From minkyupark.phys at gmail.com Thu Jul 4 06:12:07 2024 From: minkyupark.phys at gmail.com (=?utf-8?B?67CV66+86rec?=) Date: Thu, 4 Jul 2024 13:12:07 +0900 Subject: [xcrysden] Compile on M2 In-Reply-To: References: Message-ID: <0329CA1A-5BD5-49E7-8E0B-45B25E7212BC@gmail.com> Dear all, After many tries, I finally succeed to compile xcrysden 1.6.2 on Apple silicon M2 using homebrew. Here is my recipe. 1. Install homebrew. Command Line Tools (CLT) is required. 2. Install fftw using homebrew. This also installs gcc and gfortran (which is part of gcc). 3. cp system/Make.sys-semishared-macosx-x11-xquartz Make.sys 4. Add -L/opt/homebrew/lib and -I/opt/homebrew/include to FFTW3_LIB and FFTW3_INCDIR in Make.sys respectively. 5. make CC=/usr/bin/gcc all Instead of gcc installed by homebrew, use gcc provided in CLT: Apple clang version 15.0.0 (clang-1500.3.9.4) in my case. 6. The compilation will be stopped by the error from Togl. 7. Modify external/src/Togl2.0/togl.c follow the instruction https://cgit.freebsd.org/ports/commit/?id=0e77cfcef8a5677cff1ba81430b767a1089fd083 8. Since libTogl2.0.dylib is not automatically generated in external/lib, we either do 1) add -L$(TOPDIR)/external/lib/Togl2.0 to TOGL_LIB in Make.sys or 2) ln -s external/lib/Togl2.0/libTogl2.0.dylib external/lib/ 9. make CC=/usr/bin/gcc xcrysden 10. If the compilation succeed but no executable file is generated, it can be copied from Mac OS binary packages (pre-compiled packages downloadable from xcrysden homepage). 11. make install 12. If error occurs, add symbolic link of libTogl2.0.dylib to proper locations. I hope it helps to someone struggling like me. Best regards, Minkyu Park Korea Research Institute of Standards and Science > On Apr 4, 2024, at 3:40?PM, xcrysden-request at democritos.it wrote: > > 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. Compile on M2 (???) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 4 Apr 2024 14:09:24 +0900 > From: ??? > Subject: [xcrysden] Compile on M2 > To: xcrysden at democritos.it > Message-ID: <340FFBBB-0CC3-4B84-AC9D-D20AA1DC9CC2 at gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I have been trying to compile xcrysden on M2 chip without success. > > I found one relevant email > http://www.democritos.it/pipermail/xcrysden/2022-September/002116.html > But this does not work for me. > > While ago, I was able to compile xcrysden on MacBook Pro with intel chip > by installing required libraries through homebrew. > But even if I follow the same procedure, it does not work in M2. > > So does anyone succeed to compile xcrysden on M2 or any other apple silicon chips? > > Attaches are my Make.sys and output error message. > > Best, > Minkyu Park > Korea Research Institute of Standards and Science > > ?? > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: err.log > Type: application/octet-stream > Size: 33553 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment.obj > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment.htm > -------------- next part -------------- > An embedded and charset-unspecified text was scrubbed... > Name: Make.sys.txt > Url: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment.txt > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 153, Issue 1 > **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240704/7fba5e06/attachment.htm From aadeniy at purdue.edu Tue Jul 9 16:49:51 2024 From: aadeniy at purdue.edu (Aanuoluwapo Emmanuel Adeniyi) Date: Tue, 9 Jul 2024 14:49:51 +0000 Subject: [xcrysden] output file failure Message-ID: Hi, I am very new to the world of xcrysden and I am running xcrysden on ubuntu, the program successfully open pw,in (input file) but failed to open pw.out (output file), I always get " /home/winlinux/quantumEspresso_2024/xcrysden/xcrysden-1.5.60-bin-semishared/scripts/pwo2xsf.sh:1: bc: not found" I have also attached the image of another error displayed to this email. Thanks, Aanuoluwapo Emmanuel Adeniyi. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240709/bd681061/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: error.png Type: image/png Size: 15831 bytes Desc: error.png Url : http://www.democritos.it/pipermail/xcrysden/attachments/20240709/bd681061/attachment-0001.png From tone.kokalj at ijs.si Tue Jul 9 16:54:04 2024 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 09 Jul 2024 16:54:04 +0200 Subject: [xcrysden] output file failure In-Reply-To: References: Message-ID: On Tue, 2024-07-09 at 14:49 +0000, Aanuoluwapo Emmanuel Adeniyi wrote: > > Hi, > ?I am very new to the world of xcrysden and I am running xcrysden on > ubuntu, the program successfully open pw,in (input file) but failed > to open pw.out (output file),? I always get " > /home/winlinux/quantumEspresso_2024/xcrysden/xcrysden-1.5.60-bin- > semishared/scripts/pwo2xsf.sh:1: bc: not found"? You miss the "bc" program. Do: sudo apt install bc Furthermore, you are using rather old version of xcrysden, consider installing a new version, i.e.: sudo apt install xcrysden Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From surajp at iitkgp.ac.in Fri Jul 19 07:37:04 2024 From: surajp at iitkgp.ac.in (Suraj P) Date: Fri, 19 Jul 2024 11:07:04 +0530 (IST) Subject: [xcrysden] Xcrysden not opening with Ubuntu 24.04 LTS Message-ID: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> Dear xcrysden users, I have installed xcrysden 1.6.2 in Ubuntu 24.04 LTS. However its not opening and the message that came in the terminal is as attached below. Kindly help me in trouble shooting this problem. Thanks regards Suraj Research student, IIT Kharagpur _______________________________________________________________________________________________________________________________________________________________________________________________ $ xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2019 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.6.2 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=/usr/share/xcrysden XCRYSDEN_SCRATCH=/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: /usr/lib/xcrysden/ftnunit Error in startup script: Couldn't configure togl widget while executing "togl .mesa -width 400 -height 400 -ident .mesa -rgba $toglOpt(rgba) -redsize $toglOpt(redsize..." (procedure "PlaceGlobWin" line 107) invoked from within "PlaceGlobWin 0 [expr round(670 * $fac1)] [expr round(670 * $fac1)]" (procedure "ViewMol" line 25) invoked from within "ViewMol ." invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 633) ____________________________________________________________________________________________________________________________________________________________________________ From tone.kokalj at ijs.si Fri Jul 19 09:06:39 2024 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 19 Jul 2024 09:06:39 +0200 Subject: [xcrysden] Xcrysden not opening with Ubuntu 24.04 LTS In-Reply-To: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> References: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> Message-ID: <237395ac7c19a9d77ebc8eb88c91db5222e704a2.camel@ijs.si> Dear Suraj, You can try to uncomment the "#set toglOpt(accum) false" line in the custom-definitions file, i.e., create the $USER/.xcrysden directory and copy the custom-definitions file into it and then edit the file. In the Ubuntu version, the file is located in /usr/share/xcrysden/Tcl/custom-definitions For example: cd mkdir .xcrysden cd .xcrysden cp /usr/share/xcrysden/Tcl/custom-definitions . and edit the file by uncommenting the "#set toglOpt(accum) false" line. Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia On Fri, 2024-07-19 at 11:07 +0530, Suraj P wrote: > > Dear xcrysden users, > I have installed xcrysden 1.6.2 in Ubuntu 24.04 LTS. However its not > opening and the message that came in the terminal is as attached > below. Kindly help me in trouble shooting this problem. > > Thanks regards > Suraj > Research student, IIT Kharagpur > _____________________________________________________________________ > _____________________________________________________________________ > _____________________________________________________ > > $ xcrysden > > +-----------------------------------------------------------------+ > > *****************************************************************| > > *?????????????????????????????????????????????????????????????? *| > > *? XCrySDen -- (X-Window) CRYstalline Structures and DENsities? *| > > *?????????????? =???????? ===???????? =????????????? ===??????? *| > > *---------------------------------------------------------------*| > > *?????????????????????????????????????????????????????????????? *| > > *??? Anton Kokalj (tone.kokalj at ijs.si)????????????????????????? *| > > *??? Jozef Stefan Institute, Ljubljana, Slovenia??????????????? *| > > *?????????????????????????????????????????????????????????????? *| > > *??? Copyright (c) 1996--2019 by Anton Kokalj?????????????????? *| > > *?????????????????????????????????????????????????????????????? *| > > *****************************************************************| > +-----------------------------------------------------------------+ > > ? Version: 1.6.2 > > ? 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=/usr/share/xcrysden > XCRYSDEN_SCRATCH=/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: /usr/lib/xcrysden/ftnunit > Error in startup script: > Couldn't configure togl widget > ??? while executing > "togl .mesa? -width????????? 400? -height???????? 400? - > ident????????? .mesa? -rgba?????????? $toglOpt(rgba)?????????? - > redsize??????? $toglOpt(redsize..." > ??? (procedure "PlaceGlobWin" line 107) > ??? invoked from within > "PlaceGlobWin 0 [expr round(670 * $fac1)] [expr round(670 * $fac1)]" > ??? (procedure "ViewMol" line 25) > ??? invoked from within > "ViewMol ." > ??? invoked from within > "if { [llength $argv] > 2 } { > ??? parseComLinArg [lrange $argv 2 end] > } else { > ??? ViewMol . > }" > ??? (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 633) > _____________________________________________________________________ > _____________________________________________________________________ > __________________________________ > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From surajp at iitkgp.ac.in Fri Jul 19 11:35:34 2024 From: surajp at iitkgp.ac.in (Suraj P) Date: Fri, 19 Jul 2024 15:05:34 +0530 (IST) Subject: [xcrysden] Xcrysden not opening with Ubuntu 24.04 LTS In-Reply-To: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> References: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> Message-ID: <1862760160.3737084.1721381734331.JavaMail.zimbra@iitkgp.ac.in> Dear Tone, I have removed the comment #set toglOpt(accum) false from the tcl/custom directory and saved it. Still the problem persists with same error repeating. Can you please suggest me some other ways to troubleshoot the issue. Thanks regards, Suraj IIT Kharagpur From tone.kokalj at ijs.si Fri Jul 19 12:07:05 2024 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 19 Jul 2024 12:07:05 +0200 Subject: [xcrysden] Xcrysden not opening with Ubuntu 24.04 LTS In-Reply-To: <1862760160.3737084.1721381734331.JavaMail.zimbra@iitkgp.ac.in> References: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> <1862760160.3737084.1721381734331.JavaMail.zimbra@iitkgp.ac.in> Message-ID: <5e38b7431dd635feeea3b39df7de2684999f1eaf.camel@ijs.si> On Fri, 2024-07-19 at 15:05 +0530, Suraj P wrote: > Dear Tone, > I have removed the comment #set toglOpt(accum)? false from the > tcl/custom directory and saved it.? You should not remove it, but uncomment it, i.e., there should be a line: set toglOpt(accum) false Regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From khalifaiza at yahoo.fr Fri Jul 19 15:59:51 2024 From: khalifaiza at yahoo.fr (Faiza Khali) Date: Fri, 19 Jul 2024 13:59:51 +0000 (UTC) Subject: [xcrysden] Xcrysden not opening with Ubuntu 24.04 LTS In-Reply-To: <5e38b7431dd635feeea3b39df7de2684999f1eaf.camel@ijs.si> References: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> <1862760160.3737084.1721381734331.JavaMail.zimbra@iitkgp.ac.in> <5e38b7431dd635feeea3b39df7de2684999f1eaf.camel@ijs.si> Message-ID: <68533924.460343.1721397591952@mail.yahoo.com> Dear Sir,Thank you so much for your support.Please I can?t configure xcrysden with crystal17 software on windows,?I don?t know why??Best? Sent from Yahoo Mail for iPhone On Friday, July 19, 2024, 11:13, Tone Kokalj wrote: On Fri, 2024-07-19 at 15:05 +0530, Suraj P wrote: > Dear Tone, > I have removed the comment #set toglOpt(accum)? false from the > tcl/custom directory and saved it.? You should not remove it, but uncomment it, i.e., there should be a line: set toglOpt(accum)? false Regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia _______________________________________________ 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/20240719/e1717c5b/attachment-0001.htm From surajp at iitkgp.ac.in Fri Jul 19 16:20:17 2024 From: surajp at iitkgp.ac.in (Suraj P) Date: Fri, 19 