From flux_ray12 at 163.com Wed Feb 1 17:55:44 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 2 Feb 2012 00:55:44 +0800 (CST) Subject: [xcrysden] Is it possible to show two planes in one xsf file? Message-ID: <5561badc.bf65.13539d7e498.Coremail.flux_ray12@163.com> Dear XCrySDen developer and users: Hello. I am using XCrySDen for the charge density or |psi|^2 visulasition of Quantum-ESPRESSO. SInce only one plane can be generated by pp.x in one time, I always draw the figure with single DATAGRID. However, I found some person used CASTEP+Materials Studio to produce the model with two charge density planes which are not orthogonal. Therefore, I also wondering whether XCrySDen can draw the similar model. I tried to generate two xsf files corresponding to different planes by pp.x, and accumulated them by: BEGIN_BLOCK_DATAGRID_2D name DATAGRID_2D_1 nx ny x0(1) x0(2) x0(3) e1(1) e1(2) e1(3) e2(1) e2(2) e2(3) FFT Data Mesh END_DATAGRID_2D DATAGRID_2D_1 nx ny x0(1) x0(2) x0(3) v1(1) v1(2) v1(3) v2(1) v2(2) v2(3) FFT Data Mesh END_DATAGRID_2D END_BLOCK_DATAGRID_2D But finally I found that not only the nx and ny have to be the same, but also the planes in two DATAGRID should be same. Then I tried to write tow BLOCK_DATAGRID_2D, but when I imported DATAGRID to my model, I had to choose one and only one. So, now I just want to know, are there any methods to get two nonorthogonal plane to show charge density by XCrySDen? Thanks. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120202/0d124a6c/attachment.htm From arshadfarhan at hotmail.com Fri Feb 3 06:52:32 2012 From: arshadfarhan at hotmail.com (=?iso-8859-6?B?5c3lzyDH0dTPIOHRzcfm?=) Date: Fri, 3 Feb 2012 14:52:32 +0900 Subject: [xcrysden] FW: Welcome to the "XCrySDen" mailing list In-Reply-To: References: Message-ID: hi,please add me in the mailing list. so that i could post (as mentioned below)Regards,M. Arshad Farhan > Subject: Welcome to the "XCrySDen" mailing list > From: xcrysden-request at democritos.it > To: arshadfarhan at hotmail.com > Date: Fri, 3 Feb 2012 06:50:46 +0100 > > Welcome to the XCrySDen at democritos.it mailing list! The purpose of the > list is to discuss XCRYSDEN related issues among users. > > XCRYSDEN is a crystalline and molecular structure visualisation > program, (http://www.xcrysden.org/). > > To post to this list, send your email to: > > xcrysden at democritos.it > > General information about the mailing list is at: > > http://www.democritos.it/mailman/listinfo/xcrysden > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > http://www.democritos.it/mailman/options/xcrysden/arshadfarhan%40hotmail.com > > > You can also make such adjustments via email by sending a message to: > > XCrySDen-request at democritos.it > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > ilovepakistan > > Normally, Mailman will remind you of your democritos.it mailing list > passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120203/1b7419a2/attachment.htm From tone.kokalj at ijs.si Fri Feb 3 09:59:37 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 03 Feb 2012 09:59:37 +0100 Subject: [xcrysden] Is it possible to show two planes in one xsf file? In-Reply-To: <5561badc.bf65.13539d7e498.Coremail.flux_ray12@163.com> References: <5561badc.bf65.13539d7e498.Coremail.flux_ray12@163.com> Message-ID: <1328259577.5846.17.camel@catalyst.ijs.si> On Thu, 2012-02-02 at 00:55 +0800, GAO Zhe wrote: > Dear XCrySDen developer and users: > Hello. > I am using XCrySDen for the charge density or |psi|^2 visulasition of > Quantum-ESPRESSO. SInce only one plane can be generated by pp.x in one > time, I always draw the figure with single DATAGRID. > However, I found