From daniel.mazur at mcgill.ca Tue Oct 14 19:43:59 2014 From: daniel.mazur at mcgill.ca (Dan Mazur) Date: Tue, 14 Oct 2014 13:43:59 -0400 Subject: [xcrysden] BadWindow error when launching newly installed xcrysden Message-ID: Hello, I have compiled the source distribution of xcrysden v 1.5.60 on CentOS 6.3 and the compilation and installation appears to proceed without errors. When I run xcrysden, it briefly opens an X11 splash window, but then crashes with the following messages: $ xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2014 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.5.60 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, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999. Code available from http://www.xcrysden.org/. XCRYSDEN_TOPDIR=/software/CentOS-6/applications/xcrysden-1.5.60/share/xcrysden-1.5.60 XCRYSDEN_SCRATCH=/home/tfosrgm/xcrys_tmp Running on platform : unix Operating system : Linux Package ImageMagick's convert: /usr/bin/convert Package ImageMagick's import: /usr/bin/import Package Ppmtompeg: /usr/bin/ppmtompeg Package Xwd: /usr/bin/xwd Executing: /software/CentOS-6/applications/xcrysden-1.5.60/lib/xcrysden-1.5.60/ftnunit X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 ResourceID in failed request: 0xffffffff Serial number of failed request: 799 X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 ResourceID in failed request: 0xffffffff Serial number of failed request: 801 Error in startup script: Togl: couldn't get visual while executing "togl .mesa -width 400 -height 400 -ident .mesa -rgba true -redsize 1 -greensize 1 -blu..." (procedure "PlaceGlobWin" line 105) invoked from within "PlaceGlobWin 0 [expr round(650 * $fac1)] [expr round(650 * $fac1)]" (procedure "ViewMol" line 25) invoked from within "ViewMol ." invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/software/CentOS-6/applications/xcrysden-1.5.60/share/xcrysden-1.5.60/Tcl/xcInit.tcl" line 609) X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 12 ResourceID in failed request: 0xffffffff Serial number of failed request: 804 I do not have problems with other OpenGL or X11 programs. I first tried linking against libraries (including mesa) on the system, but got this error. Then, I tried downloading and compiling the external libraries by activating the required flags in Make.sys. However, I again got the above error. I am not sure of the reason for the error. If someone can help me to debug the issue and complete my installation of xcrysden, it would be appreciated. -Dan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20141014/5d96ee93/attachment.htm From member at linkedin.com Wed Oct 15 10:25:21 2014 From: member at linkedin.com (hamidreza balangi) Date: Wed, 15 Oct 2014 08:25:21 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_voc=C3=AA_poderia_me_a?= =?utf-8?q?dicionar_=C3=A0_sua_rede_do_LinkedIn=3F?= Message-ID: <745682173.3404494.1413361521629.JavaMail.app@lva1-app3751.prod> Ol?, Andr? Pereira. Fa?a parte da minha rede no LinkedIn. hamidreza balangi member at Sadra Data Processing company Aceitar: http://www.linkedin.com/blink?simpleRedirect=d30Tc3wOc3sUcj8UdPoMe38VdjR4imVLqnhxt6BSrCACc30RnP8RdP0Rdz0SdP0Re3sSc3wOejl9fkh9rmlQqioRjjhngmFCpjRVpkJApn9xq7cCe39vsClyrmlJnSlQqnpKqjRHpipBt6BSrCBTpmUJt71BoSdxbm8JrnpKqlZJrmZzbmNJpjRDrCBHoS5Ot2pTpBlpd7lBd51OrkxhgjRKpmJLl6hFripBt6BSrABQs6lzoQ5LpmMZoipNciRKtm9Vpm4NqiRNc69Id38ZpjYOtyZBbSRLoOVKqmhBqSVFr2VTtTsLbPFMt7hE&msgID=I5928067850760650752_500&markAsRead= Visualizar o perfil de hamidreza balangi: http://www.linkedin.com/blink?simpleRedirect=3cVdjsQcjkVcjR4in9BoCRBripBe4RhfmVBqSZkq7hRoipBrm5KfmlMulhEt7lx9z0MdlYOdjsMdjoMdzsMdjwTdz0UczARilYQdPwQd3oUcz4Zt71BoSd1rCZFt65QqnpKqioUcBZOpm9JpmRvpnhFtCVFfmJB9ClQqnpKqntBryRBrm5Kbm8JrnpKqlZJrmZzbmNJpjRDrCBHoS5Ot2pTpBlpd7lBd51OrkxhgjRKpmJLl6hFripSs6UZt2pNciRKtm9Vpm4NqiRNc69Id38ZpjYOtyZBbSRLoOVKqmhBqSVFr2VTtTsLbPFMt7hE&msgID=I5928067850760650752_500&markAsRead= Voc? est? recebendo