From baaouague_khaled at yahoo.fr Mon Feb 1 21:27:09 2010 From: baaouague_khaled at yahoo.fr (Khaled Baaouague) Date: Mon, 1 Feb 2010 20:27:09 +0000 (GMT) Subject: [xcrysden] please I need a help Message-ID: <592647.76575.qm@web23004.mail.ird.yahoo.com> dear sir I am beginner with CRYSTAL03 and Xcrysden when I am trying to displyay the band structure of MgO I cannot see them please help me -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100201/ca22b9f9/attachment.htm From tone.kokalj at ijs.si Fri Feb 5 17:07:46 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 05 Feb 2010 17:07:46 +0100 Subject: [xcrysden] please I need a help In-Reply-To: <592647.76575.qm@web23004.mail.ird.yahoo.com> References: <592647.76575.qm@web23004.mail.ird.yahoo.com> Message-ID: <1265386066.15638.4.camel@walk.ijs.si> On Mon, 2010-02-01 at 20:27 +0000, Khaled Baaouague wrote: > dear sir > I am beginner with CRYSTAL03 and Xcrysden > when I am trying to displyay the band structure of MgO I cannot see > them > Your description is far insufficient to help. 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 xyzfxbd at hotmail.com Sat Feb 6 05:40:53 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Sat, 6 Feb 2010 11:40:53 +0700 Subject: [xcrysden] Installation of xcrysden In-Reply-To: References: , <1264441421.5857.47.camel@walk.ijs.si>, , <1264497327.12843.1.camel@walk.ijs.si>, Message-ID: Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list I have returned now and I read the email from ??? and the big boss Anton Kokalj,,,, Now I understand that the xc-1.5.17-linux_x86-semishared.tar.gz is a compiled package.....However I found some strange result on my system,,,,so I type like this [revival at localhost ~]$ source ~/.bashrc bash: TMOUT: readonly variable Then I try to type xcrysden,,,,and this is the result : [revival at localhost ~]$ 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: 1.5.17 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/. TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared XCRYSDEN_SCRATCH=/home/revival/xcrys_temp Running on platform: unix Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 14571 Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null I can not understand the meaning of the error message written above.....Is it mean that something is missing with the $XCRYSDEN_TOPDIR and $XCRYSDEN_SCRATCH??? I think I need a help again to figure out what's wrong with my way of installation....... Thanks so much for everyone who helps until now GBU Date: Tue, 26 Jan 2010 17:40:48 +0800 From: bingmou2004 at gmail.com To: tone.kokalj at ijs.si; xcrysden at democritos.it Subject: Re: [xcrysden] Installation of xcrysden Follow the big boss Tone Kokalj and I hope you get what you want. 2010/1/26 Tone Kokalj On Tue, 2010-01-26 at 15:18 +0700, Fendy Lovefaith wrote: > Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list > > > I'm so honored to receive many replies for the installation of > XCrysden,,,,so I have download the tar file for for 32-bit linux: > http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz > > > and then I update the info in /.bashrc file like below > > > #------------------------------------------------------------------------ > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/ scripts: > $XCRYSDEN_TOPDIR/util" if your xcrysden is really in /home/revival/XCrySDen-1.5.17-bin-semishared, then all you need to do is: source ~/.bashrc xcrysden That's all. You don't need any make files, because xc-1.5.17-linux_x86-semishared.tar.gz is already compiled package. 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 -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100206/4791afdc/attachment.htm From bingmou2004 at gmail.com Sat Feb 6 07:41:27 2010 From: bingmou2004 at gmail.com (=?GB2312?B?s8LOsOnE?=) Date: Sat, 6 Feb 2010 14:41:27 +0800 Subject: [xcrysden] Installation of xcrysden In-Reply-To: References: <1264441421.5857.47.camel@walk.ijs.si> <1264497327.12843.1.camel@walk.ijs.si> Message-ID: try to read the end of your ~/.bashrc and found whether the enviroment variables XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH have been set right. I guess Xcrysden didn't write anything to your bashrc to set the approximate value and when you started your xcrysden, it used the default values. However maybe there's ~/xcrys/temp in your home directory---that's why error happened. Hope it's useful for you! ? 2010?2?6? ??12:40?Fendy Lovefaith ??? > Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list > > I have returned now and I read the email from ??? and the big boss Anton > Kokalj,,,, > > Now I understand that the xc-1.5.17-linux_x86-semishared.tar.gz is a > compiled package.....However I found some strange result on my system,,,,so > I type like this > > [revival at localhost ~]$ source ~/.bashrc > bash: TMOUT: readonly variable > > Then I try to type xcrysden,,,,and this is the result : > > [revival at localhost ~]$ 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: 1.5.17 > > 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/. > > > TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 > > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > > Running on platform: unix > Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit > /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 14571 > Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys > ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH > $ARGS > /dev/null > > I can not understand the meaning of the error message written above.....Is > it mean that something is missing with the $XCRYSDEN_TOPDIR and > $XCRYSDEN_SCRATCH??? > > I think I need a help again to figure out what's wrong with my way of > installation....... > > Thanks so much for everyone who helps until now > > GBU > ------------------------------ > Date: Tue, 26 Jan 2010 17:40:48 +0800 > From: bingmou2004 at gmail.com > To: tone.kokalj at ijs.si; xcrysden at democritos.it > > Subject: Re: [xcrysden] Installation of xcrysden > > Follow the big boss Tone Kokalj and I hope you get what you want. > > 2010/1/26 Tone Kokalj > > On Tue, 2010-01-26 at 15:18 +0700, Fendy Lovefaith wrote: > > Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list > > > > > > I'm so honored to receive many replies for the installation of > > XCrysden,,,,so I have download the tar file for for 32-bit linux: > > http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz > > > > > > and then I update the info in /.bashrc file like below > > > > > > #------------------------------------------------------------------------ > > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/ scripts: > > $XCRYSDEN_TOPDIR/util" > > if your xcrysden is really > in /home/revival/XCrySDen-1.5.17-bin-semishared, then all you need to do > is: > > source ~/.bashrc > xcrysden > > That's all. You don't need any make files, because > xc-1.5.17-linux_x86-semishared.tar.gz is already compiled package. > > 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 > > > > > -- > ??? > Chen Weibing > ????????????????? > The State Key Laboratory for Superlattices and Microstructures > Institute of Semiconductor, Chinese Academy of Science > > > ------------------------------ > New Windows 7: Find the right PC for you. Learn more. > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100206/3d7b92ad/attachment-0001.htm From xyzfxbd at hotmail.com Sat Feb 6 12:11:10 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Sat, 6 Feb 2010 18:11:10 +0700 Subject: [xcrysden] Installation of xcrysden In-Reply-To: References: , <1264441421.5857.47.camel@walk.ijs.si>, , <1264497327.12843.1.camel@walk.ijs.si>, , , Message-ID: Dear ??? I'm sure the the enviroment variables XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH have been set right in ~/.bashrc,,,,,here is the profile of ~/.bashrc #------------------------------------------------------------------------ # this is for XCRYSDEN 1.5.17; added by XCRYSDEN installation on # Sat Feb 6 18:53:17 CST 2010 #------------------------------------------------------------------------ XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared XCRYSDEN_SCRATCH=/home/revival/xcrys_temp