some person used CASTEP+Materials Studio to produce > the model with two charge density planes which are not orthogonal. > Therefore, I also wondering whether XCrySDen can draw the similar > model. XCrySDen can plot only one DATAGRID_2D at a time. However, if you have 3D datagrid (DATAGRID_3D), then xcrysden can plot there basal contour-planes (ab, ac, bc) simultaneously. For cubic/tetragonal/orthorhombic cells this implies that these planes are orthogonal, but for triclinic they are not. This can be used as a trick to achieve what you want: you need to construct a 3D datagrid with the "box" chosen such that its basal planes coincides with the planes you want to show. It is somewhat cumbersome as its needs a manual specification of the box in QE's pp.x program (i.e. e1, e2, e3, and o vectors), but this is always so if you want a given arbitrary plane. 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 Fri Feb 3 10:00:54 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 03 Feb 2012 10:00:54 +0100 Subject: [xcrysden] FW: Welcome to the "XCrySDen" mailing list In-Reply-To: References: Message-ID: <1328259654.5846.19.camel@catalyst.ijs.si> On Fri, 2012-02-03 at 14:52 +0900, ???? ???? ????? wrote: > hi, > please add me in the mailing list. so that i could post (as mentioned > below) Dear Arshad, given the fact that you can post to the list implies that you have already subscribed yourself to the list! 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 flux_ray12 at 163.com Fri Feb 3 18:06:59 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 4 Feb 2012 01:06:59 +0800 (CST) Subject: [xcrysden] Is it possible to show two planes in one xsf file? In-Reply-To: <1328259577.5846.17.camel@catalyst.ijs.si> References: <1328259577.5846.17.camel@catalyst.ijs.si> <5561badc.bf65.13539d7e498.Coremail.flux_ray12@163.com> Message-ID: <3f8abf63.ec8e.135442ee943.Coremail.flux_ray12@163.com> Dear Prof. Kokalj, thank you very much, I though I've obtained what I can do by XCrySDen. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-03 16:59:37,"Tone Kokalj" wrote: >On Thu, 2012-02-02 at 00:55 +0800, GAO Zhe wrote: >> Dear XCrySDen developer and users: >> Hello. >> I am using XCrySDen for the charge density or |psi|^2 visulasition of >> Quantum-ESPRESSO. SInce only one plane can be generated by pp.x in one >> time, I always draw the figure with single DATAGRID. >> However, I found some person used CASTEP+Materials Studio to produce >> the model with two charge density planes which are not orthogonal. >> Therefore, I also wondering whether XCrySDen can draw the similar >> model. > >XCrySDen can plot only one DATAGRID_2D at a time. > >However, if you have 3D datagrid (DATAGRID_3D), then xcrysden can plot >there basal contour-planes (ab, ac, bc) simultaneously. For >cubic/tetragonal/orthorhombic cells this implies that these planes are >orthogonal, but for triclinic they are not. > >This can be used as a trick to achieve what you want: you need to >construct a 3D datagrid with the "box" chosen such that its basal planes >coincides with the planes you want to show. It is somewhat cumbersome as >its needs a manual specification of the box in QE's pp.x program (i.e. >e1, e2, e3, and o vectors), but this is always so if you want a given >arbitrary plane. > >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 > >_______________________________________________ >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/20120204/da88687f/attachment.htm From indu.chem.mind86 at gmail.com Wed Feb 8 12:40:50 2012 From: indu.chem.mind86 at gmail.com (Indu Kaul) Date: Wed, 8 Feb 2012 17:10:50 +0530 Subject: [xcrysden] Regarding Xcrysden installation in Linux Message-ID: Hi, I have installed Xcrysden on my linux machine(OS-Redhat) version xc-1.5.24.Whenever i tries to open xcrysden,it displays the error message lib.sh not found in /Bin directory although it is present in Bin directory.Can anyone help out what problem could be there with it? With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120208/5ab4170f/attachment.htm From flux_ray12 at 163.com Wed Feb 8 14:45:20 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 8 Feb 2012 21:45:20 +0800 (CST) Subject: [xcrysden] Regarding Xcrysden installation in Linux In-Reply-To: References: Message-ID: Whether the one you downloaded is the semishared binary version? If yes, please check: 1, whether the version of your Red Hat Enterprise Linux is not lower than 6.0, otherwise you have to use XCrySDen 1.4 2, whether you have run xcConfigure before running xcrysden, if not, run the xcConfigure firstly. If the one you downloaded is the shared binary version, please make sure that your system has provided the library required by xcrysden and all the library can be found through environment variable. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-08 19:40:50,"Indu Kaul" wrote: Hi, I have installed Xcrysden on my linux machine(OS-Redhat) version xc-1.5.24.Whenever i tries to open xcrysden,it displays the error message lib.sh not found in /Bin directory although it is present in Bin directory.Can anyone help out what problem could be there with it? With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120208/c4479440/attachment.htm From tone.kokalj at ijs.si Mon Feb 13 16:40:05 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 13 Feb 2012 16:40:05 +0100 Subject: [xcrysden] Regarding Xcrysden installation in Linux In-Reply-To: References: Message-ID: <1329147605.3667.14.camel@catalyst.ijs.si> On Wed, 2012-02-08 at 17:10 +0530, Indu Kaul wrote: > Hi, > > I have installed Xcrysden on my linux machine(OS-Redhat) version > xc-1.5.24.Whenever i tries to open xcrysden,it displays the error > message lib.sh not found in /Bin directory although it is present in > Bin directory.Can anyone help out what problem could be there with > it? I very much doubt the message is "lib.sh not found in /Bin", likely it is: .... Can't open ***/xcLib.sh This likely means you set up XCRYSDEN_TOPDIR variable to point to wrong place. Note that for xcrysden 1.5.* version the use of XCRYSDEN_TOPDIR variable is deprecated. Go to xcrysden root directory and try the following: unset XCRYSDEN_TOPDIR ./xcrysden What happens? 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 indu.chem.mind86 at gmail.com Wed Feb 15 08:13:44 2012 From: indu.chem.mind86 at gmail.com (Indu Kaul) Date: Wed, 15 Feb 2012 02:13:44 -0500 Subject: [xcrysden] XCrySDen Digest, Vol 49, Issue 5 In-Reply-To: References: Message-ID: Hi Tone, I tried to unset the xcrysden_topdir and again ran xcryden but in vain..it again displays the message "./xcrysden: line 129: /scripts/xcLib.sh: No such file or directory ". On 2/14/12, 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. Re: Regarding Xcrysden installation in Linux (Tone Kokalj) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Feb 2012 16:40:05 +0100 > From: Tone Kokalj > Subject: Re: [xcrysden] Regarding Xcrysden installation in Linux > To: xcrysden at democritos.it > Message-ID: <1329147605.3667.14.