e-mails sobre Convite. Cancele a inscri??o clicando aqui: http://www.linkedin.com/blink?simpleRedirect=1NciRKtm9Vpm4NqiRNc69Id38Zp6BB9BBLsBdGcj4Rqk97qARch4BHe6Nbk51lskFHl48QnORpmCNWoSBipChiqR52i3hIoz4Jgj5pc4oMbkEStQZmdBdHlk51gl5CdzphjT9VcCZihl51fmhFrSMCe39vsClyrmlJnSlQqnpKqjRHpipBt6BSrCBTpmUJoDlPrDkJpyRJtCVFnSRJrScJr6RBfmtKqmJzon9Q9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9DdRpjRQ9D4NbmVRoDBBoj5Fbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5928067850760650752_500&markAsRead=. Este e-mail foi enviado para Andr? Pereira XCrysden (Estudante na Universidade Estadual Paulista 'J?lio de Mesquita Filho'). Saiba por que inclu?mos isso neste link: http://www.linkedin.com/blink?simpleRedirect=e3wTd3RAimlIoSBQsC4Ce39vsClyrmlJnSlQqnpKqjRHpipTpBlpd7lBd51OrkxhgjRKpmJLl6hFripIsBlBoSBSsCljsClJrThPtmcZoipNciRKtm9Vpm4NqiRNc69Id38ZpjYOtyZBbSRLoOVKqmhBqSVFr2VTtTsLbPFMt7hE&msgID=I5928067850760650752_500&markAsRead= ©2014 LinkedIn Ireland Limited, registrada na Irlanda como uma empresa privada e ltda. Registro n?mero 477441. Registrada em: 70 Sir John Roberson's Quay, Dublin 2. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20141015/4baf1145/attachment-0001.htm From oleh.menchyshyn at gmail.com Sat Oct 18 01:28:26 2014 From: oleh.menchyshyn at gmail.com (Menchyshyn Oleh) Date: Sat, 18 Oct 2014 02:28:26 +0300 Subject: [xcrysden] Visualizing the frustrated magnets lattices Message-ID: Dear all, Sorry in advance if my question sounds silly or naive. I would like to picture the pyrochlore and the gadolinium gallium garnet lattices, but not as a crystalline structure with some real chemical formula, rather as a graph of edges connecting nodes in primitive coordinates. Does it somehow relates to datagrids? How can I specify a bond between some atoms? I will appreciate some simple *.xsf as example, if possible. Best regards, Oleh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20141018/c3c0d874/attachment.htm From daniel.mazur at mcgill.ca Tue Oct 28 20:48:48 2014 From: daniel.mazur at mcgill.ca (Dan Mazur) Date: Tue, 28 Oct 2014 15:48:48 -0400 Subject: [xcrysden] BadWindow error when launching newly installed xcrysden In-Reply-To: References: Message-ID: Hello, I am still not able to install this package. I have tried linking instead with a different OpenGL library, but I get the same results. If anyone can offer any advice on how to resolve the error, it would be much appreciated. -Dan On Tue, Oct 14, 2014 at 1:43 PM, Dan Mazur wrote: > Hello, > > I have compiled the source distribution of xcrysden v 1.5.60 on CentOS 6.3 > and the compilation and installation appears to proceed without errors. > > When I run xcrysden, it briefly opens an X11 splash window, but then > crashes with the following messages: > > $ xcrysden > > +-----------------------------------------------------------------+ > |*****************************************************************| > |* *| > |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| > |* = === = === *| > |*---------------------------------------------------------------*| > |* *| > |* Anton Kokalj (tone.kokalj at ijs.si) *| > |* Jozef Stefan Institute, Ljubljana, Slovenia *| > |* *| > |* Copyright (c) 1996--2014 by Anton Kokalj *| > |* *| > |*****************************************************************| > +-----------------------------------------------------------------+ > > Version: 1.5.60 > > 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, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999. > Code available from http://www.xcrysden.org/. > > > XCRYSDEN_TOPDIR=/software/CentOS-6/applications/xcrysden-1.5.60/share/xcrysden-1.5.60 > XCRYSDEN_SCRATCH=/home/tfosrgm/xcrys_tmp > > Running on platform : unix > Operating system : Linux > Package ImageMagick's convert: /usr/bin/convert > Package ImageMagick's import: /usr/bin/import > Package Ppmtompeg: /usr/bin/ppmtompeg > Package Xwd: /usr/bin/xwd > Executing: > /software/CentOS-6/applications/xcrysden-1.5.60/lib/xcrysden-1.5.60/ftnunit > X Error of failed request: BadWindow (invalid Window parameter) > Major opcode of failed request: 3 > ResourceID in failed request: 0xffffffff > Serial number of failed request: 799 > X Error of failed request: BadWindow (invalid Window parameter) > Major opcode of failed request: 3 > ResourceID in failed request: 0xffffffff > Serial number of failed request: 801 > Error in startup script: Togl: couldn't get visual > while executing > "togl .mesa -width 400 -height 400 -ident > .mesa -rgba true -redsize 1 -greensize 1 > -blu..." > (procedure "PlaceGlobWin" line 105) > invoked from within > "PlaceGlobWin 0 [expr round(650 * $fac1)] [expr round(650 * $fac1)]" > (procedure "ViewMol" line 25) > invoked from within > "ViewMol ." > invoked from within > "if { [llength $argv] > 2 } { > parseComLinArg [lrange $argv 2 end] > } else { > ViewMol . > }" > (file > "/software/CentOS-6/applications/xcrysden-1.5.60/share/xcrysden-1.5.60/Tcl/xcInit.tcl" > line 609) > X Error of failed request: BadWindow (invalid Window parameter) > Major opcode of failed request: 12 > ResourceID in failed request: 0xffffffff > Serial number of failed request: 804 > > I do not have problems with other OpenGL or X11 programs. I first tried > linking against libraries (including mesa) on the system, but got this > error. Then, I tried downloading and compiling the external libraries by > activating the required flags in Make.sys. However, I again got the above > error. > > I am not sure of the reason for the error. If someone can help me to debug > the issue and complete my installation of xcrysden, it would be appreciated. > > > -Dan > > -- ------------------------------------------------------------------------ Dr. Dan Mazur | daniel.mazur at mcgill.ca | dan.mazur at calculquebec.ca Scientific Computing Analyst / Analyste en calcul scientifique McGill HPC Centre / Centre de Calcul Haute Performance de McGill | http://www.hpc.mcgill.ca Calcul Qu?bec | http://www.calculquebec.ca Compute/Calcul Canada | http://www.computecanada.ca Tel/T?l: 514-396-8928 | Fax/T?l?copieur: 514-396-8934 ------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20141028/fb17275a/attachment.htm From kami at chem.s.u-tokyo.ac.jp Wed Oct 29 02:52:44 2014 From: kami at chem.s.u-tokyo.ac.jp (Hideyuki KAMISAKA) Date: Wed, 29 Oct 2014 10:52:44 +0900 Subject: [xcrysden] BadWindow error when launching newly installed xcrysden In-Reply-To: References: Message-ID: Dear Dan, Did you try to fix the problem by modifying the Togl options in xcrysden-1.5.60/Tcl/Viewer.tcl and xcrysden-1.5.60/Tcl/fs/FS_{Main,Multi}.tcl ? We have compiled xcrysden-1.5.53 on CentOS 5.7 successfully. No special installation of additional middleware was needed. The "-accum*" and ?-stereo?, '-time' options in Togl was the key in our case. If you already know this, please ignore this message. Regards, Hideyuki KAMISAKA 2014-10-29 4:48 GMT+09:00 Dan Mazur : > Hello, > > I am still not able to install this package. I have tried linking instead > with a different OpenGL library, but I get the same results. If anyone can > offer any advice on how to resolve the error, it would be much appreciated. > > -Dan > > On Tue, Oct 14, 2014 at 1:43 PM, Dan Mazur wrote: >> >> Hello, >> >> I have compiled the source distribution of xcrysden v 1.5.60 on CentOS 6.3 >> and the compilation and installation appears to proceed without errors. >> >> When I run xcrysden, it briefly opens an X11 splash window, but then >> crashes with the following messages: >> >> $ xcrysden >> >> +-----------------------------------------------------------------+ >> |*****************************************************************| >> |* *| >> |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| >> |* = === = === *| >> |*---------------------------------------------------------------*| >> |* *| >> |* Anton Kokalj (tone.kokalj at ijs.si) *| >> |* Jozef Stefan Institute, Ljubljana, Slovenia *| >> |* *| >> |* Copyright (c) 1996--2014 by Anton Kokalj *| >> |* *| >> |*****************************************************************| >> +-----------------------------------------------------------------+ >> >> Version: 1.5.60 >> >> 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, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999. >> Code available from http://www.xcrysden.org/. >> >> >> XCRYSDEN_TOPDIR=/software/CentOS-6/applications/xcrysden-1.5.60/share/xcrysden-1.5.60 >> XCRYSDEN_SCRATCH=/home/tfosrgm/xcrys_tmp >> >> Running on platform : unix >> Operating system : Linux >> Package ImageMagick's convert: /usr/bin/convert >> Package ImageMagick's import: /usr/bin/import >> Package Ppmtompeg: /usr/bin/ppmtompeg >> Package Xwd: /usr/bin/xwd >> Executing: >> /software/CentOS-6/applications/xcrysden-1.5.60/lib/xcrysden-1.5.60/ftnunit >> X Error of failed request: BadWindow (invalid Window parameter) >> Major opcode of failed request: 3 >> ResourceID in failed request: 0xffffffff >> Serial number of failed request: 799 >> X Error of failed request: BadWindow (invalid Window parameter) >> Major opcode of failed request: 3 >> ResourceID in failed request: 0xffffffff >> Serial number of failed request: 801 >> Error in startup script: Togl: couldn't get visual >> while executing >> "togl .mesa -width 400 -height 400 -ident >> .mesa -rgba true -redsize 1 -greensize 1 >> -blu..." >> (procedure "PlaceGlobWin" line 105) >> invoked from within >> "PlaceGlobWin 0 [expr round(650 * $fac1)] [expr round(650 * $fac1)]" >> (procedure "ViewMol" line 25) >> invoked from within >> "ViewMol ." >> invoked from within >> "if { [llength $argv] > 2 } { >> parseComLinArg [lrange $argv 2 end] >> } else { >> ViewMol . >> }" >> (file >> "/software/CentOS-6/applications/xcrysden-1.5.60/share/xcrysden-1.5.60/Tcl/xcInit.tcl" >> line 609) >> X Error of failed request: BadWindow (invalid Window parameter) >> Major opcode of failed request: 12 >> ResourceID in failed request: 0xffffffff >> Serial number of failed request: 804 >> >> I do not have problems with other OpenGL or X11 programs. I first tried >> linking against libraries (including mesa) on the system, but got this >> error. Then, I tried downloading and compiling the external libraries by >> activating the required flags in Make.sys. However, I again got the above >> error. >> >> I am not sure of the reason for the error. If someone can help me to debug >> the issue and complete my installation of xcrysden, it would be appreciated. >> >> >> -Dan >> > > > > -- > ------------------------------------------------------------------------ > Dr. Dan Mazur | daniel.mazur at mcgill.ca | > dan.mazur at calculquebec.ca > Scientific Computing Analyst / Analyste en calcul scientifique > McGill HPC Centre / Centre de Calcul Haute Performance de McGill | > http://www.hpc.mcgill.ca > Calcul Qu?bec | http://www.calculquebec.ca > Compute/Calcul Canada | http://www.computecanada.ca > Tel/T?l: 514-396-8928 | Fax/T?l?copieur: 514-396-8934 > > ------------------------------------------------------------------------ > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Hideyuki KAMISAKA Solid State Chemistry Laboratory, Department of Chemistry, School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan E-mail: kami at chem.s.u-tokyo.ac.jp TEL/FAX: 03-5841-4354