From Oscar.Ojeda at chemail.tamu.edu Thu Sep 13 23:57:28 2007 From: Oscar.Ojeda at chemail.tamu.edu (Oscar U. Ojeda) Date: Thu, 13 Sep 2007 16:57:28 -0500 Subject: [xcrysden] Error with xcrysden for crystal03 Message-ID: <1189720648.7b12997cOscar.Ojeda@chemail.tamu.edu> Hi Im trying to run xcrysde as gui for crystal03. When I try to visualize a structure either generated by xcrysden or a previously created input file, i get the following message: ERROR while executing exec /(PATH)/xcrysden/XCrySDen-1.4.1bin-static/bin/gengeom 0 11 1 1 1 1 /(PATH)/xcrys_tmp/xc_6099/xc_gengeom.6099 The ERROR INFO is as follows: invalid integer: read unexpected character apparent state: unit 34 named fort.34 last format: list io lately reading sequential formatted external IO Anyone has any experience? Thanks Oscar From tone.kokalj at ijs.si Wed Sep 19 13:33:28 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 19 Sep 2007 13:33:28 +0200 Subject: [xcrysden] Error with xcrysden for crystal03 In-Reply-To: <1189720648.7b12997cOscar.Ojeda@chemail.tamu.edu> References: <1189720648.7b12997cOscar.Ojeda@chemail.tamu.edu> Message-ID: <1190201608.2571.4.camel@localhost.localdomain> On Thu, 2007-09-13 at 16:57 -0500, Oscar U. Ojeda wrote: > Hi > Im trying to run xcrysde as gui for crystal03. When I try to visualize a structure either generated by xcrysden or a previously created input file, i get the following message: > ERROR while executing > exec > /(PATH)/xcrysden/XCrySDen-1.4.1bin-static/bin/gengeom 0 11 1 1 1 1 > /(PATH)/xcrys_tmp/xc_6099/xc_gengeom.6099 > > The ERROR INFO is as follows: > > invalid integer: read unexpected character > apparent state: unit 34 named fort.34 > last format: list io > lately reading sequential formatted external IO To check what is going on, please send me the input and fort.34 files. You will find the latter in the XCRYSDEN_SCRATCH/xc_???? directory; copy it before exiting, because the directory will be deleted on exit. Regards, Tone From Oscar.Ojeda at chemail.tamu.edu Wed Sep 19 17:16:17 2007 From: Oscar.Ojeda at chemail.tamu.edu (Oscar Ojeda) Date: Wed, 19 Sep 2007 10:16:17 -0500 Subject: [xcrysden] Error with xcrysden for crystal03 In-Reply-To: <1190201608.2571.4.camel@localhost.localdomain> References: <1189720648.7b12997cOscar.Ojeda@chemail.tamu.edu> <1190201608.2571.4.camel@localhost.localdomain> Message-ID: <46F13D41.3030208@chemail.tamu.edu> Tone Kokalj wrote: > On Thu, 2007-09-13 at 16:57 -0500, Oscar U. Ojeda wrote: > >> Hi >> Im trying to run xcrysde as gui for crystal03. When I try to visualize a structure either generated by xcrysden or a previously created input file, i get the following message: >> ERROR while executing >> exec >> /(PATH)/xcrysden/XCrySDen-1.4.1bin-static/bin/gengeom 0 11 1 1 1 1 >> /(PATH)/xcrys_tmp/xc_6099/xc_gengeom.6099 >> >> The ERROR INFO is as follows: >> >> invalid integer: read unexpected character >> apparent state: unit 34 named fort.34 >> last format: list io >> lately reading sequential formatted external IO >> > > To check what is going on, please send me the input and fort.34 files. > You will find the latter in the XCRYSDEN_SCRATCH/xc_???? directory; > copy it before exiting, because the directory will be deleted on exit. > > Regards, Tone > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > > Hi Tone Thanks in advance for the help Oscar -------------- next part -------------- A non-text attachment was scrubbed... Name: error.out.tar.gz Type: application/x-gzip Size: 2411 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20070919/c3f796ef/attachment.bin From tone.kokalj at ijs.si Wed Sep 19 21:29:25 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 19 Sep 2007 21:29:25 +0200 Subject: [xcrysden] Error with xcrysden for crystal03 In-Reply-To: <46F13D41.3030208@chemail.tamu.edu> References: <1189720648.7b12997cOscar.Ojeda@chemail.tamu.edu> <1190201608.2571.4.camel@localhost.localdomain> <46F13D41.3030208@chemail.tamu.edu> Message-ID: <1190230165.2571.16.camel@localhost.localdomain> On Wed, 2007-09-19 at 10:16 -0500, Oscar Ojeda wrote: > Hi Tone > Thanks in advance for the help The I/O files