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Wed, 2012-02-08 at 17:10 +0530, Indu Kaul wrote: >> Hi, >> >> I have installed Xcrysden on my linux machine(OS-Redhat) version >> xc-1.5.24.Whenever i tries to open xcrysden,it displays the error >> message lib.sh not found in /Bin directory although it is present in >> Bin directory.Can anyone help out what problem could be there with >> it? > > I very much doubt the message is "lib.sh not found in /Bin", likely it > is: .... Can't open ***/xcLib.sh > > This likely means you set up XCRYSDEN_TOPDIR variable to point to wrong > place. Note that for xcrysden 1.5.* version the use of XCRYSDEN_TOPDIR > variable is deprecated. Go to xcrysden root directory and try the > following: > > unset XCRYSDEN_TOPDIR > ./xcrysden > > What happens? > > 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 > > > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 49, Issue 5 > *************************************** > -- With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA From tone.kokalj at ijs.si Thu Feb 16 09:07:32 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 16 Feb 2012 09:07:32 +0100 Subject: [xcrysden] XCrySDen Digest, Vol 49, Issue 5 In-Reply-To: References: Message-ID: <1329379652.13905.2.camel@catalyst.ijs.si> On Wed, 2012-02-15 at 02:13 -0500, Indu Kaul wrote: > Hi Tone, > > I tried to unset the xcrysden_topdir and again ran xcryden but in > vain..it again displays the message "./xcrysden: line 129: > /scripts/xcLib.sh: No such file or directory ". Seems like XCRYSDEN_TOPDIR variable has an empty value, but it is not unset. Please try (do copy&paste): unset XCRYSDEN_TOPDIR; ./xcrysden 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 emoujaes at fisica.ufmg.br Fri Feb 24 19:25:25 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Fri, 24 Feb 2012 15:25:25 -0300 Subject: [xcrysden] cannot start XCRYSDEN Message-ID: <20120224181625.M99053@proto.fisica.ufmg.br> Dear all, I have uninstalled a previous version of XCRYSDEN and now I am re installing the XCRYSDEN -1.5.24-src version on my laptop. the "untarring" of the tarred package goes fine. When I type ./xcConfigure, the program automatically assigns the $XCRYSDEN_TOPDIR and $XCRYSDN_SCRATCH to: XCRYSDEN_TOPDIR=/XcrySDen-1.5.24-src XCRYSDEN_SCRATCH=/Elie-molecules/xcrys_tmp. PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" The problem here is in XCRYSDEN_SCRATCH where Elie-molecules folder does not exist. I deleted it when I deleted the previous version. Somehow XCRYSDEN still retains this "path". This is giving an error once I run ./xcrysden : ./xcrysden: line 165:/Elie-molecules/XcrySDen-1.5.23-src-all/scripts/xcLib.sh: no such file or directory. Note the XCrysden-1.5.23 up there. Please can anyone help what shall I do to correct this error and make XCrysden forget about previous versions..I am a beginner I really appreciate a detailed solution..Thank you all Elie -- Departamento de Fisica - UFMG/ICEx From rcais at cal3.vsnl.net.in Sun Feb 26 06:37:19 2012 From: rcais at cal3.vsnl.net.in (Chandrika Varadachari) Date: Sun, 26 Feb 2012 11:27:19 +0550 Subject: [xcrysden] XCrySDen Digest, Vol 49, Issue 8 In-Reply-To: References: Message-ID: Kindly change my e-mail id to cv at rcais.res.in Chandrika Varadachari On Sat, 25 Feb 2012 09:34:49 +0100, 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. cannot start XCRYSDEN (Elie Albert Moujaes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Feb 2012 15:25:25 -0300 > From: "Elie Albert Moujaes" > Subject: [xcrysden] cannot start XCRYSDEN > To: xcrysden at democritos.it > Message-ID: <20120224181625.M99053 at proto.fisica.ufmg.br> > Content-Type: text/plain; charset=iso-8859-1 > > Dear all, > > I have uninstalled a previous version of XCRYSDEN and now I am re installing > the XCRYSDEN -1.5.24-src version on my laptop. the "untarring" of the tarred > package goes fine. When I type ./xcConfigure, the program automatically > assigns the $XCRYSDEN_TOPDIR