From ratan4321 at yahoo.com Tue Jan 6 18:28:51 2009 From: ratan4321 at yahoo.com (Abu Md. Asaduzzaman) Date: Tue, 6 Jan 2009 09:28:51 -0800 (PST) Subject: [xcrysden] Problem with Mac-OSX Message-ID: <279057.6099.qm@web54207.mail.re2.yahoo.com> Hi there I have been trying to install xcrysden (binary package xc-1.5.17-macosx-shared.tar.gz) in my Mac (PowerPC G5) machine. Each time I tried, got the following message: " XCRYSDEN_TOPDIR=/Applications/XCrySDen-1.5.17-bin-shared XCRYSDEN_SCRATCH=/Users/abuasaduzzaman/xcrys_tmp /Applications/XCrySDen-1.5.17-bin-shared/xcrysden: line 209: /Applications/XCrySDen-1.5.17-bin-shared/bin/xcrys: cannot execute binary file " Any help will be much appreciated. Abu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090106/4ed322d1/attachment.htm From tone.kokalj at ijs.si Wed Jan 7 11:27:36 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 07 Jan 2009 11:27:36 +0100 Subject: [xcrysden] Problem with Mac-OSX In-Reply-To: <279057.6099.qm@web54207.mail.re2.yahoo.com> References: <279057.6099.qm@web54207.mail.re2.yahoo.com> Message-ID: <1231324056.11250.21.camel@walk.ijs.si> On Tue, 2009-01-06 at 09:28 -0800, Abu Md. Asaduzzaman wrote: > Hi there > I have been trying to install xcrysden (binary package > xc-1.5.17-macosx-shared.tar.gz) in my Mac (PowerPC G5) machine. Each > time I tried, got the following message: > " > XCRYSDEN_TOPDIR=/Applications/XCrySDen-1.5.17-bin-shared > XCRYSDEN_SCRATCH=/Users/abuasaduzzaman/xcrys_tmp > > /Applications/XCrySDen-1.5.17-bin-shared/xcrysden: line 209: /Applications/XCrySDen-1.5.17-bin-shared/bin/xcrys: cannot execute binary file I am definitely not the right person to answer this, because my mac experience == 0. However, very recently, I had the opportunity to work couple of hours on a given mac, and I faced precisely the same problem, and as far as I remember it was powerpc machine. Hence, I compiled this version: http://www.xcrysden.org/download/xc-1.5.19-macosx_powerpc-semishared.tar.gz Try it out. Who knows, maybe it will work. 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 jasius_1 at yahoo.com Fri Jan 9 05:22:16 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Thu, 8 Jan 2009 20:22:16 -0800 (PST) Subject: [xcrysden] xcrysden Windows installation fails Message-ID: <822255.90213.qm@web54407.mail.yahoo.com> Hi, I am trying to install newest version on Windows xp (not 64 bit). I have Cygwin installed which I launch from cd and load it. The run ./xcConfigre.sh and follow instruction. The problem is creating custom-definitions folder: creating new /cygdrive/c/Documents and Settings/Jonas/Desktop/.xcrysden/custom-definitions ... cp: copying multiple files, but last argument `Settings/Jonas/Desktop/.xcrysden/custom-definitions' is not a directory and then at the end I don;t know what to do with loading the bash source: xcrysden16> echo $SHELL /bin/bash xcrysden16> source ~/.bashrc bash: /cygdrive/c/Documents and Settings/Jonas/Desktop/.bashrc: No such file or directory xcrysden16> and of course with these two problems typing xcrysden gives me command not found Could anybody help me out with that? thanks Jonas Baltrusaitis University of Iowa From tone.kokalj at ijs.si Fri Jan 9 08:43:04 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 09 Jan 2009 08:43:04 +0100 Subject: [xcrysden] xcrysden Windows installation fails In-Reply-To: <822255.90213.qm@web54407.mail.yahoo.com> References: <822255.90213.qm@web54407.mail.yahoo.com> Message-ID: <1231486984.17031.5.camel@walk.ijs.si> On Thu, 2009-01-08 at 20:22 -0800, Jonas Baltrusaitis wrote: > Hi, > > I am trying to install newest version on Windows xp (not 64 bit). I have Cygwin installed which I launch from cd and load it. The run ./xcConfigre.sh and follow instruction. The problem is creating custom-definitions folder: > > creating new /cygdrive/c/Documents and Settings/Jonas/Desktop/.xcrysden/custom-definitions ... cp: copying multiple files, but last argument `Settings/Jonas/Desktop/.xcrysden/custom-definitions' is not a directory The problem are the whitespaces in the path (i.e. Documents and Settings). It is strange that the $HOME variable points to this place. As a default it should be something line /home/jonas. Anyway ~/.xcrysden directory is optional, and xcrysden should run without running xcConfigure.sh script. But it will not work if it is installed under path that contains whitespaces. So install it to some place without whitespaces in the path. 