you provided were sufficient to debug what is going on. The problem is that you are running CRYSTAL06 and xcrysden 1.4, which are not compatible. Install the "latest snapshot" of xcrysden which is synchronized to crystal06. http://www.xcrysden.org/download/xc-latest-linuxPC-static.tar.gz Regards, Tone From Oscar.Ojeda at chemail.tamu.edu Thu Sep 20 02:20:15 2007 From: Oscar.Ojeda at chemail.tamu.edu (Oscar U. Ojeda) Date: Wed, 19 Sep 2007 19:20:15 -0500 Subject: [xcrysden] Error with xcrysden for crystal03 Message-ID: <1190247615.8127685cOscar.Ojeda@chemail.tamu.edu> Hi Tone Thanks for the pointer. Now I go through the regualr procedure, unzip, untar, run xcConfigure; after sourcing bashrc, I try running xcrysden, I get the following error message at the bottom of the startup screen: /users/grad/ouo2224/softwares/xcrysden/XCrySDen-pre1.5bbin-static/xcrysden: line 163: 5769 Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null -----Original Message----- From: Tone Kokalj To: XCrySDen mailing list Date: Wed, 19 Sep 2007 21:29:25 +0200 Subject: Re: [xcrysden] Error with xcrysden for crystal03 On Wed, 2007-09-19 at 10:16 -0500, Oscar Ojeda wrote: > Hi Tone > Thanks in advance for the help The I/O files you provided were sufficient to debug what is going on. The problem is that you are running CRYSTAL06 and xcrysden 1.4, which are not compatible. Install the "latest snapshot" of xcrysden which is synchronized to crystal06. http://www.xcrysden.org/download/xc-latest-linuxPC-static.tar.gz Regards, Tone _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From Oscar.Ojeda at chemail.tamu.edu Thu Sep 20 02:21:09 2007 From: Oscar.Ojeda at chemail.tamu.edu (Oscar U. Ojeda) Date: Wed, 19 Sep 2007 19:21:09 -0500 Subject: [xcrysden] Error with xcrysden for crystal03 Message-ID: <1190247669.8127685cOscar.Ojeda@chemail.tamu.edu> Hi Tone Thanks for the pointer. Now I go through the regualr procedure, unzip, untar, run xcConfigure; after sourcing bashrc, I try running xcrysden, I get the following error message at the bottom of the startup screen: /users/grad/ouo2224/softwares/xcrysden/XCrySDen-pre1.5bbin-static/xcrysden: line 163: 5769 Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null Regards Oscar -----Original Message----- From: Tone Kokalj To: XCrySDen mailing list Date: Wed, 19 Sep 2007 21:29:25 +0200 Subject: Re: [xcrysden] Error with xcrysden for crystal03 On Wed, 2007-09-19 at 10:16 -0500, Oscar Ojeda wrote: > Hi Tone > Thanks in advance for the help The I/O files you provided were sufficient to debug what is going on. The problem is that you are running CRYSTAL06 and xcrysden 1.4, which are not compatible. Install the "latest snapshot" of xcrysden which is synchronized to crystal06. http://www.xcrysden.org/download/xc-latest-linuxPC-static.tar.gz Regards, Tone _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From tone.kokalj at ijs.si Thu Sep 20 19:59:00 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 20 Sep 2007 19:59:00 +0200 Subject: [xcrysden] Error with xcrysden for crystal03 In-Reply-To: <1190247669.8127685cOscar.Ojeda@chemail.tamu.edu> References: <1190247669.8127685cOscar.Ojeda@chemail.tamu.edu> Message-ID: <1190311140.2547.55.camel@localhost.localdomain> On Wed, 2007-09-19 at 19:21 -0500, Oscar U. Ojeda wrote: > Hi Tone > Thanks for the pointer. Now I go through the regualr procedure, unzip, untar, run xcConfigure; after sourcing bashrc, I try running xcrysden, I get the following error message at the bottom of the startup screen: > > /users/grad/ouo2224/softwares/xcrysden/XCrySDen-pre1.5bbin-static/xcrysden: line 163: 5769 Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null That will be difficult to tell why. You may either try to compile the source or try to use the shared version, instead. Regards, Tone From hamada at cmp.sanken.osaka-u.ac.jp Fri Sep 28 20:14:45 2007 From: hamada at cmp.sanken.osaka-u.ac.jp (Ikutaro Hamada) Date: Sat, 29 Sep 2007 03:14:45 +0900 Subject: [xcrysden] Intel Mac issue Message-ID: <5E8EBC19-D328-421A-BA9D-B7C84B207F0E@cmp.sanken.osaka-u.ac.jp> Dear all, Few days ago, I have succeeded in