From g7_lugo18 at ens.cnyn.unam.mx Tue Oct 6 05:58:42 2020 From: g7_lugo18 at ens.cnyn.unam.mx (Enrique Lugo) Date: Mon, 5 Oct 2020 22:58:42 -0500 Subject: [xcrysden] Issues running XCrySDen for the first time (package require BWidget) Message-ID: Hi All, I am a new user and am having difficulty running XCrySDen for the first time. I'm using the pre-compiled Cygwin version 1.6.2. I believe I've installed all of the required packaged through the Cygwin installer. Here is what I see after I start an Xterm and send the ./xcrysden command within the parent, unpackaged tar.gz directory $ ./xcrysden ./xcrysden: line 65: cd: too many arguments +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* 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: 1.6.2 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=/cygdrive/c/Users/ENRIQUE LUGO/Documents/Materias (UNAM)/7mo Semestre/Simulaciones Computacionales/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp Error in startup script: can't find package BWidget while executing "package require BWidget" (file "/cygdrive/c/Users/ENRIQUE LUGO/Documents/Materias (UNAM)/7mo Semestre/Simulaciones Computacionales/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" line 460) I checked in my usr folder that I have a folder called bwidget-1.9.13 Here's the evidence xcrysden-1.6.2-bin-shared/external/lib/bwidget-1.9.13 Thanks in advance for any ideas. Enrique Lugo Mart?nez Ungerdraduate Student Nanotechnology | UNAM-CNyN 6871677277 g7_lugo18 at ens.cnyn.unam.mx https://nanolic.cnyn.unam.mx [image: facebook] [image: twitter] [image: linkedin] [image: instagram] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20201005/88fb6b6d/attachment.htm From tone.kokalj at ijs.si Tue Oct 6 09:26:13 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 06 Oct 2020 09:26:13 +0200 Subject: [xcrysden] Issues running XCrySDen for the first time (package require BWidget) In-Reply-To: References: Message-ID: On Mon, 2020-10-05 at 22:58 -0500, Enrique Lugo wrote: > Hi All, > > I am a new user and am having difficulty running XCrySDen for the > first time. > I'm using the pre-compiled Cygwin version 1.6.2. I believe I've > installed all of the required packaged through the > Cygwin installer. Here is what I see after I start an Xterm and send > the ./xcrysden command within the parent, > unpackaged tar.gz directory > $ ./xcrysden > ./xcrysden: line 65: cd: too many arguments > > XCRYSDEN_TOPDIR=/cygdrive/c/Users/ENRIQUE LUGO/Documents/Materias > (UNAM)/7mo Semestre/Simulaciones Computacionales/xcrysden-1.6.2-bin- > shared The problem is that you have spaces in your directory names (e.g "ENRIQUE LUGO", "Materias (UNAM)", ...). This is a very bad idea on Unix systems, as it is likely to break many things, not just xcrysden. Install xcrysden to some directory that does not contain the spaces. Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From g7_lugo18 at ens.cnyn.unam.mx Tue Oct 6 17:26:23 2020 From: g7_lugo18 at ens.cnyn.unam.mx (Enrique Lugo) Date: Tue, 6 Oct 2020 10:26:23 -0500 Subject: [xcrysden] Issues running XCrySDen for the first time (package require BWidget) In-Reply-To: References: Message-ID: Now that I moved to a directory that contains no spaces, and while using the startx I receive this error message: *couldn't fork child process: resource temporarily unavailable* Enrique Lugo Mart?nez Ungerdraduate Student Nanotechnology | UNAM-CNyN 6871677277 g7_lugo18 at ens.cnyn.unam.mx https://nanolic.cnyn.unam.mx [image: facebook] [image: twitter] [image: linkedin] [image: instagram] El mar., 6 oct. 2020 a las 2:34, Tone Kokalj () escribi?: > On Mon, 2020-10-05 at 22:58 -0500, Enrique Lugo wrote: > > Hi All, > > > > I am a new user and am having difficulty running XCrySDen for the > > first time. > > I'm using the pre-compiled Cygwin version 1.6.2. I believe I've > > installed all of the required packaged through the > > Cygwin installer. Here is what I see after I start an Xterm and send > > the ./xcrysden command within the parent, > > unpackaged tar.gz directory > > $ ./xcrysden > > ./xcrysden: line 65: cd: too many arguments > > > > XCRYSDEN_TOPDIR=/cygdrive/c/Users/ENRIQUE LUGO/Documents/Materias > > (UNAM)/7mo Semestre/Simulaciones Computacionales/xcrysden-1.6.2-bin- > > shared > > The problem is that you have spaces in your directory names (e.g > "ENRIQUE LUGO", "Materias (UNAM)", ...). This is a very bad idea on > Unix systems, as it is likely to break many things, not just xcrysden. > > Install xcrysden to some directory that does not contain the spaces. > > Best 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/20201006/bef6814a/attachment.htm