From yunpengwang85 at gmail.com Tue May 4 11:44:40 2010 From: yunpengwang85 at gmail.com (Yunpeng Wang) Date: Tue, 4 May 2010 05:44:40 -0400 Subject: [xcrysden] Error in plotting 3D scalar field, maybe a bug Message-ID: Hello all, I want to plot a 3D scalar field by XCrySDen. If the number of data-points is small (<10), I succeed to plot the scalar field and plot the isovalued surfaces. However, if I use larger (>10) value of number of data-points, the program will crash and gives error message like "child killed: segmentation violation". My xcrysden version is 1.5.21. The following is my .xsf file, in which there is only one DATAGRID_3D section: -------------------------------------------------------- BEGIN_BLOCK_DATAGRID_3D whatever BEGIN_DATAGRID_3D_this_is_it 10 10 10 -3 -3 -3 6 0 0 0 6 0 0 0 6 ...(totally 1000 numbers) END_DATAGRID_3D END_BLOCK_DATAGRID_3D ----------------------------------------------------------- Thanks very much! -- Yunpeng Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100504/8b459985/attachment.htm From tone.kokalj at ijs.si Wed May 5 10:31:54 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 05 May 2010 10:31:54 +0200 Subject: [xcrysden] [Pw_forum] Error with Xcryden for view input and output of pwscf file In-Reply-To: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> References: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> Message-ID: <1273048314.9405.60.camel@walk.ijs.si> On Tue, 2010-05-04 at 11:15 -0400, josepht at chips.ncsu.edu wrote: > Instead, the error occurs > when any parent directory containing the input file has been given a name with > spaces. > > e.g. load attempt of output file located in: > > /HOME/JT/QE/QUANTUM\ ESPRESSO\ TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > vs > /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > > where the first case leads to load failure, and the second is successful. This > occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for others. I believe having a whitespace in directory name is not a very smart idea under Unix. It may break many scripts. Nevertheless I adapted xcrysden script, and now it seems to be able to deal with it (at least it works on my computer). You may try it yourself. The script is attached to this email, you need to copy it to your $XCRYSDEN_TOPDIR. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: xcrysden Type: application/x-shellscript Size: 7623 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20100505/c6208797/attachment.bin From tone.kokalj at ijs.si Wed May 5 10:41:43 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 05 May 2010 10:41:43 +0200 Subject: [xcrysden] [Pw_forum] Error with Xcryden for view input and output of pwscf file In-Reply-To: <1273048314.9405.60.camel@walk.ijs.si> References: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> <1273048314.9405.60.camel@walk.ijs.si> Message-ID: <1273048903.9405.63.camel@walk.ijs.si> On Wed, 2010-05-05 at 10:31 +0200, Tone Kokalj wrote: > I believe having a whitespace in directory name is not a very smart idea > under Unix. It may break many scripts. > > Nevertheless I adapted xcrysden script, and now it seems to be able to > deal with it (at least it works on my computer). You may try it > yourself. The script is attached to this email, you need to copy it to > your $XCRYSDEN_TOPDIR. Well, actually I just realized that the patch works for XSF files, but not for the PWscf files. The latter is too much involved to be adapted (and it would become a mass). Hence may recommendation is: don't use the spaces in the directory names. 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 josepht at chips.ncsu.edu Tue May 4 17:15:47 2010 From: josepht at chips.ncsu.edu (josepht at chips.ncsu.edu) Date: Tue, 4 May 2010 11:15:47 -0400 (EDT) Subject: [xcrysden] [Pw_forum] Error with Xcryden for view input and output of pwscf file Message-ID: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> Hello, I am resurrecting this thread - through spring cleaning, I observed the same behavior of xcrysden reported last year by Loc Duong Dinh. The source of the error, at least for my case, was actually unrelated to the format/content of the pwscf input/output file one attempts to read into xcrysden. Instead, the error occurs when any parent directory containing the input file has been given a name with spaces. e.g. load attempt of output file located in: /HOME/JT/QE/QUANTUM\ ESPRESSO\ TESTING/postproc/uroporphyrinogen3/scf1p2r3.out vs /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out where the first case leads to load failure, and the second is successful. This occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for others. Joe Turnbull North Carolina State University On Sun, 2009-02-02 at 16:08 -0800, Tone Kokalj wrote: >You will need to provide more info! >How did you load the file (i.e. sequence of steps), what is the actual file (mail it as attachement)? Only then there is a change 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 >On Sun, 2009-02-01 at 18:53 -0800, loc duong ding wrote: >> Dear all user, >> >>I have a problem when using Xcrysden to view input and output file of pwscf. The error i got was: >>wrong # args: should be "pwInputPreset file" >>wrong # args: should be "pwInputPreset file" >> while executing >>"pwInputPreset /cygdrive/g/Research/MODELLING/output_model2" >> ("eval" body line 1) >> invoked from within >>"eval $preset $file" >> (procedure "openExtStruct" line 106) >> invoked from within >>"openExtStruct 3 crystal external {sh >>/home/cuteo/XCrySDen-1.5.18-bin-shared/scripts/pwi2xsf.sh} pwi2xsf.xsf_out {PWSCF Input File} ANGS -preset pwInpu..." >> (menu invoke) >> >>I did not see this error before. >>I great appreciate all your instructions. >>----------------------------------------------- >>Loc Duong Dinh >>Ms-Ph.D Student >>Sungkyunkwan Advanced Institute of Nanotechnology, >>Sungkyunkwan University, >>Suwon, 440-746, Korea >>Email: mambom1902 at yahoo.com From tone.kokalj at ijs.si Wed May 5 12:39:52 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 05 May 2010 12:39:52 +0200 Subject: [xcrysden] Error in plotting 3D scalar field, maybe a bug In-Reply-To: References: Message-ID: <1273055992.9405.83.camel@walk.ijs.si> On Tue, 2010-05-04 at 05:44 -0400, Yunpeng Wang wrote: > Hello all, > > I want to plot a 3D scalar field by XCrySDen. If the number of > data-points is small (<10), I succeed to plot the scalar field and > plot the isovalued surfaces. However, if I use larger (>10) value of > number of data-points, the program will crash and gives error message > like "child killed: segmentation violation". > > My xcrysden version is 1.5.21. > The following is my .xsf file, in which there is only one DATAGRID_3D > section: To be able to help, please send me the whole XSF file (to my personal email). The number of points > 10 is still a very small number. Xcrysden can display datagrids with million points or more ... 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 yunpengwang85 at gmail.com Wed May 5 17:31:23 2010 From: yunpengwang85 at gmail.com (Yunpeng Wang) Date: Wed, 5 May 2010 11:31:23 -0400 Subject: [xcrysden] XCrySDen Digest, Vol 28, Issue 1 In-Reply-To: References: Message-ID: I have settled this question. That is, to add more "\n" in the data grid. I think the problem is when xcrysden read one line of the data grid, the length of one line is limited to shorter than, say, 1000 numbers. YP On Wed, May 5, 2010 at 7:11 AM, 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. Error in plotting 3D scalar field, maybe a bug (Yunpeng Wang) > 2. Re: [Pw_forum] Error with Xcryden for view input and output > of pwscf file (Tone Kokalj) > 3. Re: [Pw_forum] Error with Xcryden for view input and output > of pwscf file (Tone Kokalj) > 4. Re: [Pw_forum] Error with Xcryden for view input and output > of pwscf file (josepht at chips.ncsu.edu) > 5. Re: Error in plotting 3D scalar field, maybe a bug (Tone Kokalj) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 4 May 2010 05:44:40 -0400 > From: Yunpeng Wang > Subject: [xcrysden] Error in plotting 3D scalar field, maybe a bug > To: xcrysden at democritos.it > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > I want to plot a 3D scalar field by XCrySDen. If the number of data-points > is small (<10), I succeed to plot the scalar field and plot the isovalued > surfaces. However, if I use larger (>10) value of number of data-points, > the > program will crash and gives error message like "child killed: segmentation > violation". > > My xcrysden version is 1.5.21. > The following is my .xsf file, in which there is only one DATAGRID_3D > section: > > -------------------------------------------------------- > BEGIN_BLOCK_DATAGRID_3D > whatever > BEGIN_DATAGRID_3D_this_is_it > 10 10 10 > -3 -3 -3 > 6 0 0 > 0 6 0 > 0 0 6 > ...