compiling XCrySDen 1.4.1 on my Intel Mac (10.4.10) with Apple X11, Tcl/Tk and Mesa installed by Fink and with minor modification of the source codes. Unfortunately, a static binary package is not available, since my gcc cannot generate static binaries. So Intel mac users who want to use XCrySDen are encouraged to compile it by themselves, using my patch and Make.sys. I put Make.sys for Intel Mac and a patch as http://www.cmp.sanken.osaka-u.ac.jp/~hamada/xcrysden/Make.macosx-x11- intel http://www.cmp.sanken.osaka-u.ac.jp/~hamada/xcrysden/xc-1.4.1- macosx.diff.gz To apply the patch, copy xc-1.4.1-macosx.diff.gz to XCrySDen-1.4.1s and do the following in the same directory after unzipping the file patch -p1 < xc-1.4.1-macosx.diff Before building XCrySDen, Don't forget to install fink (http:// finkproject.org/)!!! Try my files and let me know if it works for other intel macs than mine. Hope it helps, Regards, Ikutaro Hamada From dmwood at Mines.EDU Sat Sep 29 20:45:46 2007 From: dmwood at Mines.EDU (David M. Wood) Date: Sat, 29 Sep 2007 12:45:46 -0600 Subject: [xcrysden] Building xcd 1.4.1 for Mac OS X/Intel w/ Ikutaro Hamada's patches Message-ID: <02BC0478-DFDF-4C7E-9DE5-A500F3F828FE@Mines.EDU> Howdy all! Many thanks to Ikutaro Hamada for his work! Following the instructions of Message 1 of the 29 Sep mail, I made sure all libraries were present via fink installs and applied the patch. Alas, I get gl2ps.c: In function 'gl2psPrintPDFInfo': gl2ps.c:3474: warning: assignment makes pointer from integer without a cast gl2ps.c:3497: error: dereferencing pointer to incomplete type gl2ps.c:3498: error: dereferencing pointer to incomplete type gl2ps.c:3499: error: dereferencing pointer to incomplete type gl2ps.c:3500: error: dereferencing pointer to incomplete type gl2ps.c:3501: error: dereferencing pointer to incomplete type gl2ps.c:3502: error: dereferencing pointer to incomplete type make[2]: *** [gl2ps.o] Error 1 The good news: (i) this is the ONLY error I can find (via a make -k all), and (ii) the same holds for XCrySDen-pre1.5bs. Any suggestions? David M. Wood dmwood at Mines.EDU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20070929/f84075d2/attachment.htm From hamada at cmp.sanken.osaka-u.ac.jp Sun Sep 30 06:50:09 2007 From: hamada at cmp.sanken.osaka-u.ac.jp (Ikutaro Hamada) Date: Sun, 30 Sep 2007 13:50:09 +0900 Subject: [xcrysden] Building xcd 1.4.1 for Mac OS X/Intel w/ Ikutaro Hamada's patches In-Reply-To: <02BC0478-DFDF-4C7E-9DE5-A500F3F828FE@Mines.EDU> References: <02BC0478-DFDF-4C7E-9DE5-A500F3F828FE@Mines.EDU> Message-ID: Dear David, It seems that you don't have or don't correctly include "time.h", which is usually located in /usr/include (it may be different from sys/time.h). If you have time.h (which declares "struct tm *gmtime..."), try to explicitly include time.h by using -I option in CFLAGS or somewhere else in your Make.sys. (ex. CFLAGS=$(CFLAGS) -I/usr/include) In the case time.h is missing in your system, I don't know how to solve the problem (XCode is not installed???)... Good luck, Ikutaro Hamada On 2007/09/30, at 3:45, David M. Wood wrote: > Howdy all! > > Many thanks to Ikutaro Hamada for his work! > > Following the instructions of Message 1 of the 29 Sep mail, I made > sure all libraries were present via fink installs and applied the > patch. > > Alas, I get > > gl2ps.c: In function 'gl2psPrintPDFInfo': > gl2ps.c:3474: warning: assignment makes pointer from integer > without a cast > gl2ps.c:3497: error: dereferencing pointer to incomplete type > gl2ps.c:3498: error: dereferencing pointer to incomplete type > gl2ps.c:3499: error: dereferencing pointer to incomplete type > gl2ps.c:3500: error: dereferencing pointer to incomplete type > gl2ps.c:3501: error: dereferencing pointer to incomplete type > gl2ps.c:3502: error: dereferencing pointer to incomplete type > make[2]: *** [gl2ps.o] Error 1 > > The good news: (i) this is the ONLY error I can find (via a make -k > all), and (ii) the same holds for XCrySDen-pre1.5bs. > > Any suggestions? > > David M. Wood > dmwood at Mines.EDU > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden