From david.grifith at gmail.com Sun Jul 3 21:36:12 2011 From: david.grifith at gmail.com (David Grifith) Date: Mon, 4 Jul 2011 00:06:12 +0430 Subject: [xcrysden] ftnunit file error Message-ID: Dear XCrysden Users I get the error: while executing exec /home/.../.../xcrysden/bin/ftnunit when I try to execute "xcrysden" . The version that I use is XCrySDen-1.5.24-bin-shared. any suggession for solving the problem is appreciated in advance. -- Sincerely Yours David G. Jamess Cook University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110704/b990ee0c/attachment.htm From andreljpereira at gmail.com Tue Jul 5 10:03:05 2011 From: andreljpereira at gmail.com (=?ISO-8859-1?Q?Andr=E9_Luis_Jesus_Pereira?=) Date: Tue, 5 Jul 2011 10:03:05 +0200 Subject: [xcrysden] XCrysDen - Doubt Message-ID: Dear all I'm a newbie in XCrysDen and I would like to ask a question. When I do a band structure or a DOS, how can I get these information in a .txt, .dat or another postscript file? I would like to format these graphics more freely in another program. I believe this is a longstanding question, but I do not find anything related to it. Already thank you for help. Best regards. -- Andr? Luis de Jesus Pereira *Brazil* Universidade Estadual Paulista Grupo de Matriais Avan?ados - *MAV* Laborat?rio de Filmes Semicondutores Bauru - SP (Brazil) *Spain* Departament de Qu?mica F?sica i Anal?tica Universitat Jaume I Campus del Riu Sec E-12071 Castell?n de la Plana (Spain) +34 964 72 8069 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110705/76581100/attachment.htm From sebastijan.peljhan at ijs.si Tue Jul 5 10:22:04 2011 From: sebastijan.peljhan at ijs.si (Sebastijan Peljhan) Date: Tue, 05 Jul 2011 10:22:04 +0200 Subject: [xcrysden] XCrysDen - Doubt In-Reply-To: References: Message-ID: <1309854124.2869.25.camel@surf> The band structure and DOS files usually are in a .txt or .dat like file formats (although they don't explicitly have .txt or .dat endings) and you can plot the graphs using gnuplot or Xmgrace (or any other available graphing software). Kind regards, Sebastijan On Tue, 2011-07-05 at 10:03 +0200, Andr? Luis Jesus Pereira wrote: > Dear all > > I'm a newbie in XCrysDen and I would like to ask a question. > When I do a band structure or a DOS, how can I get these information > in a .txt, .dat or another postscript file? I would like to format > these graphics more freely in another program. I believe this is a > longstanding question, but I do not find anything related to it. -- Sebastijan Peljhan Department of Physical and Organic Chemistry "Jozef Stefan" Institute Jamova 39 1000 Ljubljana Slovenia tel.:+386 1 4773 523 fax.:+386 1 4773 822 email: sebastijan.peljhan at IJS.SI From masoudnahali at gmail.com Wed Jul 6 17:26:15 2011 From: masoudnahali at gmail.com (Masoud Nahali) Date: Wed, 6 Jul 2011 15:26:15 +0000 (UTC) Subject: [xcrysden] Invitation to connect on LinkedIn Message-ID: <1618928710.15981268.1309965975377.JavaMail.app@ela4-bed33.prod> LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Masoud Masoud Nahali Student at Sharif University of Technology Iran Confirm that you know Masoud Nahali https://www.linkedin.com/e/-fe5rcs-gpsfx3ke-1t/isd/3450206217/eTo4f7uI/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110706/ee87ff94/attachment.htm From member at linkedin.com Tue Jul 19 10:08:17 2011 From: member at linkedin.com (Yun-Peng Wang via LinkedIn) Date: Tue, 19 Jul 2011 08:08:17 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn?= Message-ID: <1780041043.9836509.1311062897957.JavaMail.app@ela4-bed34.prod> LinkedIn ------------ Yun-Peng Wang solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de Yun-Peng Wang http://www.linkedin.com/e/-fe5rcs-gqakzyfo-37/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I94783437_125/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYRcz5vdPcQcPwTd3B9bRFIs55yqPgPbP0Sc34TdP0UdjcLrCBxbOYWrSlI/EML_comm_afe/ Visualizar convite de Yun-Peng Wang http://www.linkedin.com/e/-fe5rcs-gqakzyfo-37/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I94783437_125/3kOclYTcPgPe3sQekALqnpPbOYWrSlI/svi/ ------------------------------------------ Voc? sabia que pode ser o primeiro a saber quando um usu?rio confi?vel da sua rede mudar de emprego? Com as Atualiza??es de rede na sua p?gina inicial do LinkedIn, voc? ser? notificado quando os usu?rios da sua rede mudarem de cargo. Seja o primeiro a saber e a entrar em contato! http://www.linkedin.com/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110719/999729cc/attachment.htm From member at linkedin.com Tue Jul 19 17:27:09 2011 From: member at linkedin.com (Bin Shao via LinkedIn) Date: Tue, 19 Jul 2011 15:27:09 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn?= Message-ID: <231625389.11182568.1311089229587.JavaMail.app@ela4-bed79.prod> LinkedIn ------------ Bin Shao indicou voc? como um amigo ou amiga ------------------------------------------ I'd like to add you to my professional network. - Bin Aceitar convite de Bin Shao http://www.linkedin.com/e/-fe5rcs-gqb0oc27-3u/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I95205732_125/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYRcz5vczcTdj0OdjB9bR5DmmwTuz9fbPkNdj8Pc3oUdjcLrCBxbOYWrSlI/EML_comm_afe/ Visualizar convite de Bin Shao http://www.linkedin.com/e/-fe5rcs-gqb0oc27-3u/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I95205732_125/3kOclYOcPsRc38RekALqnpPbOYWrSlI/svi/ ------------------------------------------ Por que se conectar com Bin Shao pode ser uma boa ideia? Tem alguma d?vida? A rede de Bin Shao provavelmente ter? uma resposta: Voc? pode utilizar as Respostas do LinkedIn para distribuir suas perguntas profissionais para Bin Shao e sua rede expandida. Voc? pode obter respostas precisas de profissionais experientes. http://www.linkedin.com/e/-fe5rcs-gqb0oc27-3u/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110719/5509737d/attachment.htm From chad.junkermeier.ctr at nrl.navy.mil Wed Jul 20 00:02:42 2011 From: chad.junkermeier.ctr at nrl.navy.mil (Chad Junkermeier) Date: Tue, 19 Jul 2011 18:02:42 -0400 Subject: [xcrysden] GPU acceleration Message-ID: <689C8CBB-CD2E-4B55-BC89-77D2BEFA56CD@nrl.navy.mil> Hello, I am sorry if this has been explained elsewhere but after searching the database and looking though the User's Guide that comes with the GPU accelerated QE package, I am still not sure. I would like to start doing NEB calculations, is it possible to do so with GPU accelerated QE? Chad Junkermeier, Ph.D. NRC Post-Doctoral Associate Naval Research Laboratory 4555 Overlook Ave, S.W. Washington DC 20375 Office: (202) 404-4635 Fax: (202) 767-1165 Email: chad.junkermeier.ctr(at)nrl.navy.mil ------------------------------------------- cell: (801) 380-8895 Personal email: junkermeier(at)gmail.com skype: junkermeier AIM: junkerammavich gtalk: junkermeier(at)gmail.com From germaneau at gucas.ac.cn Wed Jul 20 15:00:13 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 20 Jul 2011 09:00:13 -0400 Subject: [xcrysden] GPU acceleration In-Reply-To: <511112498.18538@test1.gucas.ac.cn> References: <511112498.18538@test1.gucas.ac.cn> Message-ID: <4E26D15D.9040300@gucas.ac.cn> Hey, this is the xcrysden mailing list!! That's not the rioght place, just make sense. Check out QE mailing and find *the* post which talk about GPU. There is a mailing list for QE on GPU. Don't post this question on QE mailing list, that's not the right place either. On 07/19/2011 06:02 PM, Chad Junkermeier wrote: > Hello, > I am sorry if this has been explained elsewhere but after searching the database and looking though the User's Guide that comes with the GPU accelerated QE package, I am still not sure. > I would like to start doing NEB calculations, is it possible to do so with GPU accelerated QE? > > > > > Chad Junkermeier, Ph.D. > NRC Post-Doctoral Associate > Naval Research Laboratory > 4555 Overlook Ave, S.W. > Washington DC 20375 > Office: (202) 404-4635 > Fax: (202) 767-1165 > Email: chad.junkermeier.ctr(at)nrl.navy.mil > ------------------------------------------- > cell: (801) 380-8895 > Personal email: junkermeier(at)gmail.com > skype: junkermeier > AIM: junkerammavich > gtalk: junkermeier(at)gmail.com > > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110720/7a00a0b7/attachment.htm From John.Tse at usask.ca Thu Jul 21 14:04:16 2011 From: John.Tse at usask.ca (John S. Tse) Date: Thu, 21 Jul 2011 06:04:16 -0600 Subject: [xcrysden] Missing libxc.so.6 routines In-Reply-To: References: Message-ID: <1311249856.4e2815c00d48c@webmail.usask.ca> Dear netter, I encountered an error when executing xcrysden on our machines. I have tried to re-compile the code and got the same error. I am using version 1.5.24 Here is the problem .. [jtse at phy891 XCrySDen-1.5.24-bin-semishared]$ ./xcrysden +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2009 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 1.5.23 Please report bugs to: Tone.Kokalj at ijs.si TERMS OF USE: ------------- XCRYSDEN is released under the GNU General Public License. Whenever graphics generated by XCRYSDEN are used in scientific publications, it shall be greatly appreciated to include an explicit reference. The preferred form is the following: [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003. Code available from http://www.xcrysden.org/. TCL_LIBRARY=/home/jtse/XCrysden/XCrySDen-1.5.23-bin-semishared/external/lib/tcl8 .5 XCRYSDEN_TOPDIR=/home/jtse/XCrysden/XCrySDen-1.5.23-bin-semishared XCRYSDEN_SCRATCH=/home/jtse/XCrysden/tmp /home/jtse/XCrysden/XCrySDen-1.5.23-bin-semishared/bin/xcrys: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home/jtse/XCrysden/XCrySDen-1.5.23-b in-semishared/bin/xcrys) /home/jtse/XCrysden/XCrySDen-1.5.23-bin-semishared/bin/xcrys: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home/jtse/XCrysden/XCrySDen-1.5.23-b in-semishared/external/lib/libtk8.5.so) /home/jtse/XCrysden/XCrySDen-1.5.23-bin-semishared/bin/xcrys: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home/jtse/XCrysden/XCrySDen-1.5.23-b in-semishared/external/lib/libtcl8.5.so) [jtse at phy891 XCrySDen-1.5.24-bin-semishared]$ Any suggestion to resolve the problem? Thanks John Dr. John S. Tse Professor Canada Research Chair (Tier I) Department of Physics and Engineering Physics University of Saskatchewan 116 Science Place Saskatoon, SK S7N 5E2 Canada (Tel) +1 306 966 6410 (Fax) +1 306 966 6400 From tone.kokalj at ijs.si Thu Jul 21 15:21:17 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 21 Jul 2011 15:21:17 +0200 Subject: [xcrysden] ftnunit file error In-Reply-To: References: Message-ID: <1311254477.3331.30.camel@catalyst.ijs.si> On Mon, 2011-07-04 at 00:06 +0430, David Grifith wrote: > Dear XCrysden Users > > I get the error: while executing > exec /home/.../.../xcrysden/bin/ftnunit when I try to execute > "xcrysden" . The version that I use is XCrySDen-1.5.24-bin-shared. any > suggession for solving the problem is appreciated in advance. The 64bit version-1.5.24 has some problems due to a gfortran-4.6 bug. I created a new 64bit version, compiled with gfortran-4.4, which should be OK. Let me know if it fixes your problem. semishared: http://www.xcrysden.org/download/xc-1.5.25-linux_x86_64-semishared.tar.gz shared: http://www.xcrysden.org/download/xc-1.5.25-linux_x86_64-shared.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 Thu Jul 21 15:47:03 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 21 Jul 2011 15:47:03 +0200 Subject: [xcrysden] Missing libxc.so.6 routines In-Reply-To: <1311249856.4e2815c00d48c@webmail.usask.ca> References: <1311249856.4e2815c00d48c@webmail.usask.ca> Message-ID: <1311256023.3331.45.camel@catalyst.ijs.si> On Thu, 2011-07-21 at 06:04 -0600, John S. Tse wrote: > Dear netter, > > I encountered an error when executing xcrysden on our machines. I have tried to > re-compile the code and got the same error. I am using version 1.5.24 Apparently you are using too old version of linux, and you don't have recent enough version of glibc. There are three possible solutions: (i) use old enough version of xcrysden, i.e., go to http://www.xcrysden.org/download/ and pick something older; older than 1.5.22. (ii) upgrade you linux box (iii) compile the xcrysden source code. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Thu Jul 21 15:51:57 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 21 Jul 2011 15:51:57 +0200 Subject: [xcrysden] info: problems with 64bit linux 1.5.24 version Message-ID: <1311256317.3331.50.camel@catalyst.ijs.si> Hello everybody, I would like to inform all of you that use the 64bit linux 1.5.24 version of xcrysden that this particular compilation has some problems, which should be fixed in the recompiled v.1.5.25, available from: http://www.xcrysden.org/Download.html Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From palex at infis.ufu.br Thu Jul 21 16:55:12 2011 From: palex at infis.ufu.br (Paulo Alex da Silva Carvalho) Date: Thu, 21 Jul 2011 11:55:12 -0300 Subject: [xcrysden] xcrysden on Mac Os X Lion Message-ID: <45279A1B-5486-4DEC-A4C7-FB290A090ED3@infis.ufu.br> Does anyone know where I can find a compiled version of Xcrysden for Mac OS X Lion? thank you From izaakw89 at yahoo.com Thu Jul 21 22:49:56 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Thu, 21 Jul 2011 13:49:56 -0700 (PDT) Subject: [xcrysden] Saving as XSF structure In-Reply-To: References: Message-ID: <1311281396.26261.YahooMailNeo@web43402.mail.sp1.yahoo.com> Hello, I know that when I save my structure as an XSF file, the atomic coordinates for the molecule are in angstroms. Is there any way that XCrySDen can print those coordinates in alat (as a function of the lattice parameter a)? Some of the structures that I create from XSF files need the precision of alat units and converting them manually is quite time consuming. Thanks for any help. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110721/2d831d0e/attachment.htm From victor.bermudez at nrl.navy.mil Fri Jul 22 10:41:53 2011 From: victor.bermudez at nrl.navy.mil (Vic Bermudez) Date: Fri, 22 Jul 2011 04:41:53 -0400 Subject: [xcrysden] Problem With AXSF Files Message-ID: Hello, I'm running XCrySDen vers. 1.5.18 under Cygwin (the latest version) on a WinXP PC. When I display an AXSF file I get frequent error messages, as shown below. This particular error occurred when using one of the example AXSF files that comes with XCrySDen, but it happens with every AXSF file. Other file types seem to work correctly and without error. Any advice would be much appreciated. ******************************************************** error copying "ANIMsymb.axsf.raw.23" to "/tmp/xc_4500/xc_struc.4500": permission denied error copying "ANIMsymb.axsf.raw.23" to "/tmp/xc_4500/xc_struc.4500": permission denied while executing "file copy -force $file $system(SCRDIR)/xc_struc.$system(PID)" (procedure "UpdateWMTitle" line 11) invoked from within "UpdateWMTitle $working_XSF_file" (procedure "xsfAnimRenderCurrent" line 6) invoked from within "xsfAnimRenderCurrent $can" ("next" arm line 7) invoked from within "switch -exact -- $what { stop { set xsfAnim(stop) [expr {$xsfAnim(stop) ? 0 : 1}] } first { if { $xsfAnim(current) == 1 } { re..." (procedure "xsfAnimAction" line 19) invoked from within "xsfAnimAction .mesa next" invoked from within ".animmesa.f1.1.nxt invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 24) invoked from within "tk::ButtonUp .animmesa.f1.1.nxt " (command bound to event) ********************************************************* Thanks, Vic Bermudez Victor M. Bermudez Code 6876 U.S. Naval Research Laboratory 4555 Overlook Ave., S.W. Washington, DC 20375-5347 Phone: 202-767-6728 FAX: 202-767-1165 E-mail: victor.bermudez at nrl.navy.mil From palex at infis.ufu.br Fri Jul 22 17:12:42 2011 From: palex at infis.ufu.br (Paulo Alex da Silva Carvalho) Date: Fri, 22 Jul 2011 12:12:42 -0300 Subject: [xcrysden] Mac OS X binary package Message-ID: I am trying to download the Mac OS X binary package xc-1.5.21-darwin-semishared.tar.gz , but this link is broken. Does anyone knows where I can get this package, please? thank you Prof. Paulo Alex da Silva Carvalho Instituto de F?sica Campus de Patos de Minas Universidade Federal de Uberl?ndia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110722/467f907c/attachment.htm