(totally 1000 numbers) > END_DATAGRID_3D > END_BLOCK_DATAGRID_3D > ----------------------------------------------------------- > > Thanks very much! > > -- > Yunpeng Wang > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/xcrysden/attachments/20100504/8b459985/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Wed, 05 May 2010 10:31:54 +0200 > From: Tone Kokalj > Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input > and output of pwscf file > To: PWSCF Forum > Cc: xcrysden at democritos.it > Message-ID: <1273048314.9405.60.camel at walk.ijs.si> > Content-Type: text/plain; charset="utf-8" > > On Tue, 2010-05-04 at 11:15 -0400, josepht at chips.ncsu.edu wrote: > > Instead, the error occurs > > when any parent directory containing the input file has been given a name > with > > spaces. > > > > e.g. load attempt of output file located in: > > > > /HOME/JT/QE/QUANTUM\ ESPRESSO\ > TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > > vs > > > /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > > > > where the first case leads to load failure, and the second is successful. > This > > occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested > for others. > > I believe having a whitespace in directory name is not a very smart idea > under Unix. It may break many scripts. > > Nevertheless I adapted xcrysden script, and now it seems to be able to > deal with it (at least it works on my computer). You may try it > yourself. The script is attached to this email, you need to copy it to > your $XCRYSDEN_TOPDIR. > > Regards, Tone > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: xcrysden > Type: application/x-shellscript > Size: 7623 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/xcrysden/attachments/20100505/c6208797/attachment-0001.bin > > ------------------------------ > > Message: 3 > Date: Wed, 05 May 2010 10:41:43 +0200 > From: Tone Kokalj > Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input > and output of pwscf file > To: PWSCF Forum > Cc: xcrysden at democritos.it > Message-ID: <1273048903.9405.63.camel at walk.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Wed, 2010-05-05 at 10:31 +0200, Tone Kokalj wrote: > > I believe having a whitespace in directory name is not a very smart idea > > under Unix. It may break many scripts. > > > > Nevertheless I adapted xcrysden script, and now it seems to be able to > > deal with it (at least it works on my computer). You may try it > > yourself. The script is attached to this email, you need to copy it to > > your $XCRYSDEN_TOPDIR. > > Well, actually I just realized that the patch works for XSF files, but > not for the PWscf files. The latter is too much involved to be adapted > (and it would become a mass). > > Hence may recommendation is: don't use the spaces in the directory > names. > > 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 > > > > ------------------------------ > > Message: 4 > Date: Tue, 4 May 2010 11:15:47 -0400 (EDT) > From: josepht at chips.ncsu.edu > Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input > and output of pwscf file > To: pw_forum at pwscf.org > Cc: xcrysden at democritos.it > Message-ID: <58446.152.14.192.32.1272986147.squirrel at chips.ncsu.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hello, > > I am resurrecting this thread - through spring cleaning, I observed the > same > behavior of xcrysden reported last year by Loc Duong Dinh. The source of > the error, > at least for my case, was actually unrelated to the format/content of the > pwscf > input/output file one attempts to read into xcrysden. Instead, the error > occurs > when any parent directory containing the input file has been given a name > with > spaces. > > e.g. load attempt of output file located in: > > /HOME/JT/QE/QUANTUM\ ESPRESSO\ > TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > vs > > /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > > where the first case leads to load failure, and the second is successful. > This > occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for > others. > > > Joe Turnbull > North Carolina State University > > > On Sun, 2009-02-02 at 16:08 -0800, Tone Kokalj wrote: > >You will need to provide more info! > >How did you load the file (i.e. sequence of steps), what is the actual > file (mail > it as attachement)? Only then there is a change 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 > >On Sun, 2009-02-01 at 18:53 -0800, loc duong ding wrote: > >> Dear all user, > >> > >>I have a problem when using Xcrysden to view input and output file of > pwscf. The > error i got was: > >>wrong # args: should be "pwInputPreset file" > >>wrong # args: should be "pwInputPreset file" > >> while executing > >>"pwInputPreset /cygdrive/g/Research/MODELLING/output_model2" > >> ("eval" body line 1) > >> invoked from within > >>"eval $preset $file" > >> (procedure "openExtStruct" line 106) > >> invoked from within > >>"openExtStruct 3 crystal external {sh > >>/home/cuteo/XCrySDen-1.5.18-bin-shared/scripts/pwi2xsf.sh} > pwi2xsf.xsf_out {PWSCF > Input File} ANGS -preset pwInpu..." > >> (menu invoke) > >> > >>I did not see this error before. > >>I great appreciate all your instructions. > >>----------------------------------------------- > >>Loc Duong Dinh > >>Ms-Ph.D Student > >>Sungkyunkwan Advanced Institute of Nanotechnology, > >>Sungkyunkwan University, > >>Suwon, 440-746, Korea > >>Email: mambom1902 at yahoo.com > > > > > > > > > ------------------------------ > > Message: 5 > Date: Wed, 05 May 2010 12:39:52 +0200 > From: Tone Kokalj > Subject: Re: [xcrysden] Error in plotting 3D scalar field, maybe a bug > To: XCrySDen mailing list > Message-ID: <1273055992.9405.83.camel at walk.