export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" After that I try your suggestion to clean the ~/xcrys/temp using xc_cleanscratch and this is what happen : [revival at localhost scripts]$ xc_cleanscratch XCRYSDEN_SCRATCH directory: /home/revival/xcrys_temp/ will be cleaned (i.e. rm -rf /home/revival/xcrys_temp/xc_*). The following files/directories will be deleted: /home/revival/xcrys_temp/xc_12460: /home/revival/xcrys_temp/xc_16975: /home/revival/xcrys_temp/xc_18305: /home/revival/xcrys_temp/xc_8401: Really delete? ([y]es/[n]o) y Deleting /home/revival/xcrys_temp/xc_* ... OK But again something strange when I want to source out the .bashrc [revival at localhost scripts]$ source ~/.bashrc bash: TMOUT: readonly variable Then I type again the execute command xcrysden and this is happen again : [revival at localhost scripts]$ 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: 1.5.17 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/. TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared XCRYSDEN_SCRATCH=/home/revival/xcrys_temp Running on platform: unix Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 19666 Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null How do you think??? Perhaps something wrong with the bash profile??? Thanks ??? ,,and ,,Anton Kokalj,,,,,your helps really affects much............I'm sure soon the XCRYSDEN can be run in my system GBU Date: Sat, 6 Feb 2010 14:41:27 +0800 From: bingmou2004 at gmail.com To: xcrysden at democritos.it Subject: Re: [xcrysden] Installation of xcrysden try to read the end of your ~/.bashrc and found whether the enviroment variables XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH have been set right. I guess Xcrysden didn't write anything to your bashrc to set the approximate value and when you started your xcrysden, it used the default values. However maybe there's ~/xcrys/temp in your home directory---that's why error happened. Hope it's useful for you! ? 2010?2?6? ??12:40?Fendy Lovefaith ??? Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list I have returned now and I read the email from ??? and the big boss Anton Kokalj,,,, Now I understand that the xc-1.5.17-linux_x86-semishared.tar.gz is a compiled package.....However I found some strange result on my system,,,,so I type like this [revival at localhost ~]$ source ~/.bashrc bash: TMOUT: readonly variable Then I try to type xcrysden,,,,and this is the result : [revival at localhost ~]$ 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: 1.5.17 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/. TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared XCRYSDEN_SCRATCH=/home/revival/xcrys_temp Running on platform: unix Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 14571 Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null I can not understand the meaning of the error message written above.....Is it mean that something is missing with the $XCRYSDEN_TOPDIR and $XCRYSDEN_SCRATCH??? I think I need a help again to figure out what's wrong with my way of installation....... Thanks so much for everyone who helps until now GBU Date: Tue, 26 Jan 2010 17:40:48 +0800 From: bingmou2004 at gmail.com To: tone.kokalj at ijs.si; xcrysden at democritos.it Subject: Re: [xcrysden] Installation of xcrysden Follow the big boss Tone Kokalj and I hope you get what you want. 2010/1/26 Tone Kokalj On Tue, 2010-01-26 at 15:18 +0700, Fendy Lovefaith wrote: > Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list > > > I'm so honored to receive many replies for the installation of > XCrysden,,,,so I have download the tar file for for 32-bit linux: > http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz > > > and then I update the info in /.bashrc file like below > > > #------------------------------------------------------------------------ > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/ scripts: > $XCRYSDEN_TOPDIR/util" if your xcrysden is really in /home/revival/XCrySDen-1.5.17-bin-semishared, then all you need to do is: source ~/.bashrc xcrysden That's all. You don't need any make files, because xc-1.5.17-linux_x86-semishared.tar.gz is already compiled package. 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 -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science New Windows 7: Find the right PC for you. Learn more. _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100206/dece22ed/attachment-0001.htm From bingmou2004 at gmail.com Sat Feb 6 13:47:29 2010 From: bingmou2004 at gmail.com (=?GB2312?B?s8LOsOnE?=) Date: Sat, 6 Feb 2010 20:47:29 +0800 Subject: [xcrysden] Installation of xcrysden In-Reply-To: References: <1264441421.5857.47.camel@walk.ijs.si> <1264497327.12843.1.camel@walk.ijs.si> Message-ID: It's weird! Line 211 in bash file xcrysden is for cygwin not Linux and you shouldn't execute this line when your system is Unix ! Is there a file named "xcrys.dll" in your bin directory in Xcrysden directory? ? 2010?2?6? ??7:11?Fendy Lovefaith ??? > Dear ??? > > I'm sure the the enviroment variables XCRYSDEN_TOPDIR XCRYSDEN_SCRATCHhave been set right in ~/.bashrc,,,,,here is the profile of ~/.bashrc > > #------------------------------------------------------------------------ > # this is for XCRYSDEN 1.5.17; added by XCRYSDEN installation on > # Sat Feb 6 18:53:17 CST 2010 > > #------------------------------------------------------------------------ > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" > > After that I try your suggestion to clean the ~/xcrys/temp using > xc_cleanscratch and this is what happen : > > [revival at localhost scripts]$ > xc_cleanscratch > > > XCRYSDEN_SCRATCH directory: /home/revival/xcrys_temp/ will be cleaned > (i.e. rm -rf /home/revival/xcrys_temp/xc_*). > > The following files/directories will be deleted: > > /home/revival/xcrys_temp/xc_12460: > /home/revival/xcrys_temp/xc_16975: > /home/revival/xcrys_temp/xc_18305: > /home/revival/xcrys_temp/xc_8401: > > Really delete? ([y]es/[n]o) y > > Deleting /home/revival/xcrys_temp/xc_* ... OK > > But again something strange when I want to source out the .bashrc > > > [revival at localhost scripts]$ source ~/.bashrc > bash: TMOUT: readonly variable > > Then I type again the execute command xcrysden and this is happen again : > > [revival at localhost scripts]$ 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: 1.5.17 > > 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/. > > > TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > > Running on platform: unix > Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit > /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 19666 > Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys > ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH > $ARGS > /dev/null > > How do you think??? > > Perhaps something wrong with the bash profile??? > > Thanks ??? ,,and ,,Anton Kokalj,,,,,your helps really affects > much............I'm sure soon the XCRYSDEN can be run in my system > > GBU > > ------------------------------ > Date: Sat, 6 Feb 2010 14:41:27 +0800 > From: bingmou2004 at gmail.com > To: xcrysden at democritos.it > > Subject: Re: [xcrysden] Installation of xcrysden > > try to read the end of your ~/.bashrc and found whether the enviroment > variables XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH have been set right. I guess > Xcrysden didn't write anything to your bashrc to set the approximate value > and when you started your xcrysden, it used the default values. However > maybe there's ~/xcrys/temp in your home directory---that's why error > happened. > Hope it's useful for you! > > > ? 