13 at 17:32 +0530, Peram sreenivasa reddy wrote: > Dear Xcrysden, > > Recently I am trying to analyze the Difference > charge density plots. I got 2D plot. But i am troubling to analyze the > plots. By using color thermo meter what can we conformed?. i.e if the > value is negative means what? and positive means means what?. Is it > indicate flow of charge from one atom to another atom from low electro > negativity to high electro negativity?. It depends how you produced the charge density difference. Say, that you calculate the difference as: \Delta\rho = \rho(A-B) - \rho(A) - \rho(B), where \rho stands for electron density, A-B is the whole system, while A and B are the two fragments that constitute the A-B. In this case the positive values mean electron excess and negative values mean electron deficit. Regards, -- 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 Jul 18 10:55:52 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Jul 2013 10:55:52 +0200 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) In-Reply-To: References: Message-ID: <1374137752.11955.24.camel@catalyst.ijs.si> On Mon, 2013-07-15 at 15:28 -0400, Ao Teng wrote: > Hello, > > > Could anybody give me a clear instruction on how to install xCrysden? > I'm using Ubuntu 12.04. As far as I know, the new versions of Ubuntu have xcrysden, which means that you can install as: sudo apt-get install xcrysden (wheter 12.04 is new enough I don't know, try). Otherwise install the precompiled version of xcrysden: 32bit: http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz 64bit: http://www.xcrysden.org/download/xcrysden-1.5.53-linux_x86_64-semishared.tar.gz Regards, -- 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 martin at ruby.chemie.uni-freiburg.de Thu Jul 18 11:53:23 2013 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Thu, 18 Jul 2013 11:53:23 +0200 (CEST) Subject: [xcrysden] Problem in printing/saving the structure and contour plots of electron density In-Reply-To: <1374136449.11955.5.camel@catalyst.ijs.si> Message-ID: <20130718095323.ACE88801B3@ruby.chemie.uni-freiburg.de> > Try to execute this same command manually (prior to exiting xcrysden, as exit deletes the /home/wien2k/xcrys_tmp/xc_24560/ directory) . > Further to Tone's message, the "convert" program is part of the ImageMagick package, possibly this is not yet installed on your computer. -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From martin at ruby.chemie.uni-freiburg.de Thu Jul 18 12:06:04 2013 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Thu, 18 Jul 2013 12:06:04 +0200 (CEST) Subject: [xcrysden] Error: grab failed: another application has grub In-Reply-To: <1374137137.11955.16.camel@catalyst.ijs.si> Message-ID: <20130718100604.5EABC801B3@ruby.chemie.uni-freiburg.de> > Shouldn't cause any harm, unless it takes away the "focus", i.e., one > can neither click the xcrysden's buttons nor type in the entries > anymore ... > Actually it may cause an immediate crash of xcrysden for him, unless he had already applied the fix from http://www.democritos.it/pipermail/xcrysden/2012-May/001186.html as there has not been a release since then. (May I also use the opportunity to remind you of the XErrorHandler issue of http://www.democritos.it/pipermail/xcrysden/2012-April/001148.html - patch sent to you back then as requested - as the problem is still very much alive on openSuSE 12.3 and probably everything else that uses a relatively recent X.org version) Martin -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From tone.kokalj at ijs.si Thu Jul 18 12:24:02 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Jul 2013 12:24:02 +0200 Subject: [xcrysden] Error: grab failed: another application has grub In-Reply-To: <20130718100604.5EABC801B3@ruby.chemie.uni-freiburg.de> References: <20130718100604.5EABC801B3@ruby.chemie.uni-freiburg.de> Message-ID: <1374143042.11955.29.camel@catalyst.ijs.si> On Thu, 2013-07-18 at 12:06 +0200, Martin Kroeker wrote: > > Shouldn't cause any harm, unless it takes away the "focus", i.e., one > > can neither click the xcrysden's buttons nor type in the entries > > anymore ... > > > Actually it may cause an immediate crash of xcrysden for him, unless he > had already applied the fix from ... Martin, Thanks