and $XCRYSDN_SCRATCH to: > > XCRYSDEN_TOPDIR=/XcrySDen-1.5.24-src > XCRYSDEN_SCRATCH=/Elie-molecules/xcrys_tmp. > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" > > The problem here is in XCRYSDEN_SCRATCH where Elie-molecules folder does not > exist. I deleted it when I deleted the previous version. Somehow XCRYSDEN > still retains this "path". This is giving an error once I run ./xcrysden : > > ./xcrysden: line > 165:/Elie-molecules/XcrySDen-1.5.23-src-all/scripts/xcLib.sh: > no such file or directory. > > Note the XCrysden-1.5.23 up there. Please can anyone help what shall I do to > correct this error and make XCrysden forget about previous versions..I am a > beginner I really appreciate a detailed solution..Thank you all > > > Elie > > -- > Departamento de Fisica - UFMG/ICEx > > > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 49, Issue 8 > *************************************** From tone.kokalj at ijs.si Mon Feb 27 08:54:32 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 27 Feb 2012 08:54:32 +0100 Subject: [xcrysden] XCrySDen Digest, Vol 49, Issue 8 In-Reply-To: References: Message-ID: <1330329272.7856.5.camel@catalyst.ijs.si> On Sun, 2012-02-26 at 11:27 +0550, Chandrika Varadachari wrote: > Kindly change my e-mail id to cv at rcais.res.in You can do it. Please go to: http://www.democritos.it/mailman/listinfo/xcrysden and at the bottom of page enter your email and password then click the button "Visit Subscriber List". Find your email there and click it. A new page will open. Change your email there at "New address:" entry and click "Change My Address and Name" button. Regards, Tone PS: Please consider to avoid sending "reply" do digest, but always explicitly state the subject of the email! -- 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 Feb 27 08:57:17 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 27 Feb 2012 08:57:17 +0100 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <20120224181625.M99053@proto.fisica.ufmg.br> References: <20120224181625.M99053@proto.fisica.ufmg.br> Message-ID: <1330329437.7856.8.camel@catalyst.ijs.si> On Fri, 2012-02-24 at 15:25 -0300, Elie Albert Moujaes wrote: > Dear all, > > I have uninstalled a previous version of XCRYSDEN and now I am re installing > the XCRYSDEN -1.5.24-src version on my laptop. the "untarring" of the tarred > package goes fine. When I type ./xcConfigure, the program automatically > assigns the $XCRYSDEN_TOPDIR and $XCRYSDN_SCRATCH to: > > XCRYSDEN_TOPDIR=/XcrySDen-1.5.24-src > XCRYSDEN_SCRATCH=/Elie-molecules/xcrys_tmp. > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" > > The problem here is in XCRYSDEN_SCRATCH where Elie-molecules folder does not > exist. I deleted it when I deleted the previous version. Somehow XCRYSDEN > still retains this "path". This is giving an error once I run ./xcrysden : > > ./xcrysden: line 165:/Elie-molecules/XcrySDen-1.5.23-src-all/scripts/xcLib.sh: > no such file or directory. Which means that you did not update the definition of XCRYSDEN_TOPDIR variable in your profile (e.g., $HOME/.bashrc). Either correct that manually or simply unset the XCRYSDEN_TOPDIR variable (preferred). 