2010?2?6? ??12:40?Fendy Lovefaith ??? > > Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list > > I have returned now and I read the email from ??? and the big boss Anton > Kokalj,,,, > > Now I understand that the xc-1.5.17-linux_x86-semishared.tar.gz is a > compiled package.....However I found some strange result on my system,,,,so > I type like this > > [revival at localhost ~]$ source ~/.bashrc > bash: TMOUT: readonly variable > > Then I try to type xcrysden,,,,and this is the result : > > [revival at localhost ~]$ 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: 1.5.17 > > 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/. > > > TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 > > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > > Running on platform: unix > Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit > /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 14571 > Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys > ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH > $ARGS > /dev/null > > I can not understand the meaning of the error message written above.....Is > it mean that something is missing with the $XCRYSDEN_TOPDIR and > $XCRYSDEN_SCRATCH??? > > I think I need a help again to figure out what's wrong with my way of > installation....... > > Thanks so much for everyone who helps until now > > GBU > ------------------------------ > Date: Tue, 26 Jan 2010 17:40:48 +0800 > From: bingmou2004 at gmail.com > To: tone.kokalj at ijs.si; xcrysden at democritos.it > > Subject: Re: [xcrysden] Installation of xcrysden > > Follow the big boss Tone Kokalj and I hope you get what you want. > > 2010/1/26 Tone Kokalj > > On Tue, 2010-01-26 at 15:18 +0700, Fendy Lovefaith wrote: > > Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list > > > > > > I'm so honored to receive many replies for the installation of > > XCrysden,,,,so I have download the tar file for for 32-bit linux: > > http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz > > > > > > and then I update the info in /.bashrc file like below > > > > > > #------------------------------------------------------------------------ > > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/ scripts: > > $XCRYSDEN_TOPDIR/util" > > if your xcrysden is really > in /home/revival/XCrySDen-1.5.17-bin-semishared, then all you need to do > is: > > source ~/.bashrc > xcrysden > > That's all. You don't need any make files, because > xc-1.5.17-linux_x86-semishared.tar.gz is already compiled package. > > 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 > > > > > -- > ??? > Chen Weibing > ????????????????? > The State Key Laboratory for Superlattices and Microstructures > Institute of Semiconductor, Chinese Academy of Science > > > ------------------------------ > New Windows 7: Find the right PC for you. Learn more. > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > -- > ??? > Chen Weibing > ????????????????? > The State Key Laboratory for Superlattices and Microstructures > Institute of Semiconductor, Chinese Academy of Science > > > ------------------------------ > New Windows 7: Find the right PC for you. Learn more. > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100206/4f10d349/attachment-0001.htm From xyzfxbd at hotmail.com Sat Feb 6 15:15:53 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Sat, 6 Feb 2010 21:15:53 +0700 Subject: [xcrysden] Installation of xcrysden In-Reply-To: References: , <1264441421.5857.47.camel@walk.ijs.si>, , <1264497327.12843.1.camel@walk.ijs.si>, , , , , Message-ID: Dear ??? I find the file xcrys in the bin directory but is it the same with xcrys.dll??? Here the command line : [revival at localhost XCrySDen-1.5.17-bin-semishared]$ cd bin/ [revival at localhost bin]$ ls atomlab* fhi_coord2xcr* fsReadBXSF* kPath* pwi2xsf* recvec* wn_readbakgen* xctclsh* calplane* fhi_inpini2ftn34* ftnunit* multislab* pwi2xsf_old* savestruct* wn_readbands* xsf2xsf* cube2xsf* fracCoor* gengeom* nn* pwKPath* str2xcr* xcrys* How do you think ?????? Thanks before.....GBU Date: Sat, 6 Feb 2010 20:47:29 +0800 From: bingmou2004 at gmail.com To: xcrysden at democritos.it Subject: Re: [xcrysden] Installation of xcrysden It's weird! Line 211 in bash file xcrysden is for cygwin not Linux and you shouldn't execute this line when your system is Unix ! Is there a file named "xcrys.dll" in your bin directory in Xcrysden directory? ? 2010?2?6? ??7:11?Fendy Lovefaith ??? Dear ??? I'm sure the the enviroment variables XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH have been set right in ~/.bashrc,,,,,here is the profile of ~/.bashrc #------------------------------------------------------------------------ # this is for XCRYSDEN 1.5.17; added by XCRYSDEN installation on # Sat Feb 6 18:53:17 CST 2010 #------------------------------------------------------------------------ XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared XCRYSDEN_SCRATCH=/home/revival/xcrys_temp export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" After that I try your suggestion to clean the ~/xcrys/temp using xc_cleanscratch and this is what happen : [revival at localhost scripts]$ xc_cleanscratch XCRYSDEN_SCRATCH directory: /home/revival/xcrys_temp/ will be cleaned (i.e. rm -rf /home/revival/xcrys_temp/xc_*). The following files/directories will be deleted: /home/revival/xcrys_temp/xc_12460: /home/revival/xcrys_temp/xc_16975: /home/revival/xcrys_temp/xc_18305: /home/revival/xcrys_temp/xc_8401: Really delete? ([y]es/[n]o) y Deleting /home/revival/xcrys_temp/xc_* ... OK But again something strange when I want to source out the .bashrc [revival at localhost scripts]$ source ~/.bashrc bash: TMOUT: readonly variable Then I type again the execute command xcrysden and this is happen again : [revival at localhost scripts]$ 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: 1.5.17 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/. TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared XCRYSDEN_SCRATCH=/home/revival/xcrys_temp Running on platform: unix Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 19666 Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null How do you think??? Perhaps something wrong with the bash profile??? Thanks ??? ,,and ,,Anton Kokalj,,,,,your helps really affects much............I'm sure soon the XCRYSDEN can be run in my system GBU Date: Sat, 6 Feb 2010 14:41:27 +0800 From: bingmou2004 at gmail.com To: xcrysden at democritos.it Subject: Re: [xcrysden] Installation of xcrysden try to read the end of your ~/.bashrc and found whether the enviroment variables XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH have been set right. I guess Xcrysden didn't write anything to your bashrc to set the approximate value and when you started your xcrysden, it used the default values. However maybe there's ~/xcrys/temp in your home directory---that's why error happened. Hope it's useful for you! ? 2010?2?6? ??12:40?Fendy Lovefaith ??? Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list I have returned now and I read the email from ??? and the big boss Anton Kokalj,,,, Now I understand that the xc-1.5.17-linux_x86-semishared.tar.gz is a compiled package.....However I found some strange result on my system,,,,so I type like this [revival at localhost ~]$ source ~/.bashrc bash: TMOUT: readonly variable Then I try to type xcrysden,,,,and this is the result : [revival at localhost ~]$ 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: 1.5.17 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/. TCL_LIBRARY=/home/revival/XCrySDen-1.5.17-bin-semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared XCRYSDEN_SCRATCH=/home/revival/xcrys_temp Running on platform: unix Executing: /home/revival/XCrySDen-1.5.17-bin-semishared/bin/ftnunit /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 14571 Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null I can not understand the meaning of the error message written above.....Is it mean that something is missing with the $XCRYSDEN_TOPDIR and $XCRYSDEN_SCRATCH??? I think I need a help again to figure out what's wrong with my way of installation....... Thanks so much for everyone who helps until now GBU Date: Tue, 26 Jan 2010 17:40:48 +0800 From: bingmou2004 at gmail.com To: tone.kokalj at ijs.si; xcrysden at democritos.it Subject: Re: [xcrysden] Installation of xcrysden Follow the big boss Tone Kokalj and I hope you get what you want. 2010/1/26 Tone Kokalj On Tue, 2010-01-26 at 15:18 +0700, Fendy Lovefaith wrote: > Dear ??? ,,,,Anton Kokalj,,,,and XCrysden mailing list > > > I'm so honored to receive many replies for the installation of > XCrysden,,,,so I have download the tar file for for 32-bit linux: > http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz > > > and then I update the info in /.bashrc file like below > > > #------------------------------------------------------------------------ > XCRYSDEN_TOPDIR=/home/revival/XCrySDen-1.5.17-bin-semishared > XCRYSDEN_SCRATCH=/home/revival/xcrys_temp > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/ scripts: > $XCRYSDEN_TOPDIR/util" if your xcrysden is really in /home/revival/XCrySDen-1.5.17-bin-semishared, then all you need to do is: source ~/.bashrc xcrysden That's all. You don't need any make files, because xc-1.5.17-linux_x86-semishared.tar.gz is already compiled package. 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 -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science New Windows 7: Find the right PC for you. Learn more. _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science New Windows 7: Find the right PC for you. Learn more. _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science _________________________________________________________________ Windows Live: Friends get your Flickr, Yelp, and Digg updates when they e-mail you. http://www.microsoft.com/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-id:SI_SB_3:092010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100206/63a4f1a8/attachment-0001.htm From paulatto at sissa.it Sat Feb 6 20:42:00 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 6 Feb 2010 20:42:00 +0100 Subject: [xcrysden] Installation of xcrysden In-Reply-To: References: , <1264441421.5857.47.camel@walk.ijs.si>, , <1264497327.12843.1.camel@walk.ijs.si>, , , , , Message-ID: <20100206204200.s9aflig2ds8oo8wk@webmail.sissa.it> > /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: > 19666 Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys > ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR > $XCRYSDEN_SCRATCH $ARGS > /dev/null I think you've met the same problem I've had and solved about one year ago. Have a look at this mailing list post: cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From xyzfxbd at hotmail.com Sun Feb 7 11:49:19 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Sun, 7 Feb 2010 17:49:19 +0700 Subject: [xcrysden] Installation of xcrysden [SOLVED] In-Reply-To: <20100206204200.s9aflig2ds8oo8wk@webmail.sissa.it> References: , , <1264441421.5857.47.camel@walk.ijs.si>, , , , <1264497327.12843.1.camel@walk.ijs.si>, , , , , , , , , , , , <20100206204200.s9aflig2ds8oo8wk@webmail.sissa.it> Message-ID: Dear Lorenzo Paulatto Woow,,,,you really save the day,,,,I try your suggestion and it works,,,,AMAZING..........I just put unset MALLOC_CHECK_ in the first line of xcrysden file and everything works well......Now I can play around with xcrysden I think now it's better we put some information in xcrysden website about this so that someone in the future will not repeat the same mistake Because I already change the subject title and I add [SOLVED],,,I write the easiest step to install xcrysden in linux system as follows : 1. We need to download one of the following: +) for 32-bit linux: http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz +) for 64-bit linux: http://www.xcrysden.org/download/xc-1.5.21-linux_x86_64-semishared.tar.gz +) for cygwin: http://www.xcrysden.org/download/xc-1.5.18-cygwin-shared.tar.gz 2. For any of this package, all we need to do is to unpack it, i.e., tar zxvf filename.tgz3. In the command line,,,inside the directory of the xcrysden that we have download,,,execute ./xcConfigure and be sure to update xcrysden info in the ~/.bashrc to point to the xcyrsden directory 4. Edit the xcrysden file and add the unset MALLOC_CHECK_ in the beginning of xcrysden file 5. In the command line type xcrysden to start the xcrysden Thanks everyone especially ???, Anton Kokalj, Lorenzo Paulatto and xcrysden mailing list.........I learn a lot from this mailing list GBU Date: Sat, 6 Feb 2010 20:42:00 +0100 > From: paulatto at sissa.it > To: xcrysden at democritos.it > Subject: Re: [xcrysden] Installation of xcrysden > > > /home/revival/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: > > 19666 Aborted ${XCRYSDEN_TOPDIR}/bin/xcrys > > ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR > > $XCRYSDEN_SCRATCH $ARGS > /dev/null > > I think you've met the same problem I've had and solved about one year > ago. Have a look at this mailing list post: > > > cheers > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100207/80a891db/attachment.htm From erwin.rossen at gmail.com Wed Feb 10 12:19:17 2010 From: erwin.rossen at gmail.com (Erwin Rossen) Date: Wed, 10 Feb 2010 12:19:17 +0100 Subject: [xcrysden] please I need a help In-Reply-To: <1265386066.15638.4.camel@walk.ijs.si> References: <592647.76575.qm@web23004.mail.ird.yahoo.com> <1265386066.15638.4.camel@walk.ijs.si> Message-ID: <6c58d9361002100319l51d623aan915dbf5fec39314f@mail.gmail.com> Hello! I have an xyz file which starts with: 52 # atoms within limits=cell_PL Ag 0.000000 0.000000 0.000000 Ag 1.467250 -0.847120 2.396000 Ag -1.467250 -0.847120 2.396000 Ag 0.000000 1.694230 2.396000 Ag -1.467250 0.847110 4.792010 Ag 0.000000 -1.694230 4.792010 .... XCrySDen does not open this. How should I change the header such that XCrySDen can open it? Best, Erwin Rossen From giovanni.cantele at na.infn.it Wed Feb 10 12:38:48 2010 From: giovanni.cantele at na.infn.it (Giovanni Cantele) Date: Wed, 10 Feb 2010 12:38:48 +0100 Subject: [xcrysden] please I need a help In-Reply-To: <6c58d9361002100319l51d623aan915dbf5fec39314f@mail.gmail.com> References: <592647.76575.qm@web23004.mail.ird.yahoo.com> <1265386066.15638.4.camel@walk.ijs.si> <6c58d9361002100319l51d623aan915dbf5fec39314f@mail.gmail.com> Message-ID: <0812DE4D-9885-4937-974D-172D136A81A0@na.infn.it> not sure but I think that xyz file format requires a blank line after the first one (the one containing the number of atoms). Giovanni On Feb 10, 2010, at 12:19 PM, Erwin Rossen wrote: > Hello! > > I have an xyz file which starts with: > > 52 # atoms within limits=cell_PL > Ag 0.000000 0.000000 0.000000 > Ag 1.467250 -0.847120 2.396000 > Ag -1.467250 -0.847120 2.396000 > Ag 0.000000 1.694230 2.396000 > Ag -1.467250 0.847110 4.792010 > Ag 0.000000 -1.694230 4.792010 > .... > > XCrySDen does not open this. How should I change the header such that > XCrySDen can open it? > > Best, > Erwin Rossen > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100210/f6b05ccc/attachment.htm From erwin.rossen at gmail.com Wed Feb 10 13:46:21 2010 From: erwin.rossen at gmail.com (Erwin Rossen) Date: Wed, 10 Feb 2010 13:46:21 +0100 Subject: [xcrysden] please I need a help In-Reply-To: <0812DE4D-9885-4937-974D-172D136A81A0@na.infn.it> References: <592647.76575.qm@web23004.mail.ird.yahoo.com> <1265386066.15638.4.camel@walk.ijs.si> <6c58d9361002100319l51d623aan915dbf5fec39314f@mail.gmail.com> <0812DE4D-9885-4937-974D-172D136A81A0@na.infn.it> Message-ID: <6c58d9361002100446ua622de9va94685900c5fcbbc@mail.gmail.com> > not sure but I think that xyz file format requires a blank line after the > first one > (the one containing the number of atoms). > Giovanni That helped. Thanks! From John.Tse at usask.ca Sun Feb 14 21:31:00 2010 From: John.Tse at usask.ca (John S. Tse) Date: Sun, 14 Feb 2010 14:31:00 -0600 Subject: [xcrysden] XCrysden setup problem on WINDOW 7 In-Reply-To: References: Message-ID: <1266179460.4b785d8491ef2@webmail.usask.ca> Dear Netter. I have setup Cygwin on a new computer running WINDOW 7. However, when I tried to confgure and run xcrysden (both the 1.5.18 and 1.4.1 version), I encountered the following errors ... ./xcConfigure.sh: line 2: $'\r': command not found ./xcConfigure.sh: line 3: syntax error near unexpected token `$'{\r'' ./xcConfigure.sh: line 3: `InstallError () { ' ./xcrysden: line 2: $'\r': command not found ./xcrysden: line 21: $'\r': command not found ./xcrysden: line 41: syntax error near unexpected token `$'do\r'' ./xcrysden: line 41: ` do ' I have not encounetered any problem when installing on an old WINDOW XP Any help is appreciated. John Dr. John S. Tse Department of Physics and Engineering Physics University of Saskatchewan 116 Science Place Saskatoon, SK S7N 5E2 Canada Quoting xcrysden-request at democritos.it: > 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: Consulting (Lorenzo Paulatto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 02 Dec 2009 09:51:30 +0100 > From: "Lorenzo Paulatto" > Subject: Re: [xcrysden] Consulting > To: "XCrySDen mailing list" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > Replying to message "[xcrysden] Consulting" from sd.wang000 (02/12/09): > > I am Ph.D in Southeast University,Nanjing,China.I want to kwon the unit > > of the contour of electron density of XcrysDen.Is it e/Angstrum3 or > > e/Bhor3 ? > > Dear S.D.Wang, > I think it does not depend on XCrysDen, which just keeps the same unit of > measure as in the data file you loaded. > > best regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 23, Issue 3 > *************************************** > From xyzfxbd at hotmail.com Fri Feb 19 06:32:02 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Fri, 19 Feb 2010 12:32:02 +0700 Subject: [xcrysden] Error printing to JPEG Message-ID: Dear everyone I open a xsf structure file and I try to print it to JPEG file but some error occurred......This is the error message : ERROR : while executing exec /usr/bin/convert /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file konversi/LOCPOT.jpg I'm sure I have installed ImageMagick-6.5.6-10 and I have the exec file in /usr/bin/convert,,,,,and I already change the ~/.xcrysden/custom-definitions file and I add two line like below set xcMisc(ImageMagick.convert) /usr/bin/convert set xcMisc(ImageMagick.convertOptions) "-quality 90 -antialias \ -blur 1x1 -trim -bordercolor white \ -border 20x20 -bordercolor black -border 3x3" Has anyone knowed how to fix this problem??? Perhaps someone used to have the same problem with me Thanks so much everyone GBU _________________________________________________________________ NEW! Get Windows Live FREE. http://www.get.live.com/wl/all -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100219/919327af/attachment.htm From sclauzer at sissa.it Fri Feb 19 11:08:20 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 19 Feb 2010 11:08:20 +0100 Subject: [xcrysden] Error printing to JPEG In-Reply-To: References: Message-ID: <4B7E6314.8060105@sissa.it> Dear Fendy, Fendy Lovefaith wrote: > Dear everyone > > I open a xsf structure file and I try to print it to JPEG file but some > error occurred......This is the error message : > > ERROR : while executing exec /usr/bin/convert > /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file > konversi/LOCPOT.jpg > > I'm sure I have installed ImageMagick-6.5.6-10 and I have the exec file > in /usr/bin/convert,,,,,and I already change the > ~/.xcrysden/|custom-definitions file and I add two line like below| > > set xcMisc(ImageMagick.convert) /usr/bin/convert In my custom-definitions file I have this line set xcMisc(ImageMagick.converter) /usr/bin/convert and it seems to work. So you could try to replace ImageMagick.convert -> ImageMagick.converter in your file. Good luck ;-) GS > set xcMisc(ImageMagick.convertOptions) "-quality 90 -antialias \ > -blur 1x1 -trim -bordercolor white \ > -border 20x20 -bordercolor black -border 3x3" > > > Has anyone knowed how to fix this problem??? Perhaps someone used to > have the same problem with me > > Thanks so much everyone > > GBU -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From xyzfxbd at hotmail.com Fri Feb 19 12:21:44 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Fri, 19 Feb 2010 18:21:44 +0700 Subject: [xcrysden] Error printing to JPEG In-Reply-To: <4B7E6314.8060105@sissa.it> References: , <4B7E6314.8060105@sissa.it> Message-ID: Dear Gabriele Sclauzero and everyone I have try your suggestion to change the set xcMisc(ImageMagick.convert) /usr/bin/convert with set xcMisc(ImageMagick.converter) /usr/bin/convert but still,,,,I can't print the xsf structure in JPEG format,,,,,,the same error message appear as before......... Is there something wrong with the ImageMagick??? Thanks Gabriele Sclauzero and everyone GBU > Date: Fri, 19 Feb 2010 11:08:20 +0100 > From: sclauzer at sissa.it > To: xcrysden at democritos.it > Subject: Re: [xcrysden] Error printing to JPEG > > Dear Fendy, > > Fendy Lovefaith wrote: > > Dear everyone > > > > I open a xsf structure file and I try to print it to JPEG file but some > > error occurred......This is the error message : > > > > ERROR : while executing exec /usr/bin/convert > > /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file > > konversi/LOCPOT.jpg > > > > I'm sure I have installed ImageMagick-6.5.6-10 and I have the exec file > > in /usr/bin/convert,,,,,and I already change the > > ~/.xcrysden/|custom-definitions file and I add two line like below| > > > > set xcMisc(ImageMagick.convert) /usr/bin/convert > > In my custom-definitions file I have this line > set xcMisc(ImageMagick.converter) /usr/bin/convert > and it seems to work. > So you could try to replace ImageMagick.convert -> ImageMagick.converter in your file. > > Good luck ;-) > > > GS > > > set xcMisc(ImageMagick.convertOptions) "-quality 90 -antialias \ > > -blur 1x1 -trim -bordercolor white \ > > -border 20x20 -bordercolor black -border 3x3" > > > > > > Has anyone knowed how to fix this problem??? Perhaps someone used to > > have the same problem with me > > > > Thanks so much everyone > > > > GBU > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden _________________________________________________________________ Windows Live: Friends get your Flickr, Yelp, and Digg updates when they e-mail you. http://www.microsoft.com/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-id:SI_SB_3:092010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100219/0c66cac2/attachment.htm From sclauzer at sissa.it Fri Feb 19 13:33:17 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 19 Feb 2010 13:33:17 +0100 Subject: [xcrysden] Error printing to JPEG In-Reply-To: References: , <4B7E6314.8060105@sissa.it> Message-ID: <4B7E850D.4070205@sissa.it> It is difficult to help you without any further information, you should specify at least which version of xcrysden you are using. Fendy Lovefaith wrote: > > Dear Gabriele Sclauzero and everyone > > I have try your suggestion to change the > > set xcMisc(ImageMagick.convert) /usr/bin/convert > > with > > set xcMisc(ImageMagick.converter) /usr/bin/convert > > but still,,,,I can't print the xsf structure in JPEG format,,,,,,the > same error message appear as before......... > > Is there something wrong with the ImageMagick??? Have you tried to save in ppm format and then convert from command line with Image Magick's convert? Does it work? GS > > Thanks Gabriele Sclauzero and everyone > > GBU > > > Date: Fri, 19 Feb 2010 11:08:20 +0100 > > From: sclauzer at sissa.it > > To: xcrysden at democritos.it > > Subject: Re: [xcrysden] Error printing to JPEG > > > > Dear Fendy, > > > > Fendy Lovefaith wrote: > > > Dear everyone > > > > > > I open a xsf structure file and I try to print it to JPEG file but > some > > > error occurred......This is the error message : > > > > > > ERROR : while executing exec /usr/bin/convert > > > /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file > > > konversi/LOCPOT.jpg > > > > > > I'm sure I have installed ImageMagick-6.5.6-10 and I have the exec > file > > > in /usr/bin/convert,,,,,and I already change the > > > ~/.xcrysden/|custom-definitions file and I add two line like below| > > > > > > set xcMisc(ImageMagick.convert) /usr/bin/convert > > > > In my custom-definitions file I have this line > > set xcMisc(ImageMagick.converter) /usr/bin/convert > > and it seems to work. > > So you could try to replace ImageMagick.convert -> > ImageMagick.converter in your file. > > > > Good luck ;-) > > > > > > GS > > > > > set xcMisc(ImageMagick.convertOptions) "-quality 90 -antialias \ > > > -blur 1x1 -trim -bordercolor white \ > > > -border 20x20 -bordercolor black -border 3x3" > > > > > > > > > Has anyone knowed how to fix this problem??? Perhaps someone used to > > > have the same problem with me > > > > > > Thanks so much everyone > > > > > > GBU > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > ------------------------------------------------------------------------ > Chat online and in real-time with friends and family! Windows