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Tue, 2010-05-04 at 05:44 -0400, Yunpeng Wang wrote: > > Hello all, > > > > I want to plot a 3D scalar field by XCrySDen. If the number of > > data-points is small (<10), I succeed to plot the scalar field and > > plot the isovalued surfaces. However, if I use larger (>10) value of > > number of data-points, the program will crash and gives error message > > like "child killed: segmentation violation". > > > > My xcrysden version is 1.5.21. > > The following is my .xsf file, in which there is only one DATAGRID_3D > > section: > > To be able to help, please send me the whole XSF file (to my personal > email). > > The number of points > 10 is still a very small number. Xcrysden can > display datagrids with million points or more ... > > 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 28, Issue 1 > *************************************** > > -- Yunpeng Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100505/666f8f17/attachment.htm From azzizuc at libero.it Fri May 7 11:47:39 2010 From: azzizuc at libero.it (azzizuc at libero.it) Date: Fri, 7 May 2010 11:47:39 +0200 (CEST) Subject: [xcrysden] XCrysDen installation Message-ID: <20297934.1190211273225659579.JavaMail.defaultUser@defaultHost> Dear everybody, I am a new member of this mailinglist. Nice to meet you! I am writing because I need some help about XCrysDen installation. I am using Ubuntu 9.10 64bit and I downloaded xc-1.5.21-linux_x86_64-shared.tar.gz. I tried to start the istallation with ./xcConfigure but it wrote: Specify CRYSTAL's crystal module (default: -p: not found crystal: not found): WARNING: file -p: not found crystal: not found is not executable !!! Specify CRYSTAL's properties module (default: -p: not found properties: not found): WARNING: file -p: not found properties: not found is not executable !!! The problem is that I actually have Crystal and Properties executables and I tried also to put these two on the same directory as XCrysDen has been downloaded but the problem is still there. How can I do? How can I check for the correct mobule of Crystal and Properties? Thanks a lot Regards Azzurra From tone.kokalj at ijs.si Fri May 7 18:07:37 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 07 May 2010 18:07:37 +0200 Subject: [xcrysden] XCrysDen installation In-Reply-To: <20297934.1190211273225659579.JavaMail.defaultUser@defaultHost> References: <20297934.1190211273225659579.JavaMail.defaultUser@defaultHost> Message-ID: <1273248457.3432.24.camel@walk.ijs.si> On Fri, 2010-05-07 at 11:47 +0200, azzizuc at libero.it wrote: > Dear everybody, > I am a new member of this mailinglist. Nice to meet you! > > I am writing because I need some help about XCrysDen installation. I am using > Ubuntu 9.10 64bit and I downloaded xc-1.5.21-linux_x86_64-shared.tar.gz. I > tried to start the istallation with ./xcConfigure but it wrote: > > Specify CRYSTAL's crystal module (default: -p: not found crystal: not > found): > > WARNING: file -p: not found crystal: not found is not executable !!! > > Specify CRYSTAL's properties module (default: -p: not found properties: not > found): > > WARNING: file -p: not found properties: not found is not executable !!! > > The problem is that I actually have Crystal and Properties executables and I > tried also to put these two on the same directory as XCrysDen has been > downloaded but the problem is still there. For new version of xcrysden you don't need to run xcConfigure. However, if you would like to set it up for CRYSTAL, then xcConfigure might be convenient as it will aid at setting it up. If it fails you may do it manually. What you need is the proper CRYSTAL specification in the $HOME/.xcrysden/custom-definitions file. See: http://www.xcrysden.org/doc/custom.html 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 kesanakd at tcd.ie Mon May 10 11:49:59 2010 From: kesanakd at tcd.ie (Sankar) Date: Mon, 10 May 2010 10:49:59 +0100 Subject: [xcrysden] Text