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 vakula.chem at gmail.com Tue Feb 28 12:50:00 2012 From: vakula.chem at gmail.com (Nikita Vakula) Date: Tue, 28 Feb 2012 12:50:00 +0100 Subject: [xcrysden] xcrysden on windows 7 (Cygwin) Message-ID: Dear all, I'm new to xcrysden. And I have a question about installation of xcrysden on windows 7/cygwin. After installation of it on windows I tried to launch it but had an error: *Application initialization failed: no display name and no $DISPLAY environment variable* *Error in startup script: no display name and no $DISPLAY environment variable* * while executing* *"load /usr/lib/tk8.5/../../bin/libtk8.5.dll Tk"* * ("package ifneeded Tk 8.5.11" script)* * invoked from within* *"load $system(TOPDIR)/bin/xcrys.dll"* * invoked from within* *"if { [file exists $system(TOPDIR)/bin/xcrys.dll] } {* * load $system(TOPDIR)/bin/xcrys.dll* *}"* * (file "/home/Nikita/XCrySDen-1.5.18-bin-shared/Tcl/xcInit.tcl" line 426)* Could you please tell me what to do in order to make it works? Thank you in advance, Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120228/302530cb/attachment.htm From tone.kokalj at ijs.si Tue Feb 28 13:45:46 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 28 Feb 2012 13:45:46 +0100 Subject: [xcrysden] xcrysden on windows 7 (Cygwin) In-Reply-To: References: Message-ID: <1330433146.26567.4.camel@catalyst.ijs.si> On Tue, 2012-02-28 at 12:50 +0100, Nikita Vakula wrote: > Dear all, > > > I'm new to xcrysden. And I have a question about installation of > xcrysden on windows 7/cygwin. After installation of it on windows I > tried to launch it but had an error: > > > Application initialization failed: no display name and no $DISPLAY > environment variable > Error in startup script: no display name and no $DISPLAY environment > variable > while executing > "load /usr/lib/tk8.5/../../bin/libtk8.5.dll Tk" This means you attempted to run xcrysden without the running X-window. Start the X-window first! 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 vakula.chem at gmail.com Tue Feb 28 14:27:20 2012 From: vakula.chem at gmail.com (Nikita Vakula) Date: Tue, 28 Feb 2012 14:27:20 +0100 Subject: [xcrysden] xcrysden on windows 7 (Cygwin) In-Reply-To: <1330433146.26567.4.camel@catalyst.ijs.si> References: <1330433146.26567.4.camel@catalyst.ijs.si> Message-ID: Hi Tone! Thanks for your reply! But after starting x window the new error occured *Error in startup script: couldn't fork child process: resource temporarily unavailable* * while executing* *"_tcl_exec sh /home/Nikita/xcrysden/scripts/launch.sh /home/Nikita/xcrysden/scripts/pwd.sh"* * ("eval" body line 1)* * invoked from within* *"eval _tcl_exec sh /home/Nikita/xcrysden/scripts/launch.sh /home/Nikita/xcrysden/scripts/pwd.sh"* * ("uplevel" body line 1)* * invoked from within* *"uplevel 1 [list eval _tcl_exec sh $env(XCRYSDEN_TOPDIR)/scripts/launch.sh] $args"* * (procedure "exec" line 8)* * invoked from within* *"exec $env(XCRYSDEN_TOPDIR)/scripts/pwd.sh"* * (procedure "pwd" line 7)* * invoked from within* *"pwd"* * invoked from within* *"set system(PWD) [pwd]"* * (file "/home/Nikita/xcrysden/Tcl/system.tcl" line 22)* * invoked from within* *"source $env(XCRYSDEN_TOPDIR)/Tcl/system.tcl"* * invoked from within* *"if [file exists $env(XCRYSDEN_TOPDIR)/Tcl/system.tcl] {* * source $env(XCRYSDEN_TOPDIR)/Tcl/system.tcl* *} else {* * set system(PWD) [pwd]* * set ..."* * (file "/home/Nikita/xcrysden/Tcl/xcInitLib.tcl" line 54)* * invoked from within* *"source $system(TOPDIR)/Tcl/xcInitLib.tcl "* * ("eval" body line 15)* * invoked from within* *"eval [info body xcInit]"* * (file "/home/Nikita/xcrysden/Tcl/xcInit.tcl" line 530)* Do you know can I overcome this problem? Thank you in advance, Nikita 28 ??????? 2012 ?. 