Live > Messenger > > > ------------------------------------------------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From xyzfxbd at hotmail.com Fri Feb 19 14:13:24 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Fri, 19 Feb 2010 20:13:24 +0700 Subject: [xcrysden] Error printing to JPEG In-Reply-To: <4B7E850D.4070205@sissa.it> References: , , <4B7E6314.8060105@sissa.it>, , <4B7E850D.4070205@sissa.it> Message-ID: Dear Gabriele Sclauzero and everyone I'm sorry I forgot to inform that I install XCrySDen-1.5.17-bin-semishared for linux 32 bit on Mandriva linux system,,,,,and I already install the ImageMagick-6.5.6-10 Please inform me if I forgot some important information,,,, Thanks so much GBU > Date: Fri, 19 Feb 2010 13:33:17 +0100 > From: sclauzer at sissa.it > To: xcrysden at democritos.it > Subject: Re: [xcrysden] Error printing to JPEG > > It is difficult to help you without any further information, you should specify at least > which version of xcrysden you are using. > > > Fendy Lovefaith wrote: > > > > Dear Gabriele Sclauzero and everyone > > > > I have try your suggestion to change the > > > > set xcMisc(ImageMagick.convert) /usr/bin/convert > > > > with > > > > set xcMisc(ImageMagick.converter) /usr/bin/convert > > > > but still,,,,I can't print the xsf structure in JPEG format,,,,,,the > > same error message appear as before......... > > > > Is there something wrong with the ImageMagick??? > > Have you tried to save in ppm format and then convert from command line with Image > Magick's convert? Does it work? > > GS > > > > > > > Thanks Gabriele Sclauzero and everyone > > > > GBU > > > > > Date: Fri, 19 Feb 2010 11:08:20 +0100 > > > From: sclauzer at sissa.it > > > To: xcrysden at democritos.it > > > Subject: Re: [xcrysden] Error printing to JPEG > > > > > > Dear Fendy, > > > > > > Fendy Lovefaith wrote: > > > > Dear everyone > > > > > > > > I open a xsf structure file and I try to print it to JPEG file but > > some > > > > error occurred......This is the error message : > > > > > > > > ERROR : while executing exec /usr/bin/convert > > > > /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file > > > > konversi/LOCPOT.jpg > > > > > > > > I'm sure I have installed ImageMagick-6.5.6-10 and I have the exec > > file > > > > in /usr/bin/convert,,,,,and I already change the > > > > ~/.xcrysden/|custom-definitions file and I add two line like below| > > > > > > > > set xcMisc(ImageMagick.convert) /usr/bin/convert > > > > > > In my custom-definitions file I have this line > > > set xcMisc(ImageMagick.converter) /usr/bin/convert > > > and it seems to work. > > > So you could try to replace ImageMagick.convert -> > > ImageMagick.converter in your file. > > > > > > Good luck ;-) > > > > > > > > > GS > > > > > > > set xcMisc(ImageMagick.convertOptions) "-quality 90 -antialias \ > > > > -blur 1x1 -trim -bordercolor white \ > > > > -border 20x20 -bordercolor black -border 3x3" > > > > > > > > > > > > Has anyone knowed how to fix this problem??? Perhaps someone used to > > > > have the same problem with me > > > > > > > > Thanks so much everyone > > > > > > > > GBU > > > > > > -- > > > > > > > > > o ------------------------------------------------ o > > > | Gabriele Sclauzero, PhD Student | > > > | c/o: SISSA & CNR-INFM Democritos, | > > > | via Beirut 2-4, 34014 Trieste (Italy) | > > > | email: sclauzer at sissa.it | > > > | phone: +39 040 3787 511 | > > > | skype: gurlonotturno | > > > o ------------------------------------------------ o > > > _______________________________________________ > > > XCrySDen mailing list > > > XCrySDen at democritos.it > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > ------------------------------------------------------------------------ > > Chat online and in real-time with friends and family! Windows Live > > Messenger > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden _________________________________________________________________ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100219/3c565176/attachment-0001.htm From tone.kokalj at ijs.si Fri Feb 19 19:27:56 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 19 Feb 2010 19:27:56 +0100 Subject: [xcrysden] XCrysden setup problem on WINDOW 7 In-Reply-To: <1266179460.4b785d8491ef2@webmail.usask.ca> References: <1266179460.4b785d8491ef2@webmail.usask.ca> Message-ID: <1266604077.23543.7.camel@walk.ijs.si> On Sun, 2010-02-14 at 14:31 -0600, John S. Tse wrote: > Dear Netter. > > I have setup Cygwin on a new computer running WINDOW 7. However, when I tried > to confgure and run xcrysden (both the 1.5.18 and 1.4.1 version), I encountered > the following errors ... For the 1.5.18 version of xcrysden you can simply skip the xcConfigure step of installation. Simply put the root directory of xcrysden to your PATH or else you have to run it as /full/path/to/xcrysden (I belive the meaning of the /full/path/to is clear). As a quick check (for 1.5.18): 1) delete all xcrysden entries from ~/.bashrc file 2) reload the cygwin 3) go to the xcrysden root directory 4) and execute: ./xcrysden Does it 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 tone.kokalj at ijs.si Fri Feb 19 19:34:14 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 19 Feb 2010 19:34:14 +0100 Subject: [xcrysden] Error printing to JPEG In-Reply-To: <4B7E6314.8060105@sissa.it> References: <4B7E6314.8060105@sissa.it> Message-ID: <1266604454.23543.12.camel@walk.ijs.si> On Fri, 2010-02-19 at 11:08 +0100, Gabriele Sclauzero wrote: > Dear Fendy, > > Fendy Lovefaith wrote: > > Dear everyone > > > > I open a xsf structure file and I try to print it to JPEG file but some > > error occurred......This is the error message : > > > > ERROR : while executing exec /usr/bin/convert > > /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file > > konversi/LOCPOT.jpg > > > > I'm sure I have installed ImageMagick-6.5.6-10 and I have the exec file > > in /usr/bin/convert,,,,,and I already change the > > ~/.xcrysden/|custom-definitions file and I add two line like below| > > > > set xcMisc(ImageMagick.convert) /usr/bin/convert > > In my custom-definitions file I have this line > set xcMisc(ImageMagick.converter) /usr/bin/convert > and it seems to work. This is wrong. The proper variable name is xcMisc(ImageMagick.convert) and not "converter". The reason it works is because the 1.5.* version finds the packages automatically, and the specification of xcMisc(ImageMagick.convert) is redundant (or optional). Fendy, did you check that your ImageMagick indeed works as expected? Find a given, say PNG, graphics file and try to convert it manually as: convert file.png file.jpg Does it work? If it does then you may try to convert some PPM file (i.e. take it from xcrysden scratch directory, e.g., /home/revival/xcrys_temp/xc_****/tmp.ppm) 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 xyzfxbd at hotmail.com Sun Feb 21 11:57:31 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Sun, 21 Feb 2010 17:57:31 +0700 Subject: [xcrysden] Error printing to JPEG In-Reply-To: <1266604454.23543.12.camel@walk.ijs.si> References: , <4B7E6314.8060105@sissa.it>, <1266604454.23543.12.camel@walk.ijs.si> Message-ID: Dear Anton Kokalj and xcrysden mailing list I try to convert a png file to jpg file and it works very well,,,,,and then I try to convert some ppm file from xcrys_temp and it also works very well too !!!!!! Now I have the jpg file on my hand,,,,,so that means I need to do it manually every time I want to print to jpg format,,,,is that right??? Is there any other solution to convert the file automatically from xcrysden??? Thanks so much to Anton Kokalj for giving smart idea,,,,, GBU > From: tone.kokalj at ijs.si > To: xcrysden at democritos.it > Date: Fri, 19 Feb 2010 19:34:14 +0100 > Subject: Re: [xcrysden] Error printing to JPEG > > On Fri, 2010-02-19 at 11:08 +0100, Gabriele Sclauzero wrote: > > Dear Fendy, > > > > Fendy Lovefaith wrote: > > > Dear everyone > > > > > > I open a xsf structure file and I try to print it to JPEG file but some > > > error occurred......This is the error message : > > > > > > ERROR : while executing exec /usr/bin/convert > > > /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file > > > konversi/LOCPOT.jpg > > > > > > I'm sure I have installed ImageMagick-6.5.6-10 and I have the exec file > > > in /usr/bin/convert,,,,,and I already change the > > > ~/.xcrysden/|custom-definitions file and I add two line like below| > > > > > > set xcMisc(ImageMagick.convert) /usr/bin/convert > > > > In my custom-definitions file I have this line > > set xcMisc(ImageMagick.converter) /usr/bin/convert > > and it seems to work. > > This is wrong. The proper variable name is xcMisc(ImageMagick.convert) > and not "converter". The reason it works is because the 1.5.