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 jasius_1 at yahoo.com Fri Jan 9 15:32:16 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Fri, 9 Jan 2009 06:32:16 -0800 (PST) Subject: [xcrysden] Error: while executing exec sh Message-ID: <276023.8826.qm@web54402.mail.yahoo.com> Managed to launch it on Windows machine remotely via CygWin. It starts no prob but can't seem to display/open anything. In particular, I tried opening every single file on espresso 4.0.4 output example 8 with calculate DOS (I chose display optimized coordinates), it always gives the same error of Error: while executing exec sh /share/apps/xcrysden-1.6/scripts/pwo2xsf.sh --optcoor /share/apps/espresso-4.0.4/examples/example08/reference/ni.dos.out > pwo2xsf.xsf no luck with other coordinate type or any other example either Jonas From jasius_1 at yahoo.com Sat Jan 10 02:43:55 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Fri, 9 Jan 2009 17:43:55 -0800 (PST) Subject: [xcrysden] xcrysden Windows installation fails In-Reply-To: <1231486984.17031.5.camel@walk.ijs.si> Message-ID: <670143.12487.qm@web54410.mail.yahoo.com> I am not sure I follow. I put xcrysden in C:/xcrysden16, so there is not gaps and I don't know why it involves ...Documents and Settings... path. Also, I have to use xcrysden.sh file as normally launching xcrysden would do nothing at all thanks JOnas --- On Thu, 1/8/09, Tone Kokalj wrote: > From: Tone Kokalj > Subject: Re: [xcrysden] xcrysden Windows installation fails > To: jasius_1 at yahoo.com, "XCrySDen mailing list" > Date: Thursday, January 8, 2009, 11:43 PM > On Thu, 2009-01-08 at 20:22 -0800, Jonas Baltrusaitis wrote: > > Hi, > > > > I am trying to install newest version on Windows xp > (not 64 bit). I have Cygwin installed which I launch from cd > and load it. The run ./xcConfigre.sh and follow instruction. > The problem is creating custom-definitions folder: > > > > creating new /cygdrive/c/Documents and > Settings/Jonas/Desktop/.xcrysden/custom-definitions ... cp: > copying multiple files, but last argument > `Settings/Jonas/Desktop/.xcrysden/custom-definitions' is > not a directory > > The problem are the whitespaces in the path (i.e. Documents > and > Settings). It is strange that the $HOME variable points to > this place. > As a default it should be something line /home/jonas. > Anyway ~/.xcrysden > directory is optional, and xcrysden should run without > running > xcConfigure.sh script. But it will not work if it is > installed under > path that contains whitespaces. > > So install it to some place without whitespaces in the > path. > > 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 jasius_1 at yahoo.com Sun Jan 11 17:24:18 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Sun, 11 Jan 2009 08:24:18 -0800 (PST) Subject: [xcrysden] xcrysden Windows installation fails In-Reply-To: <1231486984.17031.5.camel@walk.ijs.si> Message-ID: <588951.42251.qm@web54402.mail.yahoo.com> The problem is that I do specify tmp folder without white spaces, but it still tries to look at this "default" path and completely disregards the path I specified Please specify XCRYSDEN_SCRATCH directory (default: /cygdrive/c/Documents and Settings/Jonas/Desktop/xcrys_tmp): C:/xcrysden16/tmp test: and: unknown operand I am about to create the $HOME/.xcrysden/custom-definitions file, which