From dmwood at mines.edu Mon Jul 25 20:31:39 2011 From: dmwood at mines.edu (David M. Wood) Date: Mon, 25 Jul 2011 12:31:39 -0600 Subject: [xcrysden] Success: Building XCD 1.5.24 with shared libs on OS X Message-ID: <4DDBA9AA-AAD0-4ED1-B86F-9A1B33CA30AD@Mines.EDU> Howdy all! After long travails, I have succeeded in building a functioning version of 1.5.24. It is somewhat disturbing how difficult this has been. (It appears to have succeeded today only because of new Mesa and OpenGL libraries from MacPorts.) I attempt to give here a quick prescription for building xcd 1.5.24 using external libraries provided by the MacPorts system: http://www.macports.org/ . [Remember why this is potentially useful: you can use, e.g., libraries which are tweaked for your particular architecture; macports is also well maintained.] Because this process has been spread out over many weeks, I undoubtedly have forgotten to specify something; please let me know if so. I built this under Mac OS X 10.6.8 (Snow Leopard); I'll follow up if things are significantly different under Lion (10.7). 0. Make sure you have Xcode and relevant Developer (e.g, X11) packages installed 1. Install a barebones MacPort tree (again, from www.macports.org) 2. Install, in no particular order (port will take care of dependencies) atlas fftw-3 gfortran 4.5 [which will end up being named gfortran-mp-4.5 in /opt/local/bin], although earlier versions (e.g., 4.3) worked for me. This should automatically install gcc. mesa meschach tcl tk NB: port install gcc45 +variant:gfortran is an EXAMPLE of how to install a variant of a particular port package. Each install will provoke a cascade of other downloads and install; be patient. 3. Use the Make.sys file below 4. Type "make all" 5. Test on .xsf or .xcrysden files Carefully inspect the directories and libraries mentioned in Make.sys; if you don't have the ones mentioned, you may not have installed the corresponding MacPorts packages. =========BEGINNING OF Make.sys============== MAKE = make CC = /opt/local/bin/gcc-mp-4.5 #Need the have-no-getline CFLAGS = -O2 -m64 -L/opt/local/lib -DXC_HAVE_NO_GETLINE MATH = -lm FC = /opt/local/bin/gfortran-mp-4.5 FFLAGS = -O2 -m64 -L/opt/local/lib #DMW: See notes for CFLAGS above #X #port libs X_LIB = -L/opt/local/lib -lXmu -lX11 -lXext X_INCDIR = -I/opt/local/include # If you want to use your own libraries and include files, # then set *_LIB and *_INCDIR variables below accordingly: # #------------------------------------------------------------------------ COMPILE_TCLTK = no COMPILE_MESA = no # # Libraries # TK_LIB = -L/opt/local/lib -ltk8.5 TCL_LIB = -L/opt/local/lib -ltcl8.5 GLU_LIB = -L/opt/local/lib -lGLU GL_LIB = -L/opt/local/lib -lGL #DMW additions MESCHACH_LIB = -L/opt/local/lib -lmeschach FFTW3_LIB = -L/opt/local/lib -lfftw3 LDLIB = -L/opt/local/lib # # Include directories # #blank fine TCL_INCDIR = TK_INCDIR = GL_INCDIR = #DMW additions MESCHACH_INCDIR = -I/opt/local/include/meschach FFTW3_INCDIR = -I/opt/local/include =========END OF Make.sys============== I readily made a XCrySDen-1.5.24-bin-shared.tar.gz file but assume this won't work unless boatloads of libraries (above) are present. Hope this helps! David M. Wood, Dept. of Physics, Colorado School of Mines, Golden, CO 80401 Phone: (303) 273-3853; Fax: (303) 273-3919 From tone.kokalj at ijs.si Tue Jul 26 17:36:27 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 26 Jul 2011 17:36:27 +0200 Subject: [xcrysden] Saving as XSF structure In-Reply-To: <1311281396.26261.YahooMailNeo@web43402.mail.sp1.yahoo.com> References: <1311281396.26261.YahooMailNeo@web43402.mail.sp1.yahoo.com> Message-ID: <1311694587.22275.2.camel@catalyst.ijs.si> On Thu, 2011-07-21 at 13:49 -0700, Izaak Williamson wrote: > Hello, > > I know that when I save my structure as an XSF file, the atomic > coordinates for the molecule are in angstroms. Is there any way that > XCrySDen can print those coordinates in alat (as a function of the > lattice parameter a)? Some of the structures that I create from XSF > files need the precision of alat units and converting them manually is > quite time consuming. The easiest thing is to write a small, say, awk script that will do the scaling of coordinates from angstrom to alat units. 