inside xcryden Message-ID: Hi All, I'd like to add some description for the structure inside xcrysden window. At the moment I'm using xfig to add this after generating an .eps figure from xcryden. I'm just wondering if there is a way to add some text within the application. Thanks in advance Sankar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100510/ea90705b/attachment.htm From tone.kokalj at ijs.si Mon May 10 19:58:24 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 10 May 2010 19:58:24 +0200 Subject: [xcrysden] Text inside xcryden In-Reply-To: References: Message-ID: <1273514304.18468.2.camel@walk.ijs.si> On Mon, 2010-05-10 at 10:49 +0100, Sankar wrote: > Hi All, > > I'd like to add some description for the structure inside xcrysden > window. At the moment I'm using xfig to add this after generating > an .eps figure from xcryden. I'm just wondering if there is a way to > add some text within the application. No! The annotations are typical job for image-manipulation and presentation programs. In addition to xfig, you may also consider to use Gimp, OpenOffice Impress, etc. For this latter set of programs, it is recommended you print to PNG file. Actually the filesize of the PNG bitmap is much smaller than EPS bitmap. 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 mohnish.iitk at gmail.com Tue May 18 06:07:43 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 18 May 2010 09:37:43 +0530 Subject: [xcrysden] a question about isovalue Message-ID: Dear Xcrysden users, I have one trivial question about the isovalue. What exactly isovalue implies, I mean what is the physical interpretation of the isovalue? Because as I think the charge density distribution of system is same so how the value is isovalue is changing the charge density plot? Thanks in advance, -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100518/65571413/attachment.htm From bingmou2004 at gmail.com Tue May 18 07:10:30 2010 From: bingmou2004 at gmail.com (=?GB2312?B?s8LOsOnE?=) Date: Tue, 18 May 2010 13:10:30 +0800 Subject: [xcrysden] a question about isovalue In-Reply-To: References: Message-ID: Why do you say " the charge density distribution of system is same "? Shouldn't there be more electons arounding the positive nuclear than far away from the nuclear? 2010/5/18 mohnish pandey > Dear Xcrysden users, > I have one trivial question about the > isovalue. What exactly isovalue implies, I mean what is the physical > interpretation of the isovalue? Because as I think the charge density > distribution of system is same so how the value is isovalue is changing the > charge density plot? > > Thanks in advance, > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,4th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > +919235721300 > ----------------------------------------------------------------- > > _______________________________________________ > 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/20100518/8a0d91a5/attachment.htm From mohnish.iitk at gmail.com Tue May 18 07:16:30 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 18 May 2010 10:46:30 +0530 Subject: [xcrysden] a question about isovalue In-Reply-To: References: Message-ID: Dear Chen, I meant to say that charge density distribution after relaxing the structure should be unchanged , I did not mean that it will be uniform throughout the structure, I have the question that how this distribution is changing bu changing the "isovalue". Please let me know if I have not made my statement clear. Thanks alot 2010/5/18 ??? > Why do you say " the charge density distribution of system is same "? > Shouldn't there be more electons arounding the positive nuclear than far > away from the nuclear? > > 2010/5/18 mohnish pandey > >> Dear Xcrysden users, >> I have one trivial question about the >> isovalue. What exactly isovalue implies, I mean what is the physical >> interpretation of the isovalue? Because as I think the charge density >> distribution of system is same so how the value is isovalue is changing the >> charge density plot? >> >> Thanks in advance, >> >> -- >> Regards, >> MOHNISH, >> ----------------------------------------------------------------- >> Mohnish Pandey >> Y6927262,4th Year dual degree student, >> Department of Chemical Engineering, >> IIT KANPUR, UP, INDIA >> +919235721300 >> ----------------------------------------------------------------- >> >> _______________________________________________ >> 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 > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100518/0bbf6480/attachment.htm From ustunel at metu.edu.tr Tue May 18 08:29:30 2010 