for correcting me and also thanks for your precious XErrorHandler reminder! Regards, -- 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 masoodyousaf1 at yahoo.com Fri Jul 19 07:07:11 2013 From: masoodyousaf1 at yahoo.com (Masood Yousaf) Date: Thu, 18 Jul 2013 22:07:11 -0700 (PDT) Subject: [xcrysden] Problem in printing/saving the structure and contour plots of electron density In-Reply-To: <1374136449.11955.5.camel@catalyst.ijs.si> References: <1373462666.85615.YahooMailNeo@web121101.mail.ne1.yahoo.com> <1374136449.11955.5.camel@catalyst.ijs.si> Message-ID: <1374210431.724.YahooMailNeo@web121106.mail.ne1.yahoo.com> Thank you Sir Antone Its really helpful. The files appear in Xcrys_tmp directory. Now the only problem left is with the printing of Thermeter scale. When I click Print Thermo then the fallowing message comes Warning: You are about to dump the content of a widget. Please make sure that no window obscures the widget to be printed. This is because Xcrysden's print is an XWD window dump. when I press OK on this message and then try to save fallowing error appears. ERROR: while executing exec xwd -id 0*280003c-out/home/wien2k/xcrys_tmp/xc_48294/0b.xwd. I dont know where this Thermo scale is saved ? Kindly guide. Best wishes Masood >________________________________ > From: Tone Kokalj >To: xcrysden at democritos.it >Sent: Thursday, July 18, 2013 4:34 PM >Subject: Re: [xcrysden] Problem in printing/saving the structure and contour plots of electron density > > >On Wed, 2013-07-10 at 06:24 -0700, Masood Yousaf wrote: >> >> Respected Xcrystalden community and Sir Anton Kokalj >> >> >> I am working on xcrystalden embeded in WIEN2k code. I have completed >> my calculations successfully on xcrystalden but whenever I try to save >> the structure and contour plots of electron density fallowing error >> appears. >> >> Error: while executing >> exec /usr/bin/convert/home/wien2k/xcrys_tmp/xc_24560/tmp.ppm > >This is likely not the whole error message. It should be something like >this: > >exec /usr/bin/convert /home/wien2k/xcrys_tmp/xc_24560/tmp.ppm output_filename > > >where "output_filename" is the name of the file into which you intended to print. > > >Try to execute this same command manually (prior to exiting xcrysden, as exit deletes the /home/wien2k/xcrys_tmp/xc_24560/ directory) . > >What happens? > >Regards, >-- >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 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130718/43258dcc/attachment.htm From masoodyousaf1 at yahoo.com Fri Jul 19 07:09:48 2013 From: masoodyousaf1 at yahoo.com (Masood Yousaf) Date: Thu, 18 Jul 2013 22:09:48 -0700 (PDT) Subject: [xcrysden] Error: grab failed: another application has grub In-Reply-To: <1374137137.11955.16.camel@catalyst.ijs.si> References: <1373644167.75736.YahooMailNeo@web121101.mail.ne1.yahoo.com> <1374137137.11955.16.camel@catalyst.ijs.si> Message-ID: <1374210588.15013.YahooMailNeo@web121104.mail.ne1.yahoo.com> Thank you once again for your explanation Sir, I can obtain contour plots even after this message. I dont know what is the effect. I was just confused might be result will be effected by this message. Best wishes Masood >________________________________ > From: Tone Kokalj >To: xcrysden at democritos.it >Sent: Thursday, July 18, 2013 4:45 PM >Subject: Re: [xcrysden] Error: grab failed: another application has grub > > >On Fri, 2013-07-12 at 08:49 -0700, Masood Yousaf wrote: >> Dear Xcrytalden community members. >> >> I got this error while Xcrytalden was calculating electron density for >> contour plots. >> >> >> Error: grab failed: another application has grub > >There are several ways (known to me) how this can happen: >the displayed virtual desktop page has changed while the "Calculating" >popup window exists (i.e. during the calculation) or you have closed >that popup window. > >> what is the effect of this error on calculation ? > >Shouldn't cause any harm, unless it takes away the "focus", i.e., one >can neither click the xcrysden's buttons nor type in the entries >anymore ... > >Regards, >-- >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 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130718/d841a5e5/attachment.htm From peramsreenivas at gmail.com Fri