13:45 ???????????? Tone Kokalj ???????: > On Tue, 2012-02-28 at 12:50 +0100, Nikita Vakula wrote: > > Dear all, > > > > > > I'm new to xcrysden. And I have a question about installation of > > xcrysden on windows 7/cygwin. After installation of it on windows I > > tried to launch it but had an error: > > > > > > Application initialization failed: no display name and no $DISPLAY > > environment variable > > Error in startup script: no display name and no $DISPLAY environment > > variable > > while executing > > "load /usr/lib/tk8.5/../../bin/libtk8.5.dll Tk" > > This means you attempted to run xcrysden without the running X-window. > Start the X-window first! > > 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 > > _______________________________________________ > 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/20120228/2f66bb4d/attachment.htm From vakula.chem at gmail.com Tue Feb 28 14:54:14 2012 From: vakula.chem at gmail.com (Nikita Vakula) Date: Tue, 28 Feb 2012 14:54:14 +0100 Subject: [xcrysden] xcrysden on windows 7 (Cygwin) In-Reply-To: References: <1330433146.26567.4.camel@catalyst.ijs.si> Message-ID: And another issue. I have read that rebaseall can solve this problem (with fork()). But after I had done rebaseall, segfault occured *Running on platform: cygwin* *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: /home/Nikita/xcrysden/bin/ftnunit* */home/Nikita/xcrysden/xcrysden: line 206: 2680 Segmentation fault (core dumped) exec wish ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null* Maybe somebody knows how to solve it? Thanks in advance, Nikita 28 ??????? 2012 ?. 14:27 ???????????? Nikita Vakula ???????: > Hi Tone! > > Thanks for your reply! > But after starting x window the new error occured > > *Error in startup script: couldn't fork child process: resource > temporarily unavailable* > * while executing* > *"_tcl_exec sh /home/Nikita/xcrysden/scripts/launch.sh > /home/Nikita/xcrysden/scripts/pwd.sh"* > * ("eval" body line 1)* > * invoked from within* > *"eval _tcl_exec sh /home/Nikita/xcrysden/scripts/launch.sh > /home/Nikita/xcrysden/scripts/pwd.sh"* > * ("uplevel" body line 1)* > * invoked from within* > *"uplevel 1 [list eval _tcl_exec sh > $env(XCRYSDEN_TOPDIR)/scripts/launch.sh] $args"* > * (procedure "exec" line 8)* > * invoked from within* > *"exec $env(XCRYSDEN_TOPDIR)/scripts/pwd.sh"* > * (procedure "pwd" line 7)* > * invoked from within* > *"pwd"* > * invoked from within* > *"set system(PWD) [pwd]"* > * (file "/home/Nikita/xcrysden/Tcl/system.tcl" line 22)* > * invoked from within* > *"source $env(XCRYSDEN_TOPDIR)/Tcl/system.tcl"* > * invoked from within* > *"if [file exists $env(XCRYSDEN_TOPDIR)/Tcl/system.tcl] {* > * source $env(XCRYSDEN_TOPDIR)/Tcl/system.tcl* > *} else {* > * set system(PWD) [pwd]* > * set ..."* > * (file "/home/Nikita/xcrysden/Tcl/xcInitLib.tcl" line 54)* > * invoked from within* > *"source $system(TOPDIR)/Tcl/xcInitLib.tcl "* > * ("eval" body line 15)* > * invoked from within* > *"eval [info body xcInit]"* > * (file "/home/Nikita/xcrysden/Tcl/xcInit.tcl" line 530)* > > Do you know can I overcome this problem? > > Thank you in advance, > > Nikita > > 28 ??????? 2012 ?. 13:45 ???????????? Tone Kokalj ???????: > > On Tue, 2012-02-28 at 12:50 +0100, Nikita Vakula wrote: >> > Dear all, >> > >> > >> > I'm new to xcrysden. And I have a question about installation of >> > xcrysden on windows 7/cygwin. After installation of it on windows I >> > tried to launch it but had an error: >> > >> > >> > Application initialization failed: no display name and no $DISPLAY >> > environment variable >> > Error in startup script: no display name and no $DISPLAY environment >> > variable >> > while executing >> > "load /usr/lib/tk8.5/../../bin/libtk8.5.dll Tk" >> >> This means you attempted to run xcrysden without the running X-window. >> Start the X-window first! >> >> 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 >> >> _______________________________________________ >> 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/20120228/a458ec2c/attachment.htm