From fedele.stabile at fis.unical.it Wed Jun 5 12:19:19 2013 From: fedele.stabile at fis.unical.it (Fedele Stabile) Date: Wed, 05 Jun 2013 12:19:19 +0200 Subject: [xcrysden] libquadmath error Message-ID: <1370427559.2762.65.camel@tango.fis.unical.it> When i run xcrysden it givethis error: /apps/xcrysden/xcrysden-1.5.53-bin-semishared/bin/gengeom: error while loading shared libraries: libquadmath.so.O: cannot open shared object file: No such file or directory Can you help me to solve? Fedele From tone.kokalj at ijs.si Wed Jun 5 17:00:57 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 05 Jun 2013 17:00:57 +0200 Subject: [xcrysden] libquadmath error In-Reply-To: <1370427559.2762.65.camel@tango.fis.unical.it> References: <1370427559.2762.65.camel@tango.fis.unical.it> Message-ID: <1370444457.18391.23.camel@catalyst.ijs.si> On Wed, 2013-06-05 at 12:19 +0200, Fedele Stabile wrote: > When i run xcrysden it givethis error: > /apps/xcrysden/xcrysden-1.5.53-bin-semishared/bin/gengeom: > error while loading shared libraries: > libquadmath.so.O: > cannot open shared object file: Perhaps the easiest thing is to install the libquadmath library system wide. For example for Debian based linux distros that would be something like: apt-get install libquadmath0 and for PRM compatible linux distros one can use: yum install libquadmath0 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 fedele.stabile at fis.unical.it Wed Jun 5 23:55:34 2013 From: fedele.stabile at fis.unical.it (Fedele Stabile) Date: Wed, 5 Jun 2013 23:55:34 +0200 Subject: [xcrysden] R: libquadmath error In-Reply-To: <1370444457.18391.23.camel@catalyst.ijs.si> References: <1370427559.2762.65.camel@tango.fis.unical.it> <1370444457.18391.23.camel@catalyst.ijs.si> Message-ID: <020801ce6237$68339f60$389ade20$@fis.unical.it> Can you suggest me a link for Scientific Linux? Thank you -----Messaggio originale----- Da: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] Per conto di Tone Kokalj Inviato: mercoled? 5 giugno 2013 17:01 A: xcrysden at democritos.it Oggetto: Re: [xcrysden] libquadmath error On Wed, 2013-06-05 at 12:19 +0200, Fedele Stabile wrote: > When i run xcrysden it givethis error: > /apps/xcrysden/xcrysden-1.5.53-bin-semishared/bin/gengeom: > error while loading shared libraries: > libquadmath.so.O: > cannot open shared object file: Perhaps the easiest thing is to install the libquadmath library system wide. For example for Debian based linux distros that would be something like: apt-get install libquadmath0 and for PRM compatible linux distros one can use: yum install libquadmath0 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 From break_the_calculus at yahoo.com Thu Jun 6 13:59:20 2013 From: break_the_calculus at yahoo.com (Tom Marvollo Riddle) Date: Thu, 6 Jun 2013 04:59:20 -0700 (PDT) Subject: [xcrysden] Print in vector format + anti-aliasing using scripting Message-ID: <1370519960.83224.YahooMailClassic@web162204.mail.bf1.yahoo.com> Dear all, I intend to produce images from several pwscf output files. I already used produced some png files using scripting features of XCrysden (a very nice feature). Unfortunately somehow I need the picture files in vector format. The problem is I cannot find documentation about how to print to vector graphics format such as eps using scripting. I also cannot find a way to turn on anti-aliasing. Are any ways to achieve this using scripting? Any response will be much appreciated, Fadjar Fathurrahman From tone.kokalj at ijs.si Thu Jun 6 14:40:49 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 06 Jun 2013 14:40:49 +0200 Subject: [xcrysden] R: libquadmath error In-Reply-To: <020801ce6237$68339f60$389ade20$@fis.unical.it> References: <1370427559.2762.65.camel@tango.fis.unical.it> <1370444457.18391.23.camel@catalyst.ijs.si> <020801ce6237$68339f60$389ade20$@fis.unical.it> Message-ID: <1370522449.1972.36.camel@catalyst.ijs.si> On Wed, 2013-06-05 at 23:55 +0200, Fedele Stabile wrote: > Can you suggest me a link for Scientific Linux? It seems to me that scientific linux is RPM based and there is "yum", hence: yum install libquadmath0 If that doesn't work, google to locate appropriate RPM Scientific Linux libquadmath package and then you can install it as: rpm -i package.rpm Regards, Tone PS: note that you need to be root (or use sudo) to install system-wide -- 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 Jun 6 14:59:33 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 06 Jun 2013 14:59:33 +0200 Subject: [xcrysden] Print in vector format + anti-aliasing using scripting In-Reply-To: <1370519960.83224.YahooMailClassic@web162204.mail.bf1.yahoo.com> References: <1370519960.83224.YahooMailClassic@web162204.mail.bf1.yahoo.com> Message-ID: <1370523573.1972.53.camel@catalyst.ijs.si> On Thu, 2013-06-06 at 04:59 -0700, Tom Marvollo Riddle wrote: > Dear all, > > I intend to produce images from several pwscf output files. > I already used produced some png files using scripting features > of XCrysden (a very nice feature). > > Unfortunately somehow I need the picture files in vector format. I would strongly advice against it (unless you will print a few meter wide picture, you don't need it). The reason is that the vectorial EPS files are huge (easily over 100 MB unless the number of atoms is really small). My recommendation would be: 1. maximize xcrysden's display window 2. maximize the displayed structure 3. turn on antialiasing (play a bit with anti-alias settings Modify->.../Antialias Parameters for good result) 4. print in PNG > The problem is I cannot find documentation about how to print to > vector graphics format such as eps using scripting. It automatically prints vectorial EPS for "Lighting-Off" mode and a bitmap one for "Lighting-On" mode (for the above reason). You will have to modify or write a new procedure/routine (see "proc scripting::printToFile" in file Tcl/scripting.tcl). If you write a new routine just embed it into your scripting file. > I also cannot find a way to turn on anti-aliasing. There is a clever trick of how to do various features via scripting (invented by Hande Ustunel Toffoli) and it goes as follows: 1. save the scripting file (File-->Save Current State and Structure) without the feature turned on. 2. turn the feature on 3. save a new scripting file 4. compare the two scripting files and find the difference .... 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 break_the_calculus at yahoo.com Fri Jun 7 11:58:17 2013 From: break_the_calculus at yahoo.com (Fadjar Fathurrahman) Date: Fri, 7 Jun 2013 02:58:17 -0700 (PDT) Subject: [xcrysden] Print in vector format + anti-aliasing using scripting In-Reply-To: <1370523573.1972.53.camel@catalyst.ijs.si> References: <1370519960.83224.YahooMailClassic@web162204.mail.bf1.yahoo.com> <1370523573.1972.53.camel@catalyst.ijs.si> Message-ID: <1370599097.36738.YahooMailNeo@web162206.mail.bf1.yahoo.com> Thank you very much for nice trick to turn on the anti-aliasing, Tone. I tried to turn off lighting and then try to print the eps file. I got the following error: ....... Error in startup script: can't read "toglEPS(pointsize)": no such variable ??? while executing "$togl cry_gl2psPrintTogl GL2PS_EPS GL2PS_NO_SORT? $toglEPS(pointsize) $toglEPS(linewidth) $filename" ??? (procedure "scripting::printToFile" line 39) ??? invoked from within "scripting::printToFile view1.eps" ....... I tried to modify file Tcl/scripting.tcl: # # ligting-OFF mode # set toglEPS(pointsize) 2.0 set toglEPS(linewidth) 2.0 $togl cry_gl2psPrintTogl GL2PS_EPS GL2PS_NO_SORT \ ??? $toglEPS(pointsize) $toglEPS(linewidth) $filename and got the following error: Error in startup script: wrong # args: should be "toglname cry_gl2psPrintTogl format sort options pointsize linewidth filename" ??? while executing "$togl cry_gl2psPrintTogl GL2PS_EPS GL2PS_NO_SORT? $toglEPS(pointsize) $toglEPS(linewidth) $filename" ??? (procedure "scripting::printToFile" line 39) ??? invoked from within "scripting::printToFile view1.eps" I'm sorry that I don' have familiarity with Tcl language, but how to set the value of $toglEPS(pointsize) $toglEPS(linewidth)in this script? Best regards. Fadjar Graduate Student Department of Precision Science and Applied Physics Graduate School of Engineering Osaka University, Suita, Osaka 565-0871, Japan ----- Original Message ----- From: Tone Kokalj To: xcrysden at democritos.it Cc: Sent: Thursday, June 6, 2013 9:59 PM Subject: Re: [xcrysden] Print in vector format + anti-aliasing using scripting On Thu, 2013-06-06 at 04:59 -0700, Tom Marvollo Riddle wrote: > Dear all, > > I intend to produce images from several pwscf output files. > I already used produced some png files using scripting features > of XCrysden (a very nice feature). > > Unfortunately somehow I need the picture files in vector format. I would strongly advice against it (unless you will print a few meter wide picture, you don't need it). The reason is that the vectorial EPS files are huge (easily over 100 MB unless the number of atoms is really small). My recommendation would be: 1. maximize xcrysden's display window 2. maximize the displayed structure 3. turn on antialiasing (play a bit with anti-alias settings Modify->.../Antialias Parameters for good result) 4. print in PNG > The problem is I cannot find documentation about how to print to > vector graphics format such as eps using scripting. It automatically prints vectorial EPS for "Lighting-Off" mode and a bitmap one for "Lighting-On" mode (for the above reason). You will have to modify or write a new procedure/routine (see "proc scripting::printToFile" in file Tcl/scripting.tcl). If you write a new routine just embed it into your scripting file. > I also cannot find a way to turn on anti-aliasing. There is a clever trick of how to do various features via scripting (invented by Hande Ustunel Toffoli) and it goes as follows: 1. save the scripting file (File-->Save Current State and Structure) without the feature turned on. 2. turn the feature on 3. save a new scripting file 4. compare the two scripting files and find the difference .... 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/20130607/5b7a3e24/attachment.htm From castane at mpi-halle.mpg.de Tue Jun 11 23:07:26 2013 From: castane at mpi-halle.mpg.de (=?ISO-8859-1?Q?Arcesio_Casta=F1eda?=) Date: Tue, 11 Jun 2013 16:07:26 -0500 Subject: [xcrysden] General Grid Message-ID: <51B7918E.1020801@mpi-halle.mpg.de> Hello I am trying to create a xsf file with 3D periodic data. As xcrysden uses general grids this must be done by defining properly the redundant points, otherwise the atomic positions and the isosurfaces seems to be not properly localized in regard to each other. I could manage to do correctly for one unit cell, but for more than one unit cell it seems more complicated. I know xcrysden can extend the periodic data, given these in a unit cell, but I would like to know how to achieve the same result, when the data for more than one unit cell is directly read from the xsf file. Thanks before hand for any help, A. Castaneda M. MPI Halle (Saale) From tone.kokalj at ijs.si Wed Jun 12 10:55:32 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 12 Jun 2013 10:55:32 +0200 Subject: [xcrysden] Print in vector format + anti-aliasing using scripting In-Reply-To: <1370599097.36738.YahooMailNeo@web162206.mail.bf1.yahoo.com> References: <1370519960.83224.YahooMailClassic@web162204.mail.bf1.yahoo.com> <1370523573.1972.53.camel@catalyst.ijs.si> <1370599097.36738.YahooMailNeo@web162206.mail.bf1.yahoo.com> Message-ID: <1371027332.22301.0.camel@catalyst.ijs.si> On Fri, 2013-06-07 at 02:58 -0700, Fadjar Fathurrahman wrote: > I tried to turn off lighting and then try to print the eps file. > I got the following error: > ....... > > Error in startup script: can't read "toglEPS(pointsize)": no such > variable You have discovered a bug. Thanks. > I tried to modify file Tcl/scripting.tcl: > and got the following error: > > > Error in startup script: wrong # args: should be "toglname Ups, yet another bug. To fix both both bugs replace the Tcl/scripting.tcl file with the attached one. 