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 Tue Jul 26 17:46:06 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 26 Jul 2011 17:46:06 +0200 Subject: [xcrysden] Problem With AXSF Files In-Reply-To: References: Message-ID: <1311695166.22275.12.camel@catalyst.ijs.si> On Fri, 2011-07-22 at 04:41 -0400, Vic Bermudez wrote: > Hello, > > I'm running XCrySDen vers. 1.5.18 under Cygwin (the latest version) on a > WinXP PC. When I display an AXSF file I get frequent error messages, as > shown below. This particular error occurred when using one of the example > AXSF files that comes with XCrySDen, but it happens with every AXSF file. > Other file types seem to work correctly and without error. > Any advice would be much appreciated. > > ******************************************************** > > error copying "ANIMsymb.axsf.raw.23" to "/tmp/xc_4500/xc_struc.4500": > permission denied Seems like the temporary files are readonly, and hence xcrysden cannot overwrite them. Try again and see if /tmp/xc_????/xc_struc.???? is a readonly file, i.e.; ls -l /tmp/xc_4500/xc_struc.4500 should return a line strating with: -r--r--r-- Is this is so, then this has likely to do with the cygwin settings (can't help more, because my cygwin knowledge is close to zero). 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 Tue Jul 26 18:01:46 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 26 Jul 2011 18:01:46 +0200 Subject: [xcrysden] Success: Building XCD 1.5.24 with shared libs on OS X In-Reply-To: <4DDBA9AA-AAD0-4ED1-B86F-9A1B33CA30AD@Mines.EDU> References: <4DDBA9AA-AAD0-4ED1-B86F-9A1B33CA30AD@Mines.EDU> Message-ID: <1311696106.22275.27.camel@catalyst.ijs.si> On Mon, 2011-07-25 at 12:31 -0600, David M. Wood wrote: > Howdy all! > > After long travails, I have succeeded in building a functioning version of 1.5.24. It is somewhat disturbing how difficult this has been. David, This is absolutely great! > I readily made a XCrySDen-1.5.24-bin-shared.tar.gz file but assume this won't work unless boatloads of libraries (above) are present. > Hope this helps! I would recommend to also prepare a semishared version. The "bindist-semishared" target can assist you in doing that. But prior running it, copy all the necessary libraries in $XCRYSDEN_TOPDIR/external/lib/ (you need to copy Tcl/Tl, GL/GLU, fftw and meschach libraries) E.g., here is a listing from the linux semishared version: drwxr-xr-x 7 tone tone 4096 Jan 17 2011 bwidget-1.9.4 lrwxrwxrwx 1 tone tone 17 Apr 1 11:27 libfftw3.so -> libfftw3.so.3.2.4 lrwxrwxrwx 1 tone tone 17 Apr 1 11:32 libfftw3.so.3 -> libfftw3.so.3.2.4 -rw-r--r-- 1 tone tone 1044376 Apr 1 11:27 libfftw3.so.3.2.4 lrwxrwxrwx 1 tone tone 10 Apr 1 12:21 libGL.so -> libGL.so.1 lrwxrwxrwx 1 tone tone 19 Apr 1 12:21 libGL.so.1 -> libGL.so.1.5.071000 -rwxr-xr-x 1 tone tone 17465488 Jul 31 2009 libGL.so.1.5.070200 -rwxr-xr-x 1 tone tone 20022882 Apr 1 12:21 libGL.so.1.5.071000 lrwxrwxrwx 1 tone tone 11 Apr 1 12:24 libGLU.so -> libGLU.so.1 lrwxrwxrwx 1 tone tone 20 Apr 1 12:24 libGLU.so.1 -> libGLU.so.1.3.071000 -rwxr-xr-x 1 tone tone 2156047 Jul 31 2009 libGLU.so.1.3.070200 -rwxr-xr-x 1 tone tone 2284040 Apr 1 12:24 libGLU.so.1.3.071000 lrwxrwxrwx 1 tone tone 18 Apr 1 11:27 libmeschach.so -> libmeschach.so.1.2 -rw-r--r-- 1 tone tone 300152 Apr 1 11:27 libmeschach.so.1.2 -r-xr-xr-x 1 tone tone 1265855 Apr 1 11:15 libtcl8.5.so -r-xr-xr-x 1 tone tone 1479857 Apr 1 11:16 libtk8.5.so drwxr-xr-x 6 tone tone 4096 Apr 1 11:15 tcl8.5 drwxr-xr-x 5 tone tone 4096 Apr 1 11:16 tk8.5 Then edit the EXTERNAL_LIB_FILES and EXTERNAL_SHAREDLIB_FILES variables in top Makefile and finally execute make bindist-shared. Let me know your progress. 