is XCRYSDEN's customization file. Press to continue ... Answer the following question(s) please: ---------------------------------------- [: and: unknown operand CRYSTAL is an electronic structure program for periodic systems. (http://www.crystal.unito.it/) Do you have a CRYSTAL package ([y]es/[n]o): n Is this correct ([y]es/[n]o): y test: and: unknown operand creating new /cygdrive/c/Documents and Settings/Jonas/Desktop/.xcrysden/custo m-definitions ... cp: copying multiple files, but last argument `Settings/Jonas/ Desktop/.xcrysden/custom-definitions' is not a directory Try `cp --help' for more information. --- On Thu, 1/8/09, Tone Kokalj wrote: > From: Tone Kokalj > Subject: Re: [xcrysden] xcrysden Windows installation fails > To: jasius_1 at yahoo.com, "XCrySDen mailing list" > Date: Thursday, January 8, 2009, 11:43 PM > On Thu, 2009-01-08 at 20:22 -0800, Jonas Baltrusaitis wrote: > > Hi, > > > > I am trying to install newest version on Windows xp > (not 64 bit). I have Cygwin installed which I launch from cd > and load it. The run ./xcConfigre.sh and follow instruction. > The problem is creating custom-definitions folder: > > > > creating new /cygdrive/c/Documents and > Settings/Jonas/Desktop/.xcrysden/custom-definitions ... cp: > copying multiple files, but last argument > `Settings/Jonas/Desktop/.xcrysden/custom-definitions' is > not a directory > > The problem are the whitespaces in the path (i.e. Documents > and > Settings). It is strange that the $HOME variable points to > this place. > As a default it should be something line /home/jonas. > Anyway ~/.xcrysden > directory is optional, and xcrysden should run without > running > xcConfigure.sh script. But it will not work if it is > installed under > path that contains whitespaces. > > So install it to some place without whitespaces in the > path. > > 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 jasius_1 at yahoo.com Sun Jan 11 17:45:38 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Sun, 11 Jan 2009 08:45:38 -0800 (PST) Subject: [xcrysden] xcrysden Windows installation fails In-Reply-To: <588951.42251.qm@web54402.mail.yahoo.com> Message-ID: <552260.27354.qm@web54406.mail.yahoo.com> I will have to apologize for being overly active in this forum for a while but I can't seem to open anything with xcrysden: not input nor outputs of pwscf. The most common error is below. I am runnign the newest version Linux 64 bit which I am running remotely from Cygwin based windows computer In fact, it gives thesame error when I try to open the pwscf output file in the /xcrysden/test/data folder Could anybody shed some light? thanks Jonas bad window path name ".a1" bad window path name ".a1" while executing "raise $pw(disptext) ." (procedure "pwPreset" line 70) invoked from within "pwPreset $file Input " ("uplevel" body line 1) invoked from within "uplevel 1 { pwPreset $file Input }" (procedure "pwInputPreset" line 46) invoked from within "pwInputPreset /share/apps/scratch/atom-lsda/atom-lsda.in" ("eval" body line 1) invoked from within "eval $preset $file" (procedure "openExtStruct" line 106) invoked from within "openExtStruct 3 crystal external {sh /share/apps/xcrysden-1.6/scripts/pwi2xsf.sh} pwi2xsf.xsf_out {PWSCF Input} ANGS -preset pwInputPreset" invoked from within ".menu.vmfile.menu.opstr invoke active" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke active]" (procedure "tk::MenuInvoke" line 50) invoked from within "tk::MenuInvoke .menu.vmfile.menu.opstr 1" (command bound to event) From tone.kokalj at ijs.si Mon Jan 12 09:13:57 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 12 Jan 2009 09:13:57 +0100 Subject: [xcrysden] xcrysden Windows installation fails In-Reply-To: <588951.42251.qm@web54402.mail.yahoo.com> References: <588951.42251.qm@web54402.mail.yahoo.com> Message-ID: <1231748037.20024.11.camel@walk.ijs.si> On Sun, 2009-01-11 at 08:24 -0800, Jonas