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: scripting.tcl Type: text/x-tcl Size: 29152 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20130612/9c080403/attachment-0001.tcl From tone.kokalj at ijs.si Wed Jun 12 11:00:31 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 12 Jun 2013 11:00:31 +0200 Subject: [xcrysden] General Grid In-Reply-To: <51B7918E.1020801@mpi-halle.mpg.de> References: <51B7918E.1020801@mpi-halle.mpg.de> Message-ID: <1371027631.22301.3.camel@catalyst.ijs.si> On Tue, 2013-06-11 at 16:07 -0500, Arcesio Casta?eda wrote: > Hello > > I am trying to create a xsf file with 3D periodic data. As xcrysden uses > general grids this must be done by defining properly the redundant > points, otherwise the atomic positions and the isosurfaces seems to be > not properly localized in regard to each other. I could manage to do > correctly for one unit cell, but for more than one unit cell it seems > more complicated. I know xcrysden can extend the periodic data, given > these in a unit cell, but I would like to know how to achieve the same > result, when the data for more than one unit cell is directly read from > the xsf file. Treat your supercell as an XSF datagrid cell, which means that you need to add just the redundant points at the edge of the supercell. 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 break_the_calculus at yahoo.com Wed Jun 12 11:58:36 2013 From: break_the_calculus at yahoo.com (Fadjar Fathurrahman) Date: Wed, 12 Jun 2013 02:58:36 -0700 (PDT) Subject: [xcrysden] Print in vector format + anti-aliasing using scripting In-Reply-To: <1371027332.22301.0.camel@catalyst.ijs.si> References: <1370519960.83224.YahooMailClassic@web162204.mail.bf1.yahoo.com> <1370523573.1972.53.camel@catalyst.ijs.si> <1370599097.36738.YahooMailNeo@web162206.mail.bf1.yahoo.com> <1371027332.22301.0.camel@catalyst.ijs.si> Message-ID: <1371031116.40231.YahooMailNeo@web162202.mail.bf1.yahoo.com> Thanks Tone, it worked! ? Graduate Student Department of Precision Science and Applied Physics Graduate School of Engineering Osaka University, Suita, Osaka 565-0871, Japan ________________________________ From: Tone Kokalj To: xcrysden at democritos.it Sent: Wednesday, June 12, 2013 5:55 PM Subject: Re: [xcrysden] Print in vector format + anti-aliasing using scripting On Fri, 2013-06-07 at 02:58 -0700, Fadjar Fathurrahman wrote: > I tried to turn off lighting and then try to print the eps file. > I got the following error: > ....... > > Error in startup script: can't read "toglEPS(pointsize)": no such > variable You have discovered a bug. Thanks. > I tried to modify file Tcl/scripting.tcl: > and got the following error: > > > Error in startup script: wrong # args: should be "toglname Ups, yet another bug. To fix both both bugs replace the Tcl/scripting.tcl file with the attached one. 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/20130612/7c319c49/attachment.htm From al.suarez.ctr at nrl.navy.mil Thu Jun 13 15:43:18 2013 From: al.suarez.ctr at nrl.navy.mil (Alejandro Suarez) Date: Thu, 13 Jun 2013 09:43:18 -0400 Subject: [xcrysden] Issue with image printing (cygwin) Message-ID: <51B9CC76.1080309@nrl.navy.mil> Hello Everyone, I am unsure if this is a cygwin, imagemagick, or xcrysden error, but I figured I would start here. Whenever I try exporting an animation, printing to an image, or even viewing the temporary *.ppm files created during viewing of an XSF file, I am given a highly distorted image. As an example, I have attached a tarball with two files: a simple XSF file of ZnS (from the XSF format documentation) and the result of exporting the frame to PNG. The result is similar when exporting to any other format, except for the onerously data-heavy vectoral eps (bmp-based eps is still distorted). The images are distorted when viewed through imagemagick or through the native windows gallery. For reference, I am running XCrysden 1.5.53 within cygwin on a Windows 7 64-bit machine. My version of imagemagick is the latest available through cygwin's setup.exe library (version 6.7.6.3-3). Also, this issue occurs with and without openGL support enabled within cygwin. Any help in tracing the source of this issue would be greatly appreciated. Thank you for your assistance, -Alejandro -------------- next part -------------- A non-text attachment was scrubbed... Name: ZnS_test.tar.gz Type: application/gzip Size: 17321 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20130613/3780c1ef/attachment.bin From tone.kokalj at ijs.si Fri Jun 14 22:52:14 