Jul 2024 19:50:17 +0530 (IST) Subject: [xcrysden] Xcrysden not opening with Ubuntu 24.04 LTS In-Reply-To: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> References: <2146290979.3696619.1721367424048.JavaMail.zimbra@iitkgp.ac.in> Message-ID: <1591612559.3811305.1721398817440.JavaMail.zimbra@iitkgp.ac.in> Dear Tone, I have uncommented and saved it as told by you. However the issue is still persisting. Kindly can you suggest me some other method or if you could share here a workable xcrysden package (via link) it would be greatly helpful for me. Thanks in advance Suraj ----- Original Message ----- From: "Suraj" To: "xcrysden" Sent: Friday, July 19, 2024 11:07:04 AM Subject: Xcrysden not opening with Ubuntu 24.04 LTS Dear xcrysden users, I have installed xcrysden 1.6.2 in Ubuntu 24.04 LTS. However its not opening and the message that came in the terminal is as attached below. Kindly help me in trouble shooting this problem. Thanks regards Suraj Research student, IIT Kharagpur _______________________________________________________________________________________________________________________________________________________________________________________________ $ xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2019 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.6.2 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=/usr/share/xcrysden XCRYSDEN_SCRATCH=/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: /usr/lib/xcrysden/ftnunit Error in startup script: Couldn't configure togl widget while executing "togl .mesa -width 400 -height 400 -ident .mesa -rgba $toglOpt(rgba) -redsize $toglOpt(redsize..." (procedure "PlaceGlobWin" line 107) invoked from within "PlaceGlobWin 0 [expr round(670 * $fac1)] [expr round(670 * $fac1)]" (procedure "ViewMol" line 25) invoked from within "ViewMol ." invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 633) ____________________________________________________________________________________________________________________________________________________________________________ From surajp at iitkgp.ac.in Thu Jul 25 11:23:16 2024 From: surajp at iitkgp.ac.in (Suraj P) Date: Thu, 25 Jul 2024 14:53:16 +0530 (IST) Subject: [xcrysden] atoms info Message-ID: <863164984.4866148.1721899396918.JavaMail.zimbra@iitkgp.ac.in> Dear Xcrysden users, I have a vc-relaxed structure of a super cell which contains 112 atoms which is obtained as pwscf.out. I want to get the Cartesian coordinates of all these atoms where I can copy and use it for input creation in scf calculation of quantum espresso.Is there any short-key in Xcrysden where I can select all atoms and get the cartesian coordinates of all 112 atoms instead of selecting each atoms individually. Thanking you, Suraj IIT India From khalifaiza at yahoo.fr Fri Jul 26 00:25:07 2024 From: khalifaiza at yahoo.fr (Faiza Khali) Date: Thu, 25 Jul 2024 22:25:07 +0000 (UTC) Subject: [xcrysden] XCrysden installation References: <1173152132.26653.1721946307849.ref@mail.yahoo.com> Message-ID: <1173152132.26653.1721946307849@mail.yahoo.com> Dear all, I hope that you are doing fine. Please help me to install XCrysden on Windows, please I? need your help.Best Regards ***********************************Dr. Faiza Bouamra*********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240725/eab759ac/attachment.htm From gabo13279 at gmail.com Sat Jul 27 05:05:17 2024 From: gabo13279 at gmail.com (Gavin Abo) Date: Fri, 26 Jul 2024 21:05:17 -0600 Subject: [xcrysden] XCrysden installation In-Reply-To: <1173152132.26653.1721946307849@mail.yahoo.com> References: <1173152132.26653.1721946307849.ref@mail.yahoo.com> <1173152132.26653.1721946307849@mail.yahoo.com> Message-ID: <0d6cec60-63aa-49a5-8533-e5dd1c760df1@gmail.com> As seen on the XCrySDen webpage at [1], there is two installation methods for Windows 10.? Are you using WSL or are you using Cygwin64? [1] http://www.xcrysden.org/Download.html Kind Regards, Gavin XCrySDen user On 7/25/2024 4:25 PM, Faiza Khali wrote: > Dear all, > > I hope that you are doing fine. > > Please help me to install XCrysden on Windows, please I? need your help. > Best Regards > > /***********************************/ > /Dr. Faiza Bouamra/ > /***********************************/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240726/5d6ed15c/attachment.htm