* version > finds the packages automatically, and the specification of > xcMisc(ImageMagick.convert) is redundant (or optional). > > Fendy, did you check that your ImageMagick indeed works as expected? > Find a given, say PNG, graphics file and try to convert it manually as: > > convert file.png file.jpg > > Does it work? If it does then you may try to convert some PPM file > (i.e. take it from xcrysden scratch directory, > e.g., /home/revival/xcrys_temp/xc_****/tmp.ppm) > > 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 _________________________________________________________________ Windows Live: Friends get your Flickr, Yelp, and Digg updates when they e-mail you. http://www.microsoft.com/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-id:SI_SB_3:092010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100221/e94badd1/attachment.htm From tone.kokalj at ijs.si Mon Feb 22 09:06:47 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 22 Feb 2010 09:06:47 +0100 Subject: [xcrysden] Error printing to JPEG In-Reply-To: References: , <4B7E6314.8060105@sissa.it>, <1266604454.23543.12.camel@walk.ijs.si> Message-ID: <1266826007.4026.7.camel@walk.ijs.si> On Sun, 2010-02-21 at 17:57 +0700, Fendy Lovefaith wrote: > Dear Anton Kokalj and xcrysden mailing list > > I try to convert a png file to jpg file and it works very well,,,,,and > then I try to convert some ppm file from xcrys_temp and it also works > very well too !!!!!! > > Now I have the jpg file on my hand,,,,,so that means I need to do it > manually every time I want to print to jpg format,,,,is that right??? No! That was just a test to see if the convert of ImageMagick works OK. Looking back into your original email, I realized the following: ERROR : while executing exec /usr/bin/convert /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file konversi/LOCPOT.jpg You have the whitespace in the directory path. This whitespace is likely the source of problem. Note that it is not recommended to have whitespaces in directory names in Unix-like OS. This can break many things. To verify whether this is really the source of the problem, you should execute some xcrysden example (i.e. File-->XCrySDen examples ...) from e.g. your home directory "/home/revival". Try to print into JPG then. 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 xyzfxbd at hotmail.com Tue Feb 23 05:31:08 2010 From: xyzfxbd at hotmail.com (Fendy Lovefaith) Date: Tue, 23 Feb 2010 11:31:08 +0700 Subject: [xcrysden] Error printing to JPEG [SOLVED] In-Reply-To: <1266826007.4026.7.camel@walk.ijs.si> References: ,, <4B7E6314.8060105@sissa.it>, <1266604454.23543.12.camel@walk.ijs.si>, , <1266826007.4026.7.camel@walk.ijs.si> Message-ID: Dear Anton Kokalj and xcrysden mailing list I had 100% succeeded to print xcrysden examples file into png type file or even to jpeg type file,,,,, When I move my file to another directory that do not contain space,,,,,xcrysden also works very well to print into jpeg format,,,,,, so the error is actually because the space I use in my directory,,,, I learn now not to name the directory with space if I'm using Unix-like OS,,,, Thanks Anton Kokalj for informing my unawareness,,,,,I hope others could also learn from my mistakes in this thread GBU > From: tone.kokalj at ijs.si > To: xcrysden at democritos.it > Date: Mon, 22 Feb 2010 09:06:47 +0100 > Subject: Re: [xcrysden] Error printing to JPEG > > On Sun, 2010-02-21 at 17:57 +0700, Fendy Lovefaith wrote: > > Dear Anton Kokalj and xcrysden mailing list > > > > I try to convert a png file to jpg file and it works very well,,,,,and > > then I try to convert some ppm file from xcrys_temp and it also works > > very well too !!!!!! > > > > Now I have the jpg file on my hand,,,,,so that means I need to do it > > manually every time I want to print to jpg format,,,,is that right??? > > No! > > That was just a test to see if the convert of ImageMagick works OK. > > > Looking back into your original email, I realized the following: > > ERROR : while executing exec /usr/bin/convert /home/revival/xcrys_temp/xc_5886/tmp.ppm /home/revival/File-file konversi/LOCPOT.jpg > > You have the whitespace in the directory path. This whitespace is > likely the source of problem. Note that it is not recommended to have > whitespaces in directory names in Unix-like OS. This can break many > things. > > To verify whether this is really the source of the problem, you should > execute some xcrysden example (i.e. File-->XCrySDen examples ...) from > e.g. your home directory "/home/revival". Try to print into JPG then. > > 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 _________________________________________________________________ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100223/485c38a9/attachment.htm From Irvin.Telepeni at nottingham.ac.uk Tue Feb 23 13:05:14 2010 From: Irvin.Telepeni at nottingham.ac.uk (Irvin Telepeni) Date: Tue, 23 Feb 2010 12:05:14 -0000 Subject: [xcrysden] How to remove previous xcrysden versions? Message-ID: <1E0CCC81FDE82D4C8DDE1A8F44080D944FB1C3@VUIEXCHA.ad.nottingham.ac.uk> Hi, I am trying to install xcrysden on my laptop (fedora12). First I've tried to install the pre-compiled version (XCrySDen-1.4.1bin-static), but then I changed my mind and wanted to go for the source code (XCrySDen-1.5.21-src-all). After multiple attempts, I eventually (i guess) manage to compile it. However, although it looks like the compilation is looking for some files from the pre-compiled version as shown below instead. Is it a case of removing completely the pre-compiled version? if yes how? XCrySDen-1.5.21-src-all]# xcrysden --xsf 1.xsf cat: /home/epzit/XCrySDen-1.4.1bin-static/version: No such file or directory +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2009 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 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/. /home/epzit/XCrySDen-1.5.21-src-all/xcrysden: line 166: /home/epzit/XCrySDen-1.4.1bin-static/scripts/xcLib.sh: No such file or directory Cheers, Irvin This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100223/4272a6f1/attachment.htm From Irvin.Telepeni at nottingham.ac.uk Tue Feb 23 13:34:05 2010 From: Irvin.Telepeni at nottingham.ac.uk (Irvin Telepeni) Date: Tue, 23 Feb 2010 12:34:05 -0000 Subject: [xcrysden] How to remove previous xcrysden versions? References: <1E0CCC81FDE82D4C8DDE1A8F44080D944FB1C3@VUIEXCHA.ad.nottingham.ac.uk> Message-ID: <1E0CCC81FDE82D4C8DDE1A8F44080D944FB1C4@VUIEXCHA.ad.nottingham.ac.uk> Hi, I found my own mistake. I had to rerun ~/.bashrc. I -----Original Message----- From: Telepeni Irvin Sent: Tue 23/02/2010 12:05 To: xcrysden at democritos.it Subject: How to remove previous xcrysden versions? Hi, I am trying to install xcrysden on my laptop (fedora12). First I've tried to install the pre-compiled version (XCrySDen-1.4.1bin-static), but then I changed my mind and wanted to go for the source code (XCrySDen-1.5.21-src-all). After multiple attempts, I eventually (i guess) manage to compile it. However, although it looks like the compilation is looking for some files from the pre-compiled version as shown below instead. Is it a case of removing completely the pre-compiled version? if yes how? XCrySDen-1.5.21-src-all]# xcrysden --xsf 1.xsf cat: /home/epzit/XCrySDen-1.4.1bin-static/version: No such file or directory +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2009 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 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/. /home/epzit/XCrySDen-1.5.21-src-all/xcrysden: line 166: /home/epzit/XCrySDen-1.4.1bin-static/scripts/xcLib.sh: No such