From: ustunel at metu.edu.tr (hande ustunel) Date: Tue, 18 May 2010 09:29:30 +0300 (WET) Subject: [xcrysden] a question about isovalue Message-ID: Dear Mohnish, In order to plot the charge density in its entirety one would need to draw a plot in four dimensions. You can see this if you think of the charge density as a function dependent on thre variables, namely x,y and z. In order to circumvent this you can ask XCrysDen to collect all the points at which the density has a single specific value, the isovalue, and connect them through a three-dimensional plot. To put it more mathetically you are solving for the equation rho(x,y,z)=C where C is your isovalue. It has nothing to do with the system being converged or not. By changing your isovalue you are simply changing C in the above equation and thus obtaining a different solution each time. Hope this helps, Hande Toffoli On Tue, 18 May 2010, mohnish pandey wrote: > Dear Chen, > I meant to say that charge density distribution after > relaxing the structure should be unchanged , I did not mean that it will be > uniform throughout the structure, I have the question that how this > distribution is changing bu changing the "isovalue". Please let me know if I > have not made my statement clear. > > Thanks alot > -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From mohnish.iitk at gmail.com Tue May 18 08:44:43 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 18 May 2010 12:14:43 +0530 Subject: [xcrysden] a question about isovalue In-Reply-To: References: Message-ID: Thanks a lot dear Hande! Now my doubt is clear. On Tue, May 18, 2010 at 11:59 AM, hande ustunel wrote: > Dear Mohnish, > > In order to plot the charge density in its entirety one would need to draw > a plot in four dimensions. You can see this if you think of the charge > density as a function dependent on thre variables, namely x,y and z. In > order to circumvent this you can ask XCrysDen to collect all the points at > which the density has a single specific value, the isovalue, and connect > them through a three-dimensional plot. To put it more mathetically you are > solving for the equation > > rho(x,y,z)=C > > where C is your isovalue. It has nothing to do with the system being > converged or not. By changing your isovalue you are simply changing C in > the above equation and thus obtaining a different solution each time. > > Hope this helps, > Hande Toffoli > > On Tue, 18 May 2010, mohnish pandey wrote: > > > Dear Chen, > > I meant to say that charge density distribution after > > relaxing the structure should be unchanged , I did not mean that it will > be > > uniform throughout the structure, I have the question that how this > > distribution is changing bu changing the "isovalue". Please let me know > if I > > have not made my statement clear. > > > > Thanks alot > > > > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100518/b1ac9c39/attachment.htm From robolivares at gmail.com Tue May 18 21:12:55 2010 From: robolivares at gmail.com (Roberto Olivares-Amaya) Date: Tue, 18 May 2010 15:12:55 -0400 Subject: [xcrysden] Scripting of Color Parameters Message-ID: Hello: I'm new to this list, but not to xcrysden. I've managed to do some scripts for generating molecular orbitals produced from Octopus. There are times that I need to swap the color parameters for the positive and negative part of the wave function. Therefore, there are times where I want to swap the color of each parameter. Through the GUI, it would be helpful to have a swap button, but I haven't found it. I have tried at ways of doing this through tcl scripts, but i haven't been successful. Does anyone know a way of controlling the color parameters through scripting? Thanks, Roberto -- Roberto Olivares-Amaya Aspuru-Guzik Group Dept. of Chemistry and Chemical Biology Harvard University http://aspuru.chem.harvard.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100518/884ad99e/attachment.htm From henrik.lofas at fysik.uu.se Wed May 26 09:47:32 2010 From: henrik.lofas at fysik.uu.se (=?ISO-8859-1?B?SGVucmlrIEz2ZuVz?=) Date: Wed, 26 May 2010 09:47:32 +0200 Subject: [xcrysden] XCrysden via FreeNX Message-ID: Hi all! I am trying to run XCrysden via a NX-client on a windows machine, but it is not possible to start. Anyone have tried it and had it worked? The host is ubuntu 10.04. And the error I get looks as Executing: /home/lofas/prog/XCrySDen-1.5.21-bin-shared/bin/ftnunit X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 807 Current serial number in output stream: 808 Best regards! Henrik -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100526/7243f9e5/attachment.htm