Jul 19 07:13:07 2013 From: peramsreenivas at gmail.com (Peram sreenivasa reddy) Date: Fri, 19 Jul 2013 10:43:07 +0530 Subject: [xcrysden] Problem in printing/saving the structure and contour plots of electron density In-Reply-To: <1374210431.724.YahooMailNeo@web121106.mail.ne1.yahoo.com> References: <1373462666.85615.YahooMailNeo@web121101.mail.ne1.yahoo.com> <1374136449.11955.5.camel@catalyst.ijs.si> <1374210431.724.YahooMailNeo@web121106.mail.ne1.yahoo.com> Message-ID: Dear Masood, Recently, I also faced the same problem (thermometer not saving). I removed the Xcrysden and re-installed. Than the problem solved. Try .... On Fri, Jul 19, 2013 at 10:37 AM, Masood Yousaf wrote: > Thank you Sir Antone > > Its really helpful. The files appear in Xcrys_tmp directory. Now the only > problem left is with the printing of Thermeter scale. When I click Print > Thermo then the fallowing message comes > > Warning: > You are about to dump the content of a widget. Please make sure that no > window obscures the widget to be printed. This is because Xcrysden's print > is an XWD window dump. > > when I press OK on this message and then try to save fallowing error > appears. > > ERROR: while executing exec xwd -id > 0*280003c-out/home/wien2k/xcrys_tmp/xc_48294/0b.xwd. > > I dont know where this Thermo scale is saved ? > Kindly guide. > > > > Best wishes > Masood > > ------------------------------ > *From:* Tone Kokalj > *To:* xcrysden at democritos.it > *Sent:* Thursday, July 18, 2013 4:34 PM > *Subject:* Re: [xcrysden] Problem in printing/saving the structure and > contour plots of electron density > > On Wed, 2013-07-10 at 06:24 -0700, Masood Yousaf wrote: > > > > Respected Xcrystalden community and Sir Anton Kokalj > > > > > > I am working on xcrystalden embeded in WIEN2k code. I have completed > > my calculations successfully on xcrystalden but whenever I try to save > > the structure and contour plots of electron density fallowing error > > appears. > > > > Error: while executing > > exec /usr/bin/convert/home/wien2k/xcrys_tmp/xc_24560/tmp.ppm > > This is likely not the whole error message. It should be something like > this: > > exec /usr/bin/convert /home/wien2k/xcrys_tmp/xc_24560/tmp.ppm > output_filename > > > where "output_filename" is the name of the file into which you intended to > print. > > > Try to execute this same command manually (prior to exiting xcrysden, as > exit deletes the /home/wien2k/xcrys_tmp/xc_24560/ directory) . > > What happens? > > Regards, > -- > 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 > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130719/3cd59fe9/attachment.htm From peramsreenivas at gmail.com Fri Jul 19 14:09:02 2013 From: peramsreenivas at gmail.com (Peram sreenivasa reddy) Date: Fri, 19 Jul 2013 17:39:02 +0530 Subject: [xcrysden] Difference charge density In-Reply-To: <1374137480.11955.21.camel@catalyst.ijs.si> References: <1374137480.11955.21.camel@catalyst.ijs.si> Message-ID: Dear Tone, Thank you very much for your reply. I want to know the flow from where to where?. Is it from lower electro negativity element to higher electro negativity element. How can we conform the type of bonding between them from these plots?. On Thu, Jul 18, 2013 at 2:21 PM, Tone Kokalj wrote: > On Sat, 2013-07-13 at 17:32 +0530, Peram sreenivasa reddy wrote: > > Dear Xcrysden, > > > > Recently I am trying to analyze the Difference > > charge density plots. I got 2D plot. But i am troubling to analyze the > > plots. By using color thermo meter what can we conformed?. i.e if the > > value is negative means what? and positive means means what?. Is it > > indicate flow of charge from one atom to another atom from low electro > > negativity to high electro negativity?. > > It depends how you produced the charge density difference. > > Say, that you calculate the difference as: > > \Delta\rho = \rho(A-B) - \rho(A) - \rho(B), > > where \rho stands for electron density, A-B is the whole system, while A > and B are the two fragments that constitute the A-B. In this case the > positive values mean electron excess and negative values mean electron > deficit. > > Regards, > -- > 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 > -- *P.V.SREENIVASA REDDY* *Research Scholar