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 14 Jun 2013 22:52:14 +0200 Subject: [xcrysden] Issue with image printing (cygwin) In-Reply-To: <51B9CC76.1080309@nrl.navy.mil> References: <51B9CC76.1080309@nrl.navy.mil> Message-ID: <1371243134.30595.18.camel@catalyst.ijs.si> On Thu, 2013-06-13 at 09:43 -0400, Alejandro Suarez wrote: > Hello Everyone, > > I am unsure if this is a cygwin, imagemagick, or xcrysden error, but I > figured I would start here. > > Whenever I try exporting an animation, printing to an image, or even > viewing the temporary *.ppm files created during viewing of an XSF file, > I am given a highly distorted image. As an example, I have attached a > tarball with two files: a simple XSF file of ZnS (from the XSF format > documentation) and the result of exporting the frame to PNG. The result > is similar when exporting to any other format, except for the onerously > data-heavy vectoral eps (bmp-based eps is still distorted). If it gives distorted images also for the PPM format, then this implies that it is not a problem of image converting programs, but is likely some system OpenGL related issue ... I don't know, but perhaps consider updating your cygwin, maybe that will fix the problem (who knows?) > Also, this issue occurs with and without openGL support enabled within > cygwin. The OpenGL is always used, what you mean is probably the OpenGL hardware acceleration instead. 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 Jun 14 23:04:01 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 14 Jun 2013 23:04:01 +0200 Subject: [xcrysden] plot automatically DataGrid In-Reply-To: <20130613191851.095c12ec@frenz> References: <1366815976.29834.4.camel@catalyst.ijs.si> <20130613191851.095c12ec@frenz> Message-ID: <1371243841.30595.25.camel@catalyst.ijs.si> On Thu, 2013-06-13 at 19:18 +0200, Tobias wrote: > After handing over one or more .xsf-files containing one or > multiple wavefunctions. This Bourne-shell script plots the > handed over xsf-files, after deviding it into multiple xsf-files in case of multiple SUBBLOCKS. > The one wavefunction XSF files are plotted each from two different > angles and are stored in "new_wf". > > Hope it helps someone out there. Tobias, Thanks for sharing your instructive "troubleshooting" experience with xcrysden scripting and its embedding into shell-scripts. Hope it will help somebody ... For those users interested in scripting, I am add that in addition to Tobias script that is another shell script example with embedded xcrysden-scripting in xcrysden's examples/ directory, i.e.: examples/Scripting/plot_all_MO.sh (it contains some explanation). 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 Jun 14 23:10:21 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 14 Jun 2013 23:10:21 +0200 Subject: [xcrysden] plot automatically DataGrid In-Reply-To: <1371243841.30595.25.camel@catalyst.ijs.si> References: <1366815976.29834.4.camel@catalyst.ijs.si> <20130613191851.095c12ec@frenz> <1371243841.30595.25.camel@catalyst.ijs.si> Message-ID: <1371244221.30595.30.camel@catalyst.ijs.si> On Fri, 2013-06-14 at 23:04 +0200, Tone Kokalj wrote: > For those users interested in scripting, I am add that in addition to > Tobias script that is another shell script example with embedded > xcrysden-scripting in xcrysden's examples/ directory, i.e.: Ups ... :-( Well, I actually meant: "For those users interested in scripting, I may add that in addition to Tobias script there is another shell script example ...." ... it's a late hour here in Europe :-) 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 al.suarez.ctr at nrl.navy.mil Tue Jun 18 15:42:18 2013 From: al.suarez.ctr at nrl.navy.mil (Alejandro Suarez) Date: Tue, 18 Jun 2013 09:42:18 -0400 Subject: [xcrysden] Issue with image printing (cygwin) In-Reply-To: <1371243134.30595.18.camel@catalyst.ijs.si> References: <51B9CC76.1080309@nrl.navy.mil> <1371243134.30595.18.camel@catalyst.ijs.si> Message-ID: <51C063BA.6030702@nrl.navy.mil> Thank you for the reply, Anton. I have tried re-installing/updating any opengl libraries I could find in cygwin to no avail. What is strange is the image drawn within the xcrysden window is perfectly fine (aside from a known cygwin hardware acceleration issue where other windows draw on top of it). Has anyone else been using a recent copy of xcrysden within an updated cygwin environment? On 6/14/2013 4:52 PM, Tone Kokalj wrote: > On Thu, 2013-06-13 at 09:43 -0400, Alejandro Suarez wrote: >> Hello Everyone, >> >> I am unsure if this is a cygwin, imagemagick, or xcrysden error, but I >> figured I would start here. >> >> Whenever I try exporting an animation, printing to an image, or even >> viewing the temporary *.ppm files created during viewing of an XSF file, >> I am given a highly distorted image. As an example, I have attached a >> tarball with two files: a simple XSF file of ZnS (from the XSF format >> documentation) and the result of exporting the frame to PNG. The result >> is similar when exporting to any other format, except for the onerously >> data-heavy vectoral eps (bmp-based eps is still distorted). > If it gives distorted images also for the PPM format, then this implies > that it is not a problem of image converting programs, but is likely > some system OpenGL related issue ... > > I don't know, but perhaps consider updating your cygwin, maybe that will > fix the problem (who knows?) > >> Also, this issue occurs with and without openGL support enabled within >> cygwin. > The OpenGL is always used, what you mean is probably the OpenGL hardware > acceleration instead. > > Regards, -- Alejandro Suarez NRC Postdoctoral Associate Naval Research Laboratory Washington, D.C. From max_bert at web.de Thu Jun 20 08:34:02 2013 From: max_bert at web.de (max_bert at web.de) Date: Thu, 20 Jun 2013 08:34:02 +0200 Subject: [xcrysden] plot automatically DataGrid In-Reply-To: <1371244221.30595.30.camel@catalyst.ijs.si> References: <1366815976.29834.4.camel@catalyst.ijs.si> <20130613191851.095c12ec@frenz> <1371243841.30595.25.camel@catalyst.ijs.si> <1371244221.30595.30.camel@catalyst.ijs.si> Message-ID: <0MV4tp-1UonLS2ApB-00YUC8@smtp.web.de> Hey Tone, I have encountered a new problem during using my script. While I was plotting the complete set of wavefunctions of a molecule, it showed that the isovalue of "0.2" which I chose for my script isn't met by every state. Hence I get an error message like the one in the appendix. The message itself is clear by meaning, but I'm clueless how to solve this issue. At which point(s) is the isovalue specified in my script? I tried generating with the help a new script-body (*.xcrysden-file), where the isovalue was chosen to somewhat different than "0.2" and finding this value afterwards. However I failed in doing this since I couldn't find the exact value in the script. So my guess is that the value is encoded somehow. Can you may help me with this issue? In the future, I would to like to modify the script in a way that the isovalue can be chosen dynamically for each loaded *.xsf-File with datagrids, if the value of 0.2 fails. Greets Max " Error in startup script: specified isolevel -0.200000 is out of range, should be between [-0.000027 - 0.826660] while executing "xc_iso isolevel $prop(isolevel) [expr $prop(isolevel) * -1.0]" (procedure "UpdateIsosurf" line 95) invoked from within "UpdateIsosurf" (file "/tmp/xcrysden.script" line 550) invoked from within "source [gunzipFile $scriptFile]" ("uplevel" body line 4) invoked from within "uplevel \#0 { cd $system(PWD) SetWatchCursor source [gunzipFile $scriptFile] ResetCursor }" (procedure "scripting::source" line 7) invoked from within "scripting::source $filedir" ("-s" arm line 2) invoked from within "switch -glob -- $tag { "-a" - "--attrib*" { set load_attributes 1 set file_attributes $filedir } "--xsf" - "--xcr..." (procedure "parseComLinArg" line 44) invoked from within "parseComLinArg [lrange $argv 2 end]" invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file ".../XCrySDen-1.5.21-bin-semishared/Tcl/xcInit.tcl" line 546) " Am Fri, 14 Jun 2013 23:10:21 +0200 schrieb Tone Kokalj : > On Fri, 2013-06-14 at 23:04 +0200, Tone Kokalj wrote: > > For those users interested in scripting, I am add that in addition > > to Tobias script that is another shell script example with embedded > > xcrysden-scripting in xcrysden's examples/ directory, i.e.: > > Ups ... :-( > > Well, I actually meant: > "For those users interested in scripting, I may add that in addition > to Tobias script there is another shell script example ...." > > ... it's a late hour here in Europe :-) > > Regards, From tone.kokalj at ijs.si Fri Jun 21 12:25:43 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 21 Jun 2013 12:25:43 +0200 Subject: [xcrysden] plot automatically DataGrid In-Reply-To: <0MV4tp-1UonLS2ApB-00YUC8@smtp.web.de> References: <1366815976.29834.4.camel@catalyst.ijs.si> <20130613191851.095c12ec@frenz> <1371243841.30595.25.camel@catalyst.ijs.si> <1371244221.30595.30.camel@catalyst.ijs.si> <0MV4tp-1UonLS2ApB-00YUC8@smtp.web.de> Message-ID: <1371810343.4761.51.camel@catalyst.ijs.si> On Thu, 2013-06-20 at 08:34 +0200, max_bert at web.de wrote: > Hey Tone, > > I have encountered a new problem during using my script. While I was > plotting the complete set of wavefunctions of a molecule, it showed > that the isovalue of "0.2" which I chose for my script isn't met by > every state. Hence I get an error message like the one in the appendix. This is a situation I never really thought about. When used interactively the error is fine, as it signals to the user the "out-of-bounds" problem and the actual [min,max] range is provided. However, for scripts this is fatal. The proper way of handling this issue would be to modify the code and turn this error into a warning. For the time being you can catch this error to prevent abortion. How to do that depends on how you have written the script. If you locate the command in the script that actually caused the error (name it "failed_command"), you can catch it as follows: catch { failed_command } I will suppose that you used the scripting::scalarField3D::configure .... and scripting::scalarField3D::render commands. If so then you can modify the script as: scripting::scalarField3D::configure ....here specify all the options... if { [catch {scripting::scalarField3D::render}] } { set minvalue [xc_iso minvalue] set maxvalue [xc_iso maxvalue] set maxlevel [expr {abs($minvalue) < abs($maxvalue) ? abs($minvalue) : abs($maxvalue)}] # lets take the 20% of the maxvalue set level [expr 0.2*$maxlevel] scripting::scalarField3D::configure -isolevel $level scripting::scalarField3D::render } Hope that will help! Best 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 sidiqmk at gmail.com Thu Jun 27 05:46:09 2013 From: sidiqmk at gmail.com (Sidiq Khidzir) Date: Thu, 27 Jun 2013 11:46:09 +0800 Subject: [xcrysden] Fwd: Fermi surface question In-Reply-To: References: Message-ID: 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. One thing I've noticed is that, as opposed to the examples provided with xcrysden, I've received these outputs when Number of IN triangles: 0 Number of IN vertices: 0 Number of OUT triangles: 0 Number of OUT vertices: 0 I'm also wondering if it's because the range of energies per band is too small? I'm sorry I don't have a lot of experience tinkering with xcrysden. Any help is greatly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130627/5fd50aee/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: t4xo_BXSF Type: application/octet-stream Size: 24350 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20130627/5fd50aee/attachment-0001.obj From max_bert at web.de Thu Jun 27 15:25:19 2013 From: max_bert at web.de (max_bert at web.de) Date: Thu, 27 Jun 2013 15:25:19 +0200 Subject: [xcrysden] plot automatically DataGrid In-Reply-To: <1371810343.4761.51.camel@catalyst.ijs.si> References: <1366815976.29834.4.camel@catalyst.ijs.si> <20130613191851.095c12ec@frenz> <1371243841.30595.25.camel@catalyst.ijs.si> <1371244221.30595.30.camel@catalyst.ijs.si> <0MV4tp-1UonLS2ApB-00YUC8@smtp.web.de> <1371810343.4761.51.camel@catalyst.ijs.si> Message-ID: <0Meje0-1Ucq780nZQ-00ODq7@smtp.web.de> Thanks a lot. I told Tobias about your fix and he implemented it with the small change, since we are using UpdateSurface and not loading the scalarField by the corresponding method. We but we we're both looking for a command like scripting::scalarField3D::configure -isovalue foo. Greetings Max