Baltrusaitis wrote: > The problem is that I do specify tmp folder without white spaces, but it still tries to look at this "default" path and completely disregards the path I specified > > Please specify XCRYSDEN_SCRATCH directory (default: /cygdrive/c/Documents and > Settings/Jonas/Desktop/xcrys_tmp): C:/xcrysden16/tmp > test: and: unknown operand Here there are two issues: the first is general, and related to the fact that unix HOME enviromental variable points to rather unusual path that contains whitespaces. This will break not only xcrysden but also many other things. The second is that you specified the windows-type path in your answer. Instead of C:/xcrysden16/tmp you should specify: /cygdrive/c/xcrysden16/tmp (Note however that running xcConfigure is only optional) You may want set HOME variable to point to some place that does not contain whitespaces (I don't understand why in your cygwin the HOME variable points to that place at all). The default is usually /home/$USER, so you may try: cd export HOME=/home/$USER ./xcrysden > creating new /cygdrive/c/Documents and Settings/Jonas/Desktop/.xcrysden/custo > m-definitions ... cp: copying multiple files, but last argument `Settings/Jonas/ > Desktop/.xcrysden/custom-definitions' is not a directory > Try `cp --help' for more information. This is another yet failure due to whitespaces in $HOME. -- 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 Mon Jan 12 09:16:47 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 12 Jan 2009 09:16:47 +0100 Subject: [xcrysden] xcrysden Windows installation fails In-Reply-To: <552260.27354.qm@web54406.mail.yahoo.com> References: <552260.27354.qm@web54406.mail.yahoo.com> Message-ID: <1231748207.20024.14.camel@walk.ijs.si> On Sun, 2009-01-11 at 08:45 -0800, Jonas Baltrusaitis wrote: > I will have to apologize for being overly active in this forum for a while but I can't seem to open anything with xcrysden: not input nor outputs of pwscf. The most common error is below. I am runnign the newest version Linux 64 bit which I am running remotely from Cygwin based windows computer > > In fact, it gives thesame error when I try to open the pwscf output file in the /xcrysden/test/data folder > > Could anybody shed some light? > > thanks > > Jonas > > bad window path name ".a1" > bad window path name ".a1" > while executing > .... I have never seen an error like that. Please run xcrysden as: xcrysden -T >& log and proceed to produce this error. Then send me the log file. 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 jasius_1 at yahoo.com Thu Jan 15 03:21:36 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Wed, 14 Jan 2009 18:21:36 -0800 (PST) Subject: [xcrysden] exec: wish: not found In-Reply-To: <1231748037.20024.11.camel@walk.ijs.si> Message-ID: <741607.10188.qm@web54405.mail.yahoo.com> I just realized when I click reply it goes back not ti the list but to the author. So here it is: I download newest 1.6 Cygwin version go through ./xcConfigure succesfully and when I launch xcrysden I get this exec: wish: not found I've read that this means tcl not installed. But I thought 1.6 cygwin version was fully linked to tcl and any installation of it wasn't needed. Could anybody give next steps I should proceed with? thanks Jonas xc14> xcrysden +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2004 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 1.5.18 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/. XCRYSDEN_TOPDIR=/cygdrive/c/xc16 XCRYSDEN_SCRATCH=/cygdrive/c/xc16/xcrys_tmp exec: wish: not found From tone.kokalj at ijs.si Thu Jan 15 09:25:33 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 15 Jan 2009 09:25:33 +0100 Subject: [xcrysden] exec: wish: not found In-Reply-To: <741607.10188.qm@web54405.mail.yahoo.com> References: <741607.10188.qm@web54405.mail.yahoo.com> Message-ID: <1232007933.8677.2.camel@walk.ijs.si> On Wed, 2009-01-14 at 18:21 -0800, Jonas Baltrusaitis wrote: > I just realized when I click reply it goes back not ti the list but to the author. > > So here it is: I download newest 1.6 Cygwin version go through ./xcConfigure succesfully and when I launch xcrysden I get this > > exec: wish: not found Read the README.cygwin file contained in the xcrysden's root directory. Therein is a list of required cygwin packages. Install them and the problem will be fixed. 