From 1009ukumar at gmail.com Wed Jul 14 07:48:19 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Wed, 14 Jul 2010 11:18:19 +0530 Subject: [xcrysden] Drawing of Different planes in a Unit cell Using XCRYSDEN? Message-ID: Dear All, 1). Is it possible to draw planes in a unit cell using XCRYSDEN? 2). How can i draw different planes? I am using Quantum Espresso with Xcrysden. -- Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100714/91283ad9/attachment.htm From khoncj at gmail.com Fri Jul 16 08:51:19 2010 From: khoncj at gmail.com (cj gong) Date: Fri, 16 Jul 2010 14:51:19 +0800 Subject: [xcrysden] XCrySDen Digest, Vol 30, Issue 1 In-Reply-To: References: Message-ID: I think you can draw planes in a unit cell using xcrysden,but i also a greenhand, need your help? thanks a lot 2010/7/14 > Send XCrySDen mailing list submissions to > xcrysden at democritos.it > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body 'help' to > xcrysden-request at democritos.it > > You can reach the person managing the list at > xcrysden-owner at democritos.it > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. Drawing of Different planes in a Unit cell Using XCRYSDEN? > (sonu kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 14 Jul 2010 11:18:19 +0530 > From: sonu kumar <1009ukumar at gmail.com> > Subject: [xcrysden] Drawing of Different planes in a Unit cell Using > XCRYSDEN? > To: xcrysden at democritos.it > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > 1). > Is it possible to draw planes in a unit cell using > XCRYSDEN? > > 2). > How can i draw different planes? > > I am using Quantum Espresso with Xcrysden. > > -- > Sonu Kumar > > Phd Student > Physics Department > Indian Institute of Technology > Delhi-110016, India > web:-http://www.iitd.ac.in/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/xcrysden/attachments/20100714/91283ad9/attachment.html > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 30, Issue 1 > *************************************** > -- ?????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100716/1b665133/attachment.htm From sclauzer at sissa.it Fri Jul 16 10:03:38 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 16 Jul 2010 10:03:38 +0200 Subject: [xcrysden] Drawing of Different planes in a Unit cell Using XCRYSDEN? In-Reply-To: References: Message-ID: <4C40125A.20906@sissa.it> Dear Sonu, as far as I know, from PWscf data in 3D format with xcrysden you can draw only planes perpendicular to one of the three crystal axis, hence planes corresponding to FFT planes. You have as many planes as the FFT planes corresponding to the basis set of your calculation (grep FFT in the pw.x output file). If you want other planes you must either rotate your system in the PWscf calculation or use the 2D plot mode of pp.x, which allows to select an arbitrary plane and uses FFT interpolation. HTH GS On 07/14/2010 07:48 AM, sonu kumar wrote: > Dear All, > > 1). > Is it possible to draw planes in a unit cell using > XCRYSDEN? > > 2). > How can i draw different planes? > > I am using Quantum Espresso with Xcrysden. > > -- > Sonu Kumar > > Phd Student > Physics Department > Indian Institute of Technology > Delhi-110016, India > web:-http://www.iitd.ac.in/ > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100716/2e51074e/attachment.htm From masoudnahali at live.com Fri Jul 16 11:49:13 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Fri, 16 Jul 2010 14:19:13 +0430 Subject: [xcrysden] Visualizing the Atoms Generated by Vectors Message-ID: Dear XCrysden Users As all know, one must delete the atoms that is generated by vectors in the input file of PWscf. I want to visualize that atoms (generating by vectors). Would you please say me is there any keyword in the XCrysden to visualize them. Sincerely Yours Masoud Nahalii SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100716/b273d1db/attachment.htm From jxzhu at lanl.gov Tue Jul 20 19:20:11 2010 From: jxzhu at lanl.gov (Jian-Xin Zhu) Date: Tue, 20 Jul 2010 11:20:11 -0600 Subject: [xcrysden] properties of fonts In-Reply-To: <1276280389.6839.14.camel@walk.ijs.si> References: <4C11EBE5.4020200@sissa.it> <1276280389.6839.14.camel@walk.ijs.si> Message-ID: <8253EC7C-7085-45A1-9C98-0391BA05835C@lanl.gov> Dear Prof. Kokalj and XCryDen Users, I tried to open the link http://www.xcrysden.org/ but got the following ERROR The requested URL could not be retrieved While trying to retrieve the URL: http://www.xcrysden.org/ The following error was encountered: Connection to 212.235.213.51 Failed The system returned: (113) No route to host The remote host or network may be down. Please try the request again. Your cache administrator is squid at lanl.gov. Generated Tue, 20 Jul 2010 17:17:30 GMT by proxyout.lanl.gov (squid) Is this a problem with the firewall or proxy in our institute? Thanks, Jian-Xin Zhu On Jun 11, 2010, at 12:19 PM, Tone Kokalj wrote: > On Fri, 2010-06-11 at 09:55 +0200, Gabriele Sclauzero wrote: >> Dear users, >> >> I want to increase the size of the fonts in the xcrysden GUI >> (buttons, menus). I succeeded by specifying a line like this: >> >> *font: -*-helvetica-medium-r-normal--16-*-*-*-*-*-*- >> >> in the Xcrysden_defaults file. Anyway I'm not completely satisfied of >> the results, since the fonts are bigger but they look as they have >> a too >> thin body (I don't remember the technical word to say that...). Where >> can I learn all the possible options for this *font: definition > > That is nothing but the X11 specification of the font and "*" are > wildcards. Try the xfontsel. It is an ancient x11 font-selection > program > with the possibility to set all the fields. Select the font there and > paste it to Xcrysden_defaults file. > >> Is there a possibility to add an antialiasing options, in order to >> make >> those fonts to look smoother? > > While the new Tk support the antialiased fonts (actually on my system, > xcrysden uses antialiased fonts), I don't know if this will work via > Xcrysden_defaults file. > > >> Another issue which came about after increasing the font size: the >> default window size happens to be a bit too small to accomodate all >> the >> buttons with the larger fonts, so that I have to resize it manually >> after starting xcrysden. Where and how do I specify my default >> window size? > > If you are referring to xcrysden main-window, I believe there is > little > you can do: its sizes are hard-coded so as that all "buttons" fits > within the panel. Usually this works well with the default font, but > when larger font is specified one faces your problem. > > 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 -- ################################ Jian-Xin Zhu, Ph.D Theorertical Division, MS B262 Los Alamos National Laboratory Los Alamos, NM 87545 Phone: (505) 667 2363 Fax: (505) 665 4063 Emai: jxzhu at lanl.gov Email (backup): physjxzhu at gmail.com URL: http://theory.lanl.gov ################################ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100720/fa41de33/attachment.htm From 1009ukumar at gmail.com Wed Jul 21 09:49:44 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Wed, 21 Jul 2010 13:19:44 +0530 Subject: [xcrysden] Drawing of Different planes in a Unit cell Using XCRYSDEN? Message-ID: Dear Gabriele Sclauzero, I am *sorry* for the late reply. Thank you for your reply. I just want to see atoms above and below , say (111) plane . I searched for it, but i think that using Xcrysden , it's not possible to do it. With Kind Regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100721/30f496ee/attachment.htm From kirtinandan07 at gmail.com Wed Jul 21 13:33:14 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Wed, 21 Jul 2010 17:03:14 +0530 Subject: [xcrysden] Drawing of Different planes in a Unit cell Using XCRYSDEN? In-Reply-To: <4C40125A.20906@sissa.it> References: <4C40125A.20906@sissa.it> Message-ID: Dear Prof. Sclauzero sorry I could not understand the meaning of your statement 'If you want other planes you must either rotate your system in the PWscf calculation or use the 2D plot mode of pp.x, which allows to select an arbitrary plane and uses FFT interpolation.' what is the meaning or rotation here. could you please explain. with regards vickysingh research student, Bangalore On Fri, Jul 16, 2010 at 1:33 PM, Gabriele Sclauzero wrote: > Dear Sonu, > as far as I know, from PWscf data in 3D format with xcrysden you can > draw only planes perpendicular to one of the three crystal axis, hence > planes corresponding to FFT planes. You have as many planes as the FFT > planes corresponding to the basis set of your calculation (grep FFT in the > pw.x output file). If you want other planes you must either rotate your > system in the PWscf calculation or use the 2D plot mode of pp.x, which > allows to select an arbitrary plane and uses FFT interpolation. > > HTH > > GS > > > On 07/14/2010 07:48 AM, sonu kumar wrote: > > Dear All, > > 1). > Is it possible to draw planes in a unit cell using > XCRYSDEN? > > 2). > How can i draw different planes? > > I am using Quantum Espresso with Xcrysden. > > -- > Sonu Kumar > > Phd Student > Physics Department > Indian Institute of Technology > Delhi-110016, India > web:-http://www.iitd.ac.in/ > > > _______________________________________________ > XCrySDen mailing listXCrySDen at democritos.ithttp://www.democritos.it/mailman/listinfo/xcrysden > > > > -- > > Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > _______________________________________________ > 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/20100721/767445f6/attachment.htm From sclauzer at sissa.it Wed Jul 21 13:48:39 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 21 Jul 2010 13:48:39 +0200 Subject: [xcrysden] Drawing of Different planes in a Unit cell Using XCRYSDEN? In-Reply-To: References: <4C40125A.20906@sissa.it> Message-ID: <50790223-12BA-4571-A841-3E65A91F3BB2@sissa.it> Il giorno 21/lug/2010, alle ore 13.33, vicky singh ha scritto: > Dear Prof. Sclauzero Not yet Prof., if I'll ever become such :) > sorry I could not understand the meaning of your statement > > 'If you want other planes you must either rotate your system in the PWscf calculation or use the 2D plot mode of pp.x, which allows to select an arbitrary plane and uses FFT interpolation.' I meant that you have to rewrite your pw input file (changing ibrav, celldm, nat, atomic positions... whatever needed), i.e. build a supercell such that the crystallographic direction you are interested in will coincide with one of the 3 cartesian axes. GS > > what is the meaning or rotation here. could you please explain. > > with regards > vickysingh > research student, Bangalore > On Fri, Jul 16, 2010 at 1:33 PM, Gabriele Sclauzero wrote: > Dear Sonu, > as far as I know, from PWscf data in 3D format with xcrysden you can draw only planes perpendicular to one of the three crystal axis, hence planes corresponding to FFT planes. You have as many planes as the FFT planes corresponding to the basis set of your calculation (grep FFT in the pw.x output file). If you want other planes you must either rotate your system in the PWscf calculation or use the 2D plot mode of pp.x, which allows to select an arbitrary plane and uses FFT interpolation. > > HTH > > GS > > > On 07/14/2010 07:48 AM, sonu kumar wrote: >> Dear All, >> >> 1). >> Is it possible to draw planes in a unit cell using >> XCRYSDEN? >> >> 2). >> How can i draw different planes? >> >> I am using Quantum Espresso with Xcrysden. >> >> -- >> Sonu Kumar >> >> Phd Student >> Physics Department >> Indian Institute of Technology >> Delhi-110016, India >> web:-http://www.iitd.ac.in/ >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden >> > > > -- > > Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > 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 ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100721/1bb45de4/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20100721/1bb45de4/attachment.bin From tasaka at affinity-science.com Wed Jul 21 13:45:53 2010 From: tasaka at affinity-science.com (Tomohiko Tasaka) Date: Wed, 21 Jul 2010 20:45:53 +0900 Subject: [xcrysden] cannot access web server In-Reply-To: References: <4C40125A.20906@sissa.it> Message-ID: <000c01cb28ca$4cd8e9e0$e68abda0$@com> Hello, I can't access www.xcrysden.org now. could you please check the server status? Best regards, Tomo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100721/2a3919c3/attachment.htm From izaakw89 at yahoo.com Wed Jul 21 22:51:36 2010 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Wed, 21 Jul 2010 13:51:36 -0700 (PDT) Subject: [xcrysden] Error: while executing exec sh Message-ID: <683228.96804.qm@web44811.mail.sp1.yahoo.com> As posted January of 2009: >Managed to launch it on Windows machine remotely via CygWin. It starts no prob >but can't seem to display/open anything. In particular, I tried opening every >single file on espresso 4.0.4 output example 8 with calculate DOS (I chose >display optimized coordinates), it always gives the same error of > >Error: while executing exec sh /share/apps/xcrysden-1.6/ scripts/pwo2xsf.sh >--optcoor /share/apps/espresso-4.0.4/ examples/example08/reference/ ni.dos.out > >pwo2xsf.xsf > >no luck with other coordinate type or any other example either > >Jonas I received the same error message that Mr. Jonas Baltrusaitis has reported. I am using XCrySDen on linux and every one of my recent output files from a 'relax' calculation reported this same error when I attempted to "Display Optimized Coordinates" on XCrySDen. Then I noticed in the output file, there were no CELL_PARAMETERS listed so after manually putting them in and entering the following into the heading of the pwo2xsf.sh script: LANG=C LC_ALL=C export LANG LC_ALL the error goes away. However, when I try to select "reduce dimension to 2D" and "Display Optimized Coordinates", nothing is displayed and in the terminal it says: Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 Some of the older output files display the optimized coordinates correctly and in the terminal it reads this same thing but with sInfo(dim) = 2. Is that the only problem keeping my new files from working properly? How might I go about fixing this? Thanks, Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100721/e41172bd/attachment-0001.htm From lanhaiping at gmail.com Thu Jul 22 04:40:52 2010 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 22 Jul 2010 10:40:52 +0800 Subject: [xcrysden] cannot access web server In-Reply-To: <000c01cb28ca$4cd8e9e0$e68abda0$@com> References: <4C40125A.20906@sissa.it> <000c01cb28ca$4cd8e9e0$e68abda0$@com> Message-ID: i cannot either On Wed, Jul 21, 2010 at 7:45 PM, Tomohiko Tasaka < tasaka at affinity-science.com> wrote: > Hello, > > > > I can?t access www.xcrysden.org now. > > could you please check the server status? > > > > Best regards, > > Tomo > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100722/aa5d4fa1/attachment.htm From tone.kokalj at ijs.si Fri Jul 23 18:20:59 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 23 Jul 2010 18:20:59 +0200 Subject: [xcrysden] cannot access web server In-Reply-To: <000c01cb28ca$4cd8e9e0$e68abda0$@com> References: <4C40125A.20906@sissa.it> <000c01cb28ca$4cd8e9e0$e68abda0$@com> Message-ID: <1279902059.8774.8.camel@walk.ijs.si> On Wed, 2010-07-21 at 20:45 +0900, Tomohiko Tasaka wrote: > Hello, > > > > I can?t access www.xcrysden.org now. The old server died (it had a fatal hardware malfunction)! Today, I succeeded to set up a new computer as an www.xcrysden.org. Not everything is back to normal yet, but it seems that the main functionality has been restored. You may retry. I apologize for the inconvenience. Best regards, Tone PS: the cygwin and macosx binaries are currently missing. -- 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 jxzhu at lanl.gov Tue Jul 27 00:58:38 2010 From: jxzhu at lanl.gov (Jian-Xin Zhu) Date: Mon, 26 Jul 2010 16:58:38 -0600 Subject: [xcrysden] Installation of XCrySDen under Mac OSX snow leopard In-Reply-To: <1276280389.6839.14.camel@walk.ijs.si> References: <4C11EBE5.4020200@sissa.it> <1276280389.6839.14.camel@walk.ijs.si> Message-ID: <4EFB7D00-3D7C-4464-B57A-463911691D90@lanl.gov> Dear Prof. Kokalj and Respectful users, These days I tried to install the XCrySDen on the Mac Intel with OSX Snow Leopard. I downloaded xc-1.5.21-src-all.tar.gz from http://www.xcrysden.org/Download.html . I have already installed Tcl, Tk, and Mesa through fink. The OpenGL for "include" stuff is in /System/Library/Frameworks/ OpenGL.framework/Versions/A/Headers However, when I execute the command make all Many errors (as copied/pasted below) came out when the C-code was compiled. .... #------------------------------# # # # Compiling XCRYSDEN C-code # # # #------------------------------# cd C; make "TOPDIR=/Users/jxzhu/XCrySDen" compile make TOPDIR=/Users/jxzhu/XCrySDen gcc -ansi -fwritable-strings -funroll-loops -fPIC -DUSE_FONTS -dynamic -DMAC_OSX -DUSE_FONTS -I/usr/X11R6/include -c detnsplit.c In file included from /usr/X11R6/include/GL/gl.h:1386, from struct.h:44, from detnsplit.c:22: /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:37: error: expected identifier or '(' before '/' token /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:38: error: stray '#' in program /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2427: error: expected ')' before 'op' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2428: error: expected ')' before 'func' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2431: error: expected ')' before 'mode' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2432: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2435: error: expected ')' before 'mode' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2436: error: expected ')' before 'modeRGB' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2437: error: expected ')' before 'sfactor' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2439: error: expected declaration specifiers or '...' before 'GLenum' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2446: error: expected ')' before 'plane' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2480: error: expected ')' before 'face' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2481: error: expected declaration specifiers or '...' before 'GLenum' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2482: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2483: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2484: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2485: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2486: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2487: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2488: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2489: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2490: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2491: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2492: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2493: error: expected ')' before 'target' /System/Library/Frameworks/OpenGL.framework/Headers/gl.h:2494: error: expected ')' before 'target' ... In file included from struct.h:44, from detnsplit.c:22: /usr/X11R6/include/GL/gl.h:1407: error: expected ')' before 'op' /usr/X11R6/include/GL/gl.h:1408: error: expected ')' before 'func' /usr/X11R6/include/GL/gl.h:1411: error: expected ')' before 'mode' /usr/X11R6/include/GL/gl.h:1412: error: expected ')' before 'target' /usr/X11R6/include/GL/gl.h:1415: error: expected ')' before 'mode' /usr/X11R6/include/GL/gl.h:1416: error: expected ')' before 'modeRGB' /usr/X11R6/include/GL/gl.h:1417: error: expected ')' before 'sfactor' /usr/X11R6/include/GL/gl.h:1419: error: expected declaration specifiers or '...' before 'GLenum' /usr/X11R6/include/GL/gl.h:1426: error: expected ')' before 'plane' /usr/X11R6/include/GL/gl.h:1460: error: expected ')' before 'face' /usr/X11R6/include/GL/gl.h:1461: error: expected declaration specifiers or '...' before 'GLenum' /usr/X11R6/include/GL/gl.h:1462: error: expected ')' before 'target' /usr/X11R6/include/GL/gl.h:1463: error: expected ')' before 'target' /usr/X11R6/include/GL/gl.h:1464: error: expected ')' before 'target' /usr/X11R6/include/GL/gl.h:1465: error: expected ')' before 'target' /usr/X11R6/include/GL/gl.h:1466: error: expected ')' before 'target' /usr/X11R6/include/GL/gl.h:1467: error: expected ')' before 'target' ... In file included from /usr/X11R6/include/GL/gl.h:1993, from struct.h:44, from detnsplit.c:22: /usr/X11R6/include/GL/glext.h:5226: error: 'PFNGLCHECKFRAMEBUFFERSTATUSPROC' declared as function returning a function /usr/X11R6/include/GL/glext.h:7613: error: 'PFNGLCHECKFRAMEBUFFERSTATUSEXTPROC' declared as function returning a function /usr/X11R6/include/GL/glext.h:8393: error: 'PFNGLCHECKNAMEDFRAMEBUFFERSTATUSEXTPROC' declared as function returning a function In file included from detnsplit.c:22: struct.h:859: error: field 'shademodel' declared as a function make[2]: *** [detnsplit.o] Error 1 make[1]: *** [compile] Error 2 make: *** [src-C] Error 2 This kind of errors were not seen on Mac Intel with Leopard. I very much appreciate your help. Thanks, Jianxin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100726/6fe08f9b/attachment.htm From dmwood at mines.edu Tue Jul 27 18:46:26 2010 From: dmwood at mines.edu (David M. Wood) Date: Tue, 27 Jul 2010 10:46:26 -0600 Subject: [xcrysden] Installation of XCrySDen under Mac OSX snow leopard Message-ID: <67376D43-3DB3-452E-ACA7-763B479B68AF@Mines.EDU> Jian-Xin Zhu wrote: > "These days I tried to install the XCrySDen on the Mac Intel with OSX Snow Leopard. I downloaded xc-1.5.21-src-all.tar.gz from http://www.xcrysden.org/Download.html . > I have already installed Tcl, Tk, and Mesa through fink. > The OpenGL for "include" stuff is in /System/Library/Frameworks/ OpenGL.framework/Versions/A/Headers > However, when I execute the command make all > Many errors (as copied/pasted below) came out when the C-code was compiled." You don't need version 1.5.21-src-all IF you decide to use already-installed Tcl, Tk, Mesa. On the other hand, I've found getting the correct headers, library versions, etc, properly linked to was fairly difficult since there are several installations of X-related stuff on my machine. So I decided to use, as you did, xc-1.5.21-src-all . The following works for me, PROVIDED I use the Apple-distributed X11 server [version XQuartz 2.3.5 (xorg-server 1.4.2-apple53) in /Applications/Utilities/X11.app] rather than, for example XQuartz 2.5.2, which produces another X11 server entitled XQquartz.app in the same directory. The only problem I'm having is that the xcrysden display flickers rapidly. So: here's the process, using XCrySDen-1.5.21-src-all 1. My make.sys is the same as system/Make.macosx-x11-tone-elettra Make.sys except for the use of gfortran (installed via Fink) rather than g77 (no longer in fink?) FC = gfortran 2. make all 3. Make sure to run xcConfigure, or that something like # this is for XCRYSDEN 1.5.21; added by XCRYSDEN installation on # Sat Jul 24 17:34:57 MDT 2010 #------------------------------------------------------------------------ XCRYSDEN_TOPDIR=/usr/local/src/XCrySDen-1.5.21-src-all XCRYSDEN_SCRATCH=/Users/dmwood/xcrys_tmp export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" is at the bottom of your .bashrc (or equivalent) file and that you've run source ~/.bash_profile (which also sources .bashrc) 4. Launch the Apple (not XQuartz) X11.app and add an entry for xcrysden via Application->Customize Name: xcd Command: /usr/local/src/XCrySDen-1.5.21-src-all/xcrysden 5. Close the Application menu editor, 6. Select from the Apple X11 app: Applications->xcd For me, this pops open the usual XCrySDen window. As noted above, it APPEARS to work normally, except that the contents of the display window flickers annoyingly at about 10 Hz--enough that anyone with epilepsy should be careful! WARNING/FYI: attempts to launch XCrySDen via xcrysden in a terminal window (or, presumably, via the XQuartz server) for me yield Executing: /usr/local/src/XCrySDen-1.5.21-src-all/bin/ftnunit X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 147 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 566 Current serial number in output stream: 566 There is actually nothing the matter with ftnunit; the issue appears to be use of XQuartz libraries. Hope this helps. I'd LOVE to hear how to get rid of the nasty flickering! David M. Wood dmwood at Mines.EDU From dmwood at mines.edu Tue Jul 27 22:07:50 2010 From: dmwood at mines.edu (David M. Wood) Date: Tue, 27 Jul 2010 14:07:50 -0600 Subject: [xcrysden] More on: Installation of XCrySDen under Mac OSX snow leopard In-Reply-To: References: Message-ID: <37D7898D-D533-4645-84DD-59532DEB0DFC@Mines.EDU> Please see: http://xquartz.macosforge.org/trac/ticket/423 for the origins of problems I mentioned with XQuartz 2.5.2. These give rise to errors of the sort X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 147 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 566 Current serial number in output stream: 566 The PRELIMINARY patched bins (for Leopard AND Snow Leopard), to which there are links at the bottom of the page mentioned, should be placed in /Applications/Utilities/XQuartz.app/Contents/MacOS renamed to X11.bin, then made executable via chmod a+x *.bin and you can then use XQuartz with XCD 1.5.21 The damnably flickering [a stead re-update? hardware acceleration?] with XCD display contents persists, alas. David M. Wood dmwood at Mines.EDU From jxzhu at lanl.gov Wed Jul 28 01:03:39 2010 From: jxzhu at lanl.gov (Jian-Xin Zhu) Date: Tue, 27 Jul 2010 17:03:39 -0600 Subject: [xcrysden] More on: Installation of XCrySDen under Mac OSX snow leopard In-Reply-To: <37D7898D-D533-4645-84DD-59532DEB0DFC@Mines.EDU> References: <37D7898D-D533-4645-84DD-59532DEB0DFC@Mines.EDU> Message-ID: <7A1A4B31-8EE7-496E-87C9-909FBA3AA7D5@lanl.gov> Dear David, Thanks a lot. With your help, I just installed XCrySDen 1.5.21 successfully on Snow Leopard. I don't see the flicker but I do notice that the color contrast and font style (now thinner) of the interface are different from those in version 1.5.17. Otherwise, it looks fine (not dig deep yet). Regards, Jianxin On Jul 27, 2010, at 2:07 PM, David M. Wood wrote: > Please see: > > http://xquartz.macosforge.org/trac/ticket/423 > > for the origins of problems I mentioned with XQuartz 2.5.2. These > give rise to errors of the sort > > X Error of failed request: BadMatch (invalid parameter attributes) > Major opcode of failed request: 147 (GLX) > Minor opcode of failed request: 5 (X_GLXMakeCurrent) > Serial number of failed request: 566 > Current serial number in output stream: 566 > > The PRELIMINARY patched bins (for Leopard AND Snow Leopard), to > which there are links at the bottom of the page mentioned, should be > placed in > > /Applications/Utilities/XQuartz.app/Contents/MacOS > > renamed to X11.bin, then made executable via chmod a+x *.bin > > and you can then use XQuartz with XCD 1.5.21 > > The damnably flickering [a stead re-update? hardware acceleration?] > with XCD display contents persists, alas. > > David M. Wood > dmwood at Mines.EDU > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- ################################ Jian-Xin Zhu, Ph.D Theorertical Division, MS B262 Los Alamos National Laboratory Los Alamos, NM 87545 Phone: (505) 667 2363 Fax: (505) 665 4063 Emai: jxzhu at lanl.gov Email (backup): physjxzhu at gmail.com URL: http://theory.lanl.gov ################################ From mohnish.iitk at gmail.com Wed Jul 28 04:59:00 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 28 Jul 2010 08:29:00 +0530 Subject: [xcrysden] unable to exploit advanced geometric features Message-ID: Dear Xcrysden users, I am unable to exploit the advanced geometric options which I need to delete some atoms or to visualize some Miller planes. In adv. geo. option nothing comes after clicking. Can anybody please tell me where the problem might be or help me out. Thanks a lot in advance -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100728/d3fdab0c/attachment.htm