From manuel.izquierdo at xfel.eu Wed Oct 7 16:27:33 2020 From: manuel.izquierdo at xfel.eu (Izquierdo, Manuel) Date: Wed, 7 Oct 2020 16:27:33 +0200 (CEST) Subject: [xcrysden] Problems running xcrysden without screen shots Message-ID: <0d5401d69cb5$fee87870$fcb96950$@xfel.eu> Hi there, I am starting to use xcrysden on my local computer and after overcoming the typical problems during installation: 1- Error to open libTogl2.0.dll 2- DISPLAY error That I solved by editing the ~./bashrc and adding two lines: 1- export PATH=$PATH:/lib/Togl2.0 2- export DISPLAY=:0.0 I managed to run the ./xcrysden. However upon running I get the following errors I do not know how to solve: While executing ./xcrysden the Xming server I am using gives me the following error: ERROR: while executing exec/cygdrive/cygwin64/xcrysden-1.2.2-bin-shared/bin/ftnu The error info says: C:/cygwin64/xcrysden-1.6.2-bin-shared/bin/ftnunit.exe: error while loading shared libraries: cyggfortran-4.dll: cannot open shared object file: No such file or directory However the library it was installed by cygwin64 in: C:\cygwin64\usr\i686-pc-cygwin\sys-root\usr\bin I can acknowledge the error and the XCrysDen window opens However when I try to load a file, I started with a xsf structure from the examples I get the following error ERROR: while executing exec/cygdrive/cygwin64/xcrysden-1.2.2-bin-shared/bin/gen geom 0 1 11 1 1 1 1 xc_gengeom.1304/tmp/xc_1304/GaAsH.xsf.raw The detail info says: C:/cygwin64/xcrysden-1.6.2-bin-shared/bin/gengeom.exe: error while loading shared libraries: cyggfortran-4.dll: cannot open shared object file: No such file or directory Could you please let me know how I could solve the problem? It seem is related to the path of the cyggfortran-4.dll but I do not think I can redefine a different path for this library without affecting the opening of the libTogl2.0.dll one Thanks in advance for your help Manuel -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20201007/7c59f8a8/attachment.htm From tone.kokalj at ijs.si Wed Oct 7 16:33:26 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 07 Oct 2020 16:33:26 +0200 Subject: [xcrysden] Problems running xcrysden without screen shots In-Reply-To: <0d5401d69cb5$fee87870$fcb96950$@xfel.eu> References: <0d5401d69cb5$fee87870$fcb96950$@xfel.eu> Message-ID: <5a6383f868737e5d50a4fa183ebce25a0a8ff044.camel@ijs.si> On Wed, 2020-10-07 at 16:27 +0200, Izquierdo, Manuel wrote: > > Hi there, > > I am starting to use xcrysden on my local computer and after > overcoming the typical problems during installation: > > 1- Error to open libTogl2.0.dll > 2- DISPLAY error > > That I solved by editing the ~./bashrc and adding two lines: > > 1- export PATH=$PATH:/lib/Togl2.0 > 2- export DISPLAY=:0.0 > > I managed to run the ./xcrysden. However upon running I get the > following errors I do not know how to solve: > > While executing ./xcrysden the Xming server I am using gives me the > following error: > > ERROR: while executing exec/cygdrive/cygwin64/xcrysden-1.2.2-bin- > shared/bin/ftnu > The error info says: > C:/cygwin64/xcrysden-1.6.2-bin-shared/bin/ftnunit.exe: error while > loading shared libraries: cyggfortran-4.dll: cannot open shared > object file: No such file or directory This means that you miss the cyggfortran-4.dll system file, which is in the libgfortran4 package: install it. See: https://cygwin.com/cgi-bin2/package-grep.cgi?grep=cyggfortran-4.dll&arch=x86_64 Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20201007/feb00970/attachment.htm From manuel.izquierdo at xfel.eu Wed Oct 7 16:51:54 2020 From: manuel.izquierdo at xfel.eu (Izquierdo, Manuel) Date: Wed, 7 Oct 2020 16:51:54 +0200 (CEST) Subject: [xcrysden] Problems running xcrysden without screen shots In-Reply-To: <5a6383f868737e5d50a4fa183ebce25a0a8ff044.camel@ijs.si> References: <0d5401d69cb5$fee87870$fcb96950$@xfel.eu> <5a6383f868737e5d50a4fa183ebce25a0a8ff044.camel@ijs.si> Message-ID: <0d7701d69cb9$65a6a070$30f3e150$@xfel.eu> Ths for the quick reply Tone, the problem is now solved! From: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] On Behalf Of Tone Kokalj Sent: Wednesday, October 7, 2020 4:33 PM To: xcrysden at democritos.it Subject: Re: [xcrysden] Problems running xcrysden without screen shots On Wed, 2020-10-07 at 16:27 +0200, Izquierdo, Manuel wrote: Hi there, I am starting to use xcrysden on my local computer and after overcoming the typical problems during installation: 1- Error to open libTogl2.0.dll 2- DISPLAY error That I solved by editing the ~./bashrc and adding two lines: 1- export PATH=$PATH:/lib/Togl2.0 2- export DISPLAY=:0.0 I managed to