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 jasius_1 at yahoo.com Thu Jan 15 16:21:02 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Thu, 15 Jan 2009 07:21:02 -0800 (PST) Subject: [xcrysden] exec: wish: not found In-Reply-To: <1232007933.8677.2.camel@walk.ijs.si> Message-ID: <355934.64010.qm@web54406.mail.yahoo.com> I apologize but there seems to be no readme.cywin anywhere in the home directory. there is a regular readme but nothing is mentioned about cygwin. Could anybody send me the readme.cygwin file? thanks Jonas --- On Thu, 1/15/09, Tone Kokalj wrote: > From: Tone Kokalj > Subject: Re: [xcrysden] exec: wish: not found > To: jasius_1 at yahoo.com, "XCrySDen mailing list" > Date: Thursday, January 15, 2009, 12:25 AM > On Wed, 2009-01-14 at 18:21 -0800, Jonas Baltrusaitis wrote: > > I just realized when I click reply it goes back not ti > the list but to the author. > > > > So here it is: I download newest 1.6 Cygwin version go > through ./xcConfigure succesfully and when I launch xcrysden > I get this > > > > exec: wish: not found > > Read the README.cygwin file contained in the xcrysden's > root directory. > Therein is a list of required cygwin packages. Install them > and the > problem will be fixed. > > 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 Jan 15 16:53:11 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 15 Jan 2009 16:53:11 +0100 Subject: [xcrysden] exec: wish: not found In-Reply-To: <355934.64010.qm@web54406.mail.yahoo.com> References: <355934.64010.qm@web54406.mail.yahoo.com> Message-ID: <1232034791.8677.42.camel@walk.ijs.si> On Thu, 2009-01-15 at 07:21 -0800, Jonas Baltrusaitis wrote: > I apologize but there seems to be no readme.cywin anywhere in the home directory. > there is a regular readme but nothing is mentioned about cygwin. > Could anybody send me the readme.cygwin file? Indeed, you are right! This can be treated as a bug, thanks. I attach the file. 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: README.cygwin Type: text/x-readme Size: 816 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20090115/24bf061d/attachment.bin From jasius_1 at yahoo.com Thu Jan 15 21:10:57 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Thu, 15 Jan 2009 12:10:57 -0800 (PST) Subject: [xcrysden] exec: wish: not found In-Reply-To: <1232034791.8677.42.camel@walk.ijs.si> Message-ID: <101879.91112.qm@web54409.mail.yahoo.com> Ok, so here is my problem. I am using Cygwin XLiveCD from xlivecd.indiana.edu, so I don't actually have cygwin installed on hdd Which directory should I compile mesa from in this case (make cygwin-sl)? Is that all there is needed to finally run xcrysden? thanks JOnas --- On Thu, 1/15/09, Tone Kokalj wrote: > From: Tone Kokalj > Subject: Re: [xcrysden] exec: wish: not found > To: jasius_1 at yahoo.com, "XCrySDen mailing list" > Date: Thursday, January 15, 2009, 7:53 AM > On Thu, 2009-01-15 at 07:21 -0800, Jonas Baltrusaitis wrote: > > I apologize but there seems to be no readme.cywin > anywhere in the home directory. > > there is a regular readme but nothing is mentioned > about cygwin. > > Could anybody send me the readme.cygwin file? > > Indeed, you are right! This can be treated as a bug, > thanks. > > I attach the file. > > 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 jasius_1 at yahoo.com Fri Jan 16 05:22:42 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Thu, 15 Jan 2009 20:22:42 -0800 (PST) Subject: [xcrysden] exec: wish: not found In-Reply-To: <1232034791.8677.42.camel@walk.ijs.si> Message-ID: <383028.77874.qm@web54402.mail.yahoo.com> Ok, now I installed cygwin on the hard drive but can't launch make cygwin-sl as all it does it's command not found. Should I cd to a particular folder? I am not familiar very well with Linux so I would ask for the help here thanks Jonas From tone.kokalj at ijs.si Fri Jan 16 05:35:53 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 16 Jan 2009 05:35:53 +0100 Subject: [xcrysden] exec: wish: not found In-Reply-To: <101879.91112.qm@web54409.mail.yahoo.com> References: <101879.91112.qm@web54409.mail.yahoo.com> Message-ID: <1232080553.20151.14.camel@walk.ijs.si> On Thu, 2009-01-15 at 12:10 -0800, Jonas Baltrusaitis wrote: > Ok, so here is my problem. I am using Cygwin XLiveCD from xlivecd.indiana.edu, so I don't actually have cygwin installed on hdd > > Which directory should I compile mesa from in this case (make cygwin-sl)? Is that all there is needed to finally run xcrysden? You don't need to compile anything. Just install the cygwin packages listed in README.cygwin (Tcl/Tk and OpenGL is provided by these, and that is all you need), and the cygwin-version of xcrysden will run out of the box. However, if you insist on compiling Mesa and Tcl/Tk: I never tried to compile Mesa under cygwin, but it is quite difficult to compile working Tcl/Tk under cygwin. Even if you succed, you will make xcrysden dependent on X11, which is not the case if you use the cygwin packages. 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 zucco at dipteris.unige.it Wed Jan 21 11:14:34 2009 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Wed, 21 Jan 2009 11:14:34 +0100 Subject: [xcrysden] XCrysden and crystal* on Macosx Message-ID: <773E867F-23DE-41FE-94E7-4C378C912169@dipteris.unige.it> Ciao Tone and all users, i've a simple question about the integration between XCrysden on Macosx and the crystal* output. I've installed crystal* on our linux-based clusters but I use, as you know, XCrysden on my osx laptop (mainly with QE). For macosx crystal03/06 are not released yet. Then I cannot specify crystal* on XC preferences. There is the way to read a crystal* output on my laptop without crystal installed? My tests were totally unseccessful... Thanks marino ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From tone.kokalj at ijs.si Wed Jan 21 12:49:40 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 21 Jan 2009 12:49:40 +0100 Subject: [xcrysden] XCrysden and crystal* on Macosx In-Reply-To: <773E867F-23DE-41FE-94E7-4C378C912169@dipteris.unige.it> References: <773E867F-23DE-41FE-94E7-4C378C912169@dipteris.unige.it> Message-ID: <1232538580.6092.21.camel@walk.ijs.si> On Wed, 2009-01-21 at 11:14 +0100, Marino Vetuschi Zuccolini wrote: > Ciao Tone and all users, > > i've a simple question about the integration between XCrysden on > Macosx and the crystal* output. > I've installed crystal* on our linux-based clusters but I use, as you > know, XCrysden on my osx laptop (mainly with QE). For macosx > crystal03/06 are not released yet. Then I cannot specify crystal* on > XC preferences. > > There is the way to read a crystal* output on my laptop without > crystal installed? My tests were totally unseccessful... xcrysden does not read crystal output. Instead it can read crystal input and file unit 9 (i.e. fort.9, which is "properties" file). The fort.9 is a binary file and hence platform dependent. Moreover, xcrysden uses crystal's "properties" program when loading fort.9. This means that so far, you can only read crystal input files with xcrysden on macosx. Note however that if you are doing geometry optimization, then crystal produces file fort.34, which is an animated XYZ file, with all the snapshots of the structure evolution. You may load it as: xcrysden --xyz fort.34 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