file or directory Cheers, Irvin This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100223/0529541b/attachment.htm From dvdcwangcc at gmail.com Wed Feb 24 06:08:10 2010 From: dvdcwangcc at gmail.com (Chenchen Wang) Date: Wed, 24 Feb 2010 00:08:10 -0500 Subject: [xcrysden] vibrational frequency Message-ID: <74be62651002232108h5bb0b964s5bd1132af21b01f7@mail.gmail.com> Hi, I just start to use xcrysden and want to use it to visualize vibrational frequencies calculated from VASP.But I don't know how to do this.Can anyone help me with this? Thank you! CC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100224/abba04ab/attachment.htm From tone.kokalj at ijs.si Wed Feb 24 09:03:41 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 24 Feb 2010 09:03:41 +0100 Subject: [xcrysden] vibrational frequency In-Reply-To: <74be62651002232108h5bb0b964s5bd1132af21b01f7@mail.gmail.com> References: <74be62651002232108h5bb0b964s5bd1132af21b01f7@mail.gmail.com> Message-ID: <1266998621.10493.5.camel@walk.ijs.si> On Wed, 2010-02-24 at 00:08 -0500, Chenchen Wang wrote: > Hi, > I just start to use xcrysden and want to use it to visualize > vibrational frequencies calculated from VASP.But I don't know how to > do this.Can anyone help me with this? Not the frequencies (eigenvalues), but the normal modes you can. You can plot the eigenmodes as arrows. This means you use the Display->Forces features. Of course you first need to prepare a proper XSF files, see: http://www.xcrysden.org/doc/XSF.html#__toc__5 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 masoudnahali at live.com Wed Feb 24 10:19:04 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Wed, 24 Feb 2010 09:19:04 +0000 Subject: [xcrysden] Installing XCrysden on SUSE 11.2 (64) Message-ID: Dear XCrysden Users I tried to install XCrysden(XCrySDen-1.5.21) on my PC. The installed compilers are Gfortran, gcc, g++; and also I have the default TCL of SUSE 11.2. but I took the below lines included errors when I typed make all : cd C; make "TOPDIR=/root/LinSoft/QSPRESSO4.1.2/XCrySDen-1.5.21-src-all" compile make[1]: Entering directory `/root/LinSoft/QSPRESSO4.1.2/XCrySDen-1.5.21-src-all/C' make TOPDIR=/root/LinSoft/QSPRESSO4.1.2/XCrySDen-1.5.21-src-all make[2]: Entering directory `/root/LinSoft/QSPRESSO4.1.2/XCrySDen-1.5.21-src-all/C' gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c detnsplit.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcAppInit.c xcAppInit.c: In function ?Xcrys_Init?: xcAppInit.c:508: warning: initialization from incompatible pointer type xcAppInit.c:509: warning: initialization from incompatible pointer type xcAppInit.c:510: warning: initialization from incompatible pointer type xcAppInit.c:511: warning: initialization from incompatible pointer type xcAppInit.c:512: warning: initialization from incompatible pointer type xcAppInit.c:513: warning: initialization from incompatible pointer type xcAppInit.c:514: warning: initialization from incompatible pointer type xcAppInit.c:515: warning: initialization from incompatible pointer type xcAppInit.c:534: warning: assignment from incompatible pointer type xcAppInit.c:746: warning: passing argument 2 of ?Togl_CreateCommand? from incompatible pointer type togl.h:136: note: expected ?int (*)(struct Togl *, int, const char **)? but argument is of type ?int (*)(struct Togl *, int, char **)? xcAppInit.c:748: warning: passing argument 2 of ?Togl_CreateCommand? from incompatible pointer type togl.h:136: note: expected ?int (*)(struct Togl *, int, const char **)? but argument is of type ?int (*)(struct Togl *, int, char **)? xcAppInit.c:750: warning: passing argument 2 of ?Togl_CreateCommand? from incompatible pointer type togl.h:136: note: expected ?int (*)(struct Togl *, int, const char **)? but argument is of type ?int (*)(struct Togl *, int, char **)? xcAppInit.c:752: warning: passing argument 2 of ?Togl_CreateCommand? from incompatible pointer type togl.h:136: note: expected ?int (*)(struct Togl *, int, const char **)? but argument is of type ?int (*)(struct Togl *, int, char **)? xcAppInit.c:754: warning: passing argument 2 of ?Togl_CreateCommand? from incompatible pointer type togl.h:136: note: expected ?int (*)(struct Togl *, int, const char **)? but argument is of type ?int (*)(struct Togl *, int, char **)? xcAppInit.c:756: warning: passing argument 2 of ?Togl_CreateCommand? from incompatible pointer type togl.h:136: note: expected ?int (*)(struct Togl *, int, const char **)? but argument is of type ?int (*)(struct Togl *, int, char **)? xcAppInit.c:758: warning: passing argument 2 of ?Togl_CreateCommand? from incompatible pointer type togl.h:136: note: expected ?int (*)(struct Togl *, int, const char **)? but argument is of type ?int (*)(struct Togl *, int, char **)? gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcballstick.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcviewport.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcLabels.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c vectors.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcDisplayFunc2.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcAtomAdd.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c loadValues.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c hpsort.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c auxilproc.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcdebug.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c 3D.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcDisplayFunc.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c readstrf.c In file included from readstrf.c:33: getline.h:4: error: conflicting types for ?getline? /usr/include/stdio.h:653: note: previous declaration of ?getline? was here getline.h:5: error: conflicting types for ?getdelim? /usr/include/stdio.h:643: note: previous declaration of ?getdelim? was here readstrf.c: In function ?ReadCoor?: readstrf.c:1103: warning: passing argument 2 of ?getline? from incompatible pointer type getline.h:4: note: expected ?size_t *? but argument is of type ?int *? readstrf.c: In function ?ReadAtoms?: readstrf.c:1172: warning: passing argument 2 of ?getline? from incompatible pointer type getline.h:4: note: expected ?size_t *? but argument is of type ?int *? make[2]: *** [readstrf.o] Error 1 make[2]: Leaving directory `/root/LinSoft/QSPRESSO4.1.2/XCrySDen-1.5.21-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/root/LinSoft/QSPRESSO4.1.2/XCrySDen-1.5.21-src-all/C' make: *** [src-C] Error 2 then I decided to use the pre-compiled one(XCrySDen0.9.3) but I got another error: line 114: /root/LinSoft/QSPRESSO4.1.2/XCrySDen-1.5.21-src-all/scripts/xcLib.sh: No such file or directory I think that the program can not forget the memory of the XCrySDen-1.5.21 when I am installing the pre-compiled one. XCrysden is necessary to view the output of Quantum Espresso and your help is a good gift to me. Masoud Nahali Sharif University of Technology Physical Chemistry _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100224/46944ed3/attachment-0001.htm From burnus at net-b.de Wed Feb 24 11:24:01 2010 From: burnus at net-b.de (Tobias Burnus) Date: Wed, 24 Feb 2010 11:24:01 +0100 Subject: [xcrysden] Installing XCrysden on SUSE 11.2 (64) In-Reply-To: References: Message-ID: <4B84FE41.9010806@net-b.de> Hello, On 02/24/2010 10:19 AM, Masoud Nahali wrote: > I tried to install XCrysden(XCrySDen-1.5.21) on my PC. The installed > compilers are Gfortran, gcc, g++; and also I have the default TCL of > SUSE 11.2. but I took the below lines included errors when I typed > make all: Here, building XCrysden worked. You can find my build for openSUSE 11.2 at http://software.opensuse.org/search?baseproject=openSUSE%3A11.2&p=1&q=XCrySDen Note: You need to install the i586 version and not the x86-64 version of XCrysden as there is a bug in XCrysden, which causes a segfault; MESA closed their bugreport as not-our-bug thus it needs to be fixed in XCrysden. Cf. http://www.democritos.it/pipermail/xcrysden/2010-January/000732.html If you have comments to the openSUSE build, I am interested to hear them. Tobias -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100224/fccfdee1/attachment.htm