Department of Physics * *Indian Institute of Technology* *Hyderabad* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130719/9332e0c6/attachment.htm From tone.kokalj at ijs.si Fri Jul 19 17:54:30 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 19 Jul 2013 17:54:30 +0200 Subject: [xcrysden] Problem in printing/saving the structure and contour plots of electron density In-Reply-To: <1374210431.724.YahooMailNeo@web121106.mail.ne1.yahoo.com> References: <1373462666.85615.YahooMailNeo@web121101.mail.ne1.yahoo.com> <1374136449.11955.5.camel@catalyst.ijs.si> <1374210431.724.YahooMailNeo@web121106.mail.ne1.yahoo.com> Message-ID: <1374249270.4336.8.camel@catalyst.ijs.si> On Thu, 2013-07-18 at 22:07 -0700, Masood Yousaf wrote: > when I press OK on this message and then try to save fallowing error > appears. > > ERROR: while executing exec xwd -id > 0*280003c-out/home/wien2k/xcrys_tmp/xc_48294/0b.xwd. > > I dont know where this Thermo scale is saved ? As for printing the thermometer the following is important: 1. Thermometer can be printed only when it is displayed in a separate toplevel window (tick the "thermometer in toplevel" checkbutton) 2. It is printed by pressing the "Print Thermo" button. It is saved in the file specified in the popup window. As the message suggests the printing is done as a window dump; xcrysden either uses xwd or ImageMagicks's import program for dumping windows. It appears that there was a problem dumping a content of a thermometer window with the xwd program, which is likely the reason you didn't get the thermometer printed. You can try manually to dump the thermometer window as: xwd -out thermo.xwd then click on the thermometer window (not the border, but somewhere in the middle of the window) and the thermometer will be printed in file thermo.xwd Regards, -- 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 Fri Jul 19 18:04:11 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 19 Jul 2013 18:04:11 +0200 Subject: [xcrysden] Difference charge density In-Reply-To: References: <1374137480.11955.21.camel@catalyst.ijs.si> Message-ID: <1374249851.4336.17.camel@catalyst.ijs.si> On Fri, 2013-07-19 at 17:39 +0530, Peram sreenivasa reddy wrote: > Dear Tone, > Thank you very much for your reply. I want to know the > flow from where to where?. It depends how you calculate your charge density difference. > Is it from lower electro negativity element to higher electro > negativity element. Usually that is so, yes. But what you see in charge density difference plot depends how you calculate the difference. If you calculate it as a deformation density: \delta\rho = \rho(system) - \sum_{i=1}^{natoms} \rho(atom_i) then you may see what you proposed. But say you want to see a chemical bond between the fragment1 and fragment2 in a system that is composed of fragment1+fragment2 (where fragment means some group of atoms), then you may do: \delta\rho = \rho(system) - \rho(fragment1) - \rho(fragment2) where the geometries of system, fragment1, and fragment2 are kept compatible. So you see, what charge density difference shows depends on how it was calculated. Regards, -- 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 member at linkedin.com Wed Jul 24 09:39:24 2013 From: member at linkedin.com (priya goud via LinkedIn) Date: Wed, 24 Jul 2013 07:39:24 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn=2E?= Message-ID: <1374387608.8696230.1374651564061.JavaMail.app@ela4-app3607.prod> LinkedIn ------------ priya goud solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de priya goud http://www.linkedin.com/e/-fe5rcs-hji81r7m-4a/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I432694746_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnPoQdPgVdz8Pd4ALd6ViknBJs78LdPwSczgMe38Odj4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=15L7c88IebBRQ1 Visualizar perfil de priya goud http://www.linkedin.com/e/-fe5rcs-hji81r7m-4a/rso/146773710/Hixn/name/128644874_I432694746_125/?hs=false&tok=09uGp-k4GbBRQ1 ------------------------------------------ Voc? est? recebendo e-mails de convites. Este e-mail era para Andr? Pereira XCrysden. Saiba por que isto est? inclu?do: http://www.linkedin.com/e/-fe5rcs-hji81r7m-4a/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=3bl0VStlqbBRQ1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043 - EUA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130724/c5942d62/attachment.htm From morganteng at gmail.com Wed Jul 24 20:52:27 2013 From: morganteng at gmail.com (Ao Teng) Date: Wed, 24 Jul 2013 14:52:27 -0400 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) In-Reply-To: References: Message-ID: Hello dadaniu, Thank you for your suggestion last time. Here is the problem I have: I have tried different instructions, for example, this one http://conquer-ur-computer.blogspot.com/2012/10/install-xcrysden-simplest-way-for-all.html After I followed all the procedure, the executable file was not found in the designated directory, as indicated by the error message" "/home/ao/Desktop/XCrySDen-1.5.24-src-all/xcrysden: 223: /home/ao/Desktop/XCrySDen-1.5.24-src-all/xcrysden: /home/ao/Desktop/XCrySDen-1.5.24-src-all/bin/xcrys: not found " Do you know what might be the problem? Thank you! Morgan On Mon, Jul 15, 2013 at 4:16 PM, dadaniu <1272370076 at qq.com> wrote: > there is an file named "INSTALL" or ?README? which will tell you in the > package you downloaded. > > > ------------------ Original ------------------ > *From: * "Ao Teng"; > *Date: * Tue, Jul 16, 2013 03:28 AM > *To: * "xcrysden"; ** > *Subject: * [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) > > Hello, > > Could anybody give me a clear instruction on how to install xCrysden? I'm > using Ubuntu 12.04. I searched quite a bit on INTERNET, but all the > instructions I found led to failure. Thank you in advance! > > Morgan > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130724/f05ff66f/attachment.htm From morganteng at gmail.com Wed Jul 24 21:44:41 2013 From: morganteng at gmail.com (Ao Teng) Date: Wed, 24 Jul 2013 15:44:41 -0400 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) In-Reply-To: <1374137752.11955.24.camel@catalyst.ijs.si> References: <1374137752.11955.24.camel@catalyst.ijs.si> Message-ID: Hi Anton, I tried with the link you gave to me. However, I was confused at this step: "To compile the source package the file Make.sys should be present in the package root directory. Templates can be find in ./system/ subdirectory. Copy an appropriate template file: - cp ./system/Make.MY-SISTEM Make.sys Now edit the file Make.sys to suit your needs. Then if you are impatient simply try: - make all - ./xcConfigure " Would you please let me know where can I find the template "Make.sys file"? Thank you! Morgan On Thu, Jul 18, 2013 at 4:55 AM, Tone Kokalj wrote: > On Mon, 2013-07-15 at 15:28 -0400, Ao Teng wrote: > > Hello, > > > > > > Could anybody give me a clear instruction on how to install xCrysden? > > I'm using Ubuntu 12.04. > > As far as I know, the new versions of Ubuntu have xcrysden, which means > that you can install as: > > sudo apt-get install xcrysden > > (wheter 12.04 is new enough I don't know, try). Otherwise install the > precompiled version of xcrysden: > > 32bit: > http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz > > 64bit: > > http://www.xcrysden.org/download/xcrysden-1.5.53-linux_x86_64-semishared.tar.gz > > Regards, > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130724/47ee37c5/attachment.htm From ora at georgetown.edu Thu Jul 25 03:09:21 2013 From: ora at georgetown.edu (Oliver Albertini) Date: Wed, 24 Jul 2013 18:09:21 -0700 Subject: [xcrysden] has anyone compiled xcrysden on AIX ? Message-ID: Hello, I am trying to compile xcrysden on AIX 6.1, and have run into trouble building the static library Mesa. It is complaining that getopt.h is not present. The built-in header file for getopt in AIX is unistd.h instead. But it doesn't have all the functions: compiler_opts in src/glsl/main.cpp gives the following error: xlC -c -I. -I../mesa -I../mapi -I../../include -q64 -O -DAIXV3 -DPTHREADS main.cpp -o main.o "main.cpp", line 161.21: 1540-1118 (S) The declaration of "compiler_opts" uses the undefined class "option" when the class must be complete. "main.cpp", line 182.34: 1540-0274 (S) The name lookup for "compiler_opts" did not find a declaration. "main.cpp", line 182.50: 1540-0251 (S) The "->" operator cannot be applied to the undefined class "struct option". "main.cpp", line 182.65: 1540-0253 (S) This