run the ./xcrysden. However upon running I get the following errors I do not know how to solve: While executing ./xcrysden the Xming server I am using gives me the following error: ERROR: while executing exec/cygdrive/cygwin64/xcrysden-1.2.2-bin-shared/bin/ftnu The error info says: C:/cygwin64/xcrysden-1.6.2-bin-shared/bin/ftnunit.exe: error while loading shared libraries: cyggfortran-4.dll: cannot open shared object file: No such file or directory This means that you miss the cyggfortran-4.dll system file, which is in the libgfortran4 package: install it. See: https://cygwin.com/cgi-bin2/package-grep.cgi?grep=cyggfortran-4.dll &arch=x86_64 Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20201007/3a27c438/attachment-0001.htm From g7_lugo18 at ens.cnyn.unam.mx Wed Oct 7 18:22:14 2020 From: g7_lugo18 at ens.cnyn.unam.mx (Enrique Lugo) Date: Wed, 7 Oct 2020 11:22:14 -0500 Subject: [xcrysden] Issues running XCrySDen for the first time (package require BWidget) In-Reply-To: References: Message-ID: I checked the rebase thing but it didn't work or maybe I didn't make it correctly. The error that prompts is: $ ./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: 1.6.2 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=/cygdrive/c/Users/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp Running on platform : unix Operating system : CYGWIN_NT-10.0 0 [main] xcrys 1300 dofork: child -1 - forked process 9300 died unexpected ly, retry 0, exit code 0xC0000135, errno 11 48702 [main] xcrys 1300 dofork: child -1 - forked process 16024 died unexpecte dly, retry 0, exit code 0xC0000135, errno 11 63702 [main] xcrys 1300 dofork: child -1 - forked process 20944 died unexpecte dly, retry 0, exit code 0xC0000135, errno 11 74962 [main] xcrys 1300 dofork: child -1 - forked process 10912 died unexpecte dly, retry 0, exit code 0xC0000135, errno 11 Executing: /cygdrive/c/Users/xcrysden-1.6.2-bin-shared/bin/ftnunit 145402 [main] xcrys 1300 dofork: child -1 - forked process 18028 died unexpecte dly, retry 0, exit code 0xC0000135, errno 11 TEXT-WIDGET: .a0.f1.t libGL error: Windows-DRI extension not available Viewer: mesaWid = .mesa ************************************************************************ Deleting directory /tmp/xc_1300 ; Please Wait !!! ************************************************************************ Directory deleted ! Enrique Lugo Mart?nez Undergraduate Student Nanotechnology | UNAM-CNyN 6871677277 g7_lugo18 at ens.cnyn.unam.mx https://nanolic.cnyn.unam.mx [image: facebook] [image: twitter] [image: linkedin] [image: instagram] El mar., 6 oct. 2020 a las 10:26, Enrique Lugo () escribi?: > Now that I moved to a directory that contains no spaces, and while using > the startx I receive this error message: > *couldn't fork child process: resource temporarily unavailable* > Enrique Lugo Mart?nez > > Ungerdraduate Student > > Nanotechnology | UNAM-CNyN > 6871677277 > g7_lugo18 at ens.cnyn.unam.mx > https://nanolic.cnyn.unam.mx > [image: facebook] > [image: twitter] > [image: linkedin] > > [image: instagram] > > > > El mar., 6 oct. 2020 a las 2:34, Tone Kokalj () > escribi?: > >> On Mon, 2020-10-05 at 22:58 -0500, Enrique Lugo wrote: >> > Hi All, >> > >> > I am a new user and am having difficulty running XCrySDen for the >> > first time. >> > I'm using the pre-compiled Cygwin version 1.6.2. I believe I've >> > installed all of the required packaged through the >> > Cygwin installer. Here is what I see after I start an Xterm and send >> > the ./xcrysden command within the parent, >> > unpackaged tar.gz directory >> > $ ./xcrysden >> > ./xcrysden: line 65: cd: too many arguments >> > >> > XCRYSDEN_TOPDIR=/cygdrive/c/Users/ENRIQUE LUGO/Documents/Materias >> > (UNAM)/7mo Semestre/Simulaciones Computacionales/xcrysden-1.6.2-bin- >> > shared >> >> The problem is that you have spaces in your directory names (e.g >> "ENRIQUE LUGO", "Materias (UNAM)", ...). This is a very bad idea on >> Unix systems, as it is likely to break many things, not just xcrysden. >> >> Install xcrysden to some directory that does not contain the spaces. >> >> Best 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/20201007/4fe6d8ee/attachment.htm From manuel.izquierdo at xfel.eu Tue Oct 13 11:53:50 2020 From: manuel.izquierdo at xfel.eu (Izquierdo, Manuel) Date: Tue, 13 Oct 2020 11:53:50 +0200 (CEST) Subject: [xcrysden] Displaying atoms as empty circles with atom color Message-ID: <00ce01d6a146$c07df070$4179d150$@xfel.eu> Hi, I would like to display a structure with the atoms as empty circles with the color of the circle the same as the default atom color. How can I do this? Cheers Manuel