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 palex at infis.ufu.br Tue Jul 26 22:10:01 2011 From: palex at infis.ufu.br (Paulo Alex da Silva Carvalho) Date: Tue, 26 Jul 2011 17:10:01 -0300 Subject: [xcrysden] Success: Building XCD 1.5.24 with shared libs on OS X In-Reply-To: <4DDBA9AA-AAD0-4ED1-B86F-9A1B33CA30AD@Mines.EDU> References: <4DDBA9AA-AAD0-4ED1-B86F-9A1B33CA30AD@Mines.EDU> Message-ID: Thanks a lot David! I am following your steps. It takes some time. When I finished I let you know if it works for me. Again, thank you! Prof. Paulo Alex da Silva Carvalho Instituto de F?sica Campus de Patos de Minas Universidade Federal de Uberl?ndia 2011/7/25 David M. Wood > Howdy all! > > After long travails, I have succeeded in building a functioning version of > 1.5.24. It is somewhat disturbing how difficult this has been. (It appears > to have succeeded today only because of new Mesa and OpenGL libraries from > MacPorts.) > > I attempt to give here a quick prescription for building xcd 1.5.24 using > external libraries provided by the MacPorts system: > http://www.macports.org/ . [Remember why this is potentially useful: you > can use, e.g., libraries which are tweaked for your particular architecture; > macports is also well maintained.] Because this process has been spread out > over many weeks, I undoubtedly have forgotten to specify something; please > let me know if so. I built this under Mac OS X 10.6.8 (Snow Leopard); I'll > follow up if things are significantly different under Lion (10.7). > > 0. Make sure you have Xcode and relevant Developer (e.g, X11) packages > installed > > 1. Install a barebones MacPort tree (again, from www.macports.org) > > 2. Install, in no particular order (port will take care of dependencies) > > atlas > fftw-3 > gfortran 4.5 [which will end up being named gfortran-mp-4.5 in > /opt/local/bin], although earlier versions (e.g., 4.3) worked for me. This > should automatically install gcc. > mesa > meschach > tcl > tk > > NB: port install gcc45 +variant:gfortran is an EXAMPLE of how to install a > variant of a particular port package. > > Each install will provoke a cascade of other downloads and install; be > patient. > > 3. Use the Make.sys file below > > 4. Type "make all" > > 5. Test on .xsf or .xcrysden files > > Carefully inspect the directories and libraries mentioned in Make.sys; if > you don't have the ones mentioned, you may not have installed the > corresponding MacPorts packages. > > =========BEGINNING OF Make.sys============== > > MAKE = make > > CC = /opt/local/bin/gcc-mp-4.5 > #Need the have-no-getline > CFLAGS = -O2 -m64 -L/opt/local/lib -DXC_HAVE_NO_GETLINE > MATH = -lm > > FC = /opt/local/bin/gfortran-mp-4.5 > FFLAGS = -O2 -m64 -L/opt/local/lib > #DMW: See notes for CFLAGS above > > #X > #port libs > X_LIB = -L/opt/local/lib -lXmu -lX11 -lXext > X_INCDIR = -I/opt/local/include > > # If you want to use your own libraries and include files, > # then set *_LIB and *_INCDIR variables below accordingly: > # > #------------------------------------------------------------------------ > > COMPILE_TCLTK = no > COMPILE_MESA = no > > # > # Libraries > # > TK_LIB = -L/opt/local/lib -ltk8.5 > TCL_LIB = -L/opt/local/lib -ltcl8.5 > GLU_LIB = -L/opt/local/lib -lGLU > GL_LIB = -L/opt/local/lib -lGL > > #DMW additions > MESCHACH_LIB = -L/opt/local/lib -lmeschach > FFTW3_LIB = -L/opt/local/lib -lfftw3 > LDLIB = -L/opt/local/lib > > # > # Include directories > # > > #blank fine > TCL_INCDIR = > TK_INCDIR = > GL_INCDIR = > > #DMW additions > MESCHACH_INCDIR = -I/opt/local/include/meschach > FFTW3_INCDIR = -I/opt/local/include > > =========END OF Make.sys============== > > I readily made a XCrySDen-1.5.24-bin-shared.tar.gz file but assume this > won't work unless boatloads of libraries (above) are present. > Hope this helps! > > David M. Wood, Dept. of Physics, Colorado School of Mines, Golden, CO 80401 > Phone: (303) 273-3853; Fax: (303) 273-3919 > > _______________________________________________ > 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/20110726/9fbd5071/attachment.htm From palex at infis.ufu.br Wed Jul 27 17:43:28 2011 From: palex at infis.ufu.br (Paulo Alex da Silva Carvalho) Date: Wed, 27 Jul 2011 12:43:28 -0300 Subject: [xcrysden] Success: Building XCD 1.5.24 with shared libs on OS X In-Reply-To: <4DDBA9AA-AAD0-4ED1-B86F-9A1B33CA30AD@Mines.EDU> References: <4DDBA9AA-AAD0-4ED1-B86F-9A1B33CA30AD@Mines.EDU> Message-ID: Helo David I did your steps on Snow Leopard and it works nicely, thank you very much! But then I install Lion and Xcrysden continues working but now there is an annoying flickering of the Xcrysden display. It is practically impossible to use it. I know that you have this trouble last year. Do you have any idea of how to fix that? again, thanks Prof. Paulo Alex da Silva Carvalho Instituto de F?sica Campus de Patos de Minas Universidade Federal de Uberl?ndia 2011/7/25 David M. Wood > Howdy all! > > After long travails, I have succeeded in building a functioning version of > 1.5.24. It is somewhat disturbing how difficult this has been. (It appears > to have succeeded today only because of new Mesa and OpenGL libraries from > MacPorts.) > > I attempt to give here a quick prescription for building xcd 1.5.24 using > external libraries provided by the MacPorts system: > http://www.macports.org/ . [Remember why this is potentially useful: you > can use, e.g., libraries which are tweaked for your particular architecture; > macports is also well maintained.] Because this process has been spread out > over many weeks, I undoubtedly have forgotten to specify something; please > let me know if so. I built this under Mac OS X 10.6.8 (Snow Leopard); I'll > follow up if things are significantly different under Lion (10.7). > > 0. Make sure you have Xcode and relevant Developer (e.g, X11) packages > installed > > 1. Install a barebones MacPort tree (again, from www.macports.org) > > 2. Install, in no particular order (port will take care of dependencies) > > atlas > fftw-3 > gfortran 4.5 [which will end up being named gfortran-mp-4.5 in > /opt/local/bin], although earlier versions (e.g., 4.3) worked for me. This > should automatically install gcc. > mesa > meschach > tcl > tk > > NB: port install gcc45 +variant:gfortran is an EXAMPLE of how to install a > variant of a particular port package. > > Each install will provoke a cascade of other downloads and install; be > patient. > > 3. Use the Make.sys file below > > 4. Type "make all" > > 5. Test on .xsf or .xcrysden files > > Carefully inspect the directories and libraries mentioned in Make.sys; if > you don't have the ones mentioned, you may not have installed the > corresponding MacPorts packages. > > =========BEGINNING OF Make.sys============== > > MAKE = make > > CC = /opt/local/bin/gcc-mp-4.5 > #Need the have-no-getline > CFLAGS = -O2 -m64 -L/opt/local/lib -DXC_HAVE_NO_GETLINE > MATH = -lm > > FC = /opt/local/bin/gfortran-mp-4.5 > FFLAGS = -O2 -m64 -L/opt/local/lib > #DMW: See notes for CFLAGS above > > #X > #port libs > X_LIB = -L/opt/local/lib -lXmu -lX11 -lXext > X_INCDIR = -I/opt/local/include > > # If you want to use your own libraries and include files, > # then set *_LIB and *_INCDIR variables below accordingly: > # > #------------------------------------------------------------------------ > > COMPILE_TCLTK = no > COMPILE_MESA = no > > # > # Libraries > # > TK_LIB = -L/opt/local/lib -ltk8.5 > TCL_LIB = -L/opt/local/lib -ltcl8.5 > GLU_LIB = -L/opt/local/lib -lGLU > GL_LIB = -L/opt/local/lib -lGL > > #DMW additions > MESCHACH_LIB = -L/opt/local/lib -lmeschach > FFTW3_LIB = -L/opt/local/lib -lfftw3 > LDLIB = -L/opt/local/lib > > # > # Include directories > # > > #blank fine > TCL_INCDIR = > TK_INCDIR = > GL_INCDIR = > > #DMW additions > MESCHACH_INCDIR = -I/opt/local/include/meschach > FFTW3_INCDIR = -I/opt/local/include > > =========END OF Make.sys============== > > I readily made a XCrySDen-1.5.24-bin-shared.tar.gz file but assume this > won't work unless boatloads of libraries (above) are present. > Hope this helps! > > David M. Wood, Dept. of Physics, Colorado School of Mines, Golden, CO 80401 > Phone: (303) 273-3853; Fax: (303) 273-3919 > > _______________________________________________ > 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/20110727/614c571c/attachment.htm