use of undefined class "option" is not valid. "main.cpp", line 183.29: 1540-0251 (S) The "->" operator cannot be applied to the undefined class "struct option". "main.cpp", line 268.44: 1540-0274 (S) The name lookup for "compiler_opts" did not find a declaration. Also I cannot find a way to specify that ARCH_FLAGS=ar -X64. Any help with this would be greatly appreciated, Sincerely, Oliver Albertini -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130724/a5502aa0/attachment.htm From h.henri.hay at gmail.com Thu Jul 25 21:48:25 2013 From: h.henri.hay at gmail.com (Henri Hay) Date: Thu, 25 Jul 2013 13:48:25 -0600 Subject: [xcrysden] Datagrid format Message-ID: Dear XCrySDen users, Excuse me if my question has been asked before, I could not find any direct answer to it. I would like to plot the difference in charge density for three systems: pristine graphene, p-doped graphene, and n-doped graphene. For that purpose I thought I could subtract the different charge densities and plot the difference in order to see where the excess charge is located (if it is delocalized or not, for instance) . But I have some trouble understanding the Datagrid format, and in particular what is described on the XCrySDen website as "5x5x5 datagrid values in column-major mode". What does this part of the charge density data grid represent? 0.17727E+00 0.19333E+00 0.23076E+00 0.26773E+00 0.28800E+00 0.28904E+00 I am using PW of QE and the postprocessing tools to output the 3D charge density. Thank you for your help. Best regards, Henri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130725/6ae2a2d2/attachment.htm From tone.kokalj at ijs.si Wed Jul 31 23:27:34 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 31 Jul 2013 23:27:34 +0200 Subject: [xcrysden] instruction on installation xCrysden (Ubuntu 12.04) In-Reply-To: References: <1374137752.11955.24.camel@catalyst.ijs.si> Message-ID: <1375306054.6590.27.camel@catalyst.ijs.si> On Wed, 2013-07-24 at 15:44 -0400, Ao Teng wrote: > > Would you please let me know where can I find the template "Make.sys > file"? Thank you! According to instructions, the templates are located in xcrysden's system/ subdirectory. You may also try the pre-compiled xcrysden package (I assume your ubuntu is 32bit): http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz 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 Wed Jul 31 23:29:40 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 31 Jul 2013 23:29:40 +0200 Subject: [xcrysden] has anyone compiled xcrysden on AIX ? In-Reply-To: References: Message-ID: <1375306180.6590.30.camel@catalyst.ijs.si> On Wed, 2013-07-24 at 18:09 -0700, Oliver Albertini wrote: > Hello, > > > I am trying to compile xcrysden on AIX 6.1, Why? I assume you want to compile xcrysden on some supercomputer, right? If this is so, forget about it. Running xcrysden remotely will be "remotely" slow. Instead, compile xcrysden on your desktop computer. Regards, -- 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 Wed Jul 31 23:36:45 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 31 Jul 2013 23:36:45 +0200 Subject: [xcrysden] Datagrid format In-Reply-To: References: Message-ID: <1375306605.6590.37.camel@catalyst.ijs.si> On Thu, 2013-07-25 at 13:48 -0600, Henri Hay wrote: > Dear XCrySDen users, > > > Excuse me if my question has been asked before, I could not find any direct answer to it. > > > I would like to plot the difference in charge density ... > I am using PW of QE and the postprocessing tools to output the 3D > charge density. Why don't you let your pp.x of QE to calculate the charge density difference. How to do it? Well, see the description of PLOT namelist here: http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html#id3712314 > What does this part of the charge density data grid represent? > > 0.17727E+00 0.19333E+00 0.23076E+00 0.26773E+00 0.28800E+00 0.28904E+00 You are the only one that can possible know the answer, because you know how you obtained these values. I may only presume that they are some, say, charge density values inside the DATAGRID section. Otherwise, the XSF's datagrid format is described here: http://www.xcrysden.org/doc/XSF.html#__toc__11 Regards, -- 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