From sd.wang000 at 163.com Wed Dec 2 07:43:49 2009 From: sd.wang000 at 163.com (sd.wang000) Date: Wed, 2 Dec 2009 14:43:49 +0800 (CST) Subject: [xcrysden] Consulting Message-ID: <13773904.1033171259736229876.JavaMail.coremail@app181.163.com> Dear developers: 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 ? Thanks! Yours S.D.Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091202/cbfb226f/attachment.htm From paulatto at sissa.it Wed Dec 2 09:51:30 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 02 Dec 2009 09:51:30 +0100 Subject: [xcrysden] Consulting In-Reply-To: <13773904.1033171259736229876.JavaMail.coremail@app181.163.com> References: <13773904.1033171259736229876.JavaMail.coremail@app181.163.com> Message-ID: 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/ From ppzang at gmail.com Fri Dec 4 00:01:10 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Fri, 4 Dec 2009 07:01:10 +0800 Subject: [xcrysden] About display contours of charge density Message-ID: I want to display the contours of charge density on certain plane with XCrysDen. While it is quite successful to display that on the three basal planes, I cannot find a way to display charge density on other planes. For example, if I am interested in charge density on the plane [1,1,1], what can I do? I got my data from vasp with CHGCAR file, and use v2xsf to translate it into the xsf form. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091204/0f9f0fae/attachment.htm From bingmou2004 at gmail.com Fri Dec 4 04:07:24 2009 From: bingmou2004 at gmail.com (=?GB2312?B?s8LOsOnE?=) Date: Fri, 4 Dec 2009 11:07:24 +0800 Subject: [xcrysden] About display contours of charge density In-Reply-To: References: Message-ID: why don't you try lev00? It is quite easy to get the contours of charge on certain plane in lev00. 2009/12/4 Chenpeng Zang > I want to display the contours of charge density on certain plane with > XCrysDen. While it is quite successful to display that on the three basal > planes, I cannot find a way to display charge density on other planes. For > example, if I am interested in charge density on the plane [1,1,1], what can > I do? > I got my data from vasp with CHGCAR file, and use v2xsf to translate it > into the xsf form. > > _______________________________________________ > 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/20091204/7cdcf54d/attachment.htm From ppzang at gmail.com Fri Dec 4 05:11:45 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Fri, 4 Dec 2009 12:11:45 +0800 Subject: [xcrysden] About display contours of charge density In-Reply-To: References: Message-ID: Thank you! It seems that I should learn how to use it. So, there is no way to do such things in XCRYSDEN? 2009/12/4 ??? > why don't you try lev00? It is quite easy to get the contours of charge on > certain plane in lev00. > > 2009/12/4 Chenpeng Zang > >> I want to display the contours of charge density on certain plane with >> XCrysDen. While it is quite successful to display that on the three basal >> planes, I cannot find a way to display charge density on other planes. For >> example, if I am interested in charge density on the plane [1,1,1], what can >> I do? >> I got my data from vasp with CHGCAR file, and use v2xsf to translate it >> into the xsf form. >> >> _______________________________________________ >> 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091204/3aab31e0/attachment.htm From panda.deng.pan at gmail.com Mon Dec 7 10:35:17 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 7 Dec 2009 17:35:17 +0800 Subject: [xcrysden] Problem in Ploting Fermi-Surface Message-ID: Dear All, I was going to plot Fermi-Surface of TiC with SCF done by Wien2k. I had clicked every button in the pop up window. When I in the last step the "Render Fermi Surface" button, I clicked and got the message "ERROR:Please generate the k-mesh first". The meassage in command line is: TCL_LIBRARY=/home/XCrySDen-1.5.21-bin-semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home/XCrySDen-1.5.21-bin-semishared XCRYSDEN_SCRATCH=/home/xcrys_tmp Running on platform : unix Operating system : Linux Package ImageMagick's convert: /usr/bin/convert Package ImageMagick's import: /usr/bin/import Package Ppmtompeg: /usr/bin/ppmtompeg Package Xwd: /usr/bin/xwd Executing: /home/XCrySDen-1.5.21-bin-semishared/bin/ftnunit exec /home/XCrySDen-1.5.21-bin-semishared/bin/gengeom 1 1 21 1 1 1 1 /home/pan/xcrys_tmp/xc_6569/xc_struc.6569 /home/xcrys_tmp/xc_6569/xc_str2xcr.6569 Executing: /home/XCrySDen-1.5.21-bin-semishared/bin/gengeom 1 1 21 1 1 1 1 /home/xcrys_tmp/xc_6569/xc_struc.6569 /home/pan/xcrys_tmp/xc_6569/xc_str2xcr.6569 reading PRIMCOORD reading CONVCOORD Number of Atoms: 9 Number of Frames: 12 natoms: 9 , ndel: 0 Filtered number of atoms: 9 Estimated number of bonds = 12 KGEN INPUT: 500 0 wien: output-file=/home/data/Wien2k/test/TiC/TiC.output1 wien: output-file=/home/data/Wien2k/test/TiC/TiC.output2 DEBUG -- args: /home/data/Wien2k/test/TiC/TiC.outputkgen Please tell me what is wrong here.My xcrysden version is 1.5.21. Have a nice day! Pan Deng Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091207/64fc7381/attachment.htm From pblaha at theochem.tuwien.ac.at Mon Dec 7 10:58:05 2009 From: pblaha at theochem.tuwien.ac.at (Peter Blaha) Date: Mon, 07 Dec 2009 10:58:05 +0100 Subject: [xcrysden] Problem in Ploting Fermi-Surface In-Reply-To: References: Message-ID: <4B1CD1AD.9040505@theochem.tuwien.ac.at> Your WIEN2k and xcrysden versions are not compatible in kgen. (Either you use an old WIEN2k and new xcrysden or vice versa). Run x kgen at the command line (or from w2web) and NOT in xcrysden (Fermi surface). ?? schrieb: > Dear All, > > I was going to plot Fermi-Surface of TiC with SCF done by Wien2k. > I had clicked every button in the pop up window. When I in the last step > the "Render Fermi Surface" button, I clicked and got the message > "ERROR:Please generate the k-mesh first". > The meassage in command line is: > TCL_LIBRARY=/home/XCrySDen-1.5.21-bin-semishared/external/lib/tcl8.5 > XCRYSDEN_TOPDIR=/home/XCrySDen-1.5.21-bin-semishared > XCRYSDEN_SCRATCH=/home/xcrys_tmp > > Running on platform : unix > Operating system : Linux > Package ImageMagick's convert: /usr/bin/convert > Package ImageMagick's import: /usr/bin/import > Package Ppmtompeg: /usr/bin/ppmtompeg > Package Xwd: /usr/bin/xwd > Executing: /home/XCrySDen-1.5.21-bin-semishared/bin/ftnunit > exec /home/XCrySDen-1.5.21-bin-semishared/bin/gengeom 1 1 21 1 1 1 1 > /home/pan/xcrys_tmp/xc_6569/xc_struc.6569 > /home/xcrys_tmp/xc_6569/xc_str2xcr.6569 > Executing: /home/XCrySDen-1.5.21-bin-semishared/bin/gengeom 1 1 21 1 1 1 > 1 /home/xcrys_tmp/xc_6569/xc_struc.6569 > /home/pan/xcrys_tmp/xc_6569/xc_str2xcr.6569 > reading PRIMCOORD > reading CONVCOORD > Number of Atoms: 9 > Number of Frames: 12 > natoms: 9 , ndel: 0 > Filtered number of atoms: 9 > Estimated number of bonds = 12 > KGEN INPUT: 500 > 0 > > wien: output-file=/home/data/Wien2k/test/TiC/TiC.output1 > wien: output-file=/home/data/Wien2k/test/TiC/TiC.output2 > DEBUG -- args: /home/data/Wien2k/test/TiC/TiC.outputkgen > > Please tell me what is wrong here.My xcrysden version is 1.5.21. > > Have a nice day! > > > Pan Deng > Nanjing University > > > ------------------------------------------------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- P.Blaha -------------------------------------------------------------------------- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/ -------------------------------------------------------------------------- From panda.deng.pan at gmail.com Mon Dec 7 12:52:40 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 7 Dec 2009 19:52:40 +0800 Subject: [xcrysden] Problem in Ploting Fermi-Surface In-Reply-To: <4B1CD1AD.9040505@theochem.tuwien.ac.at> References: <4B1CD1AD.9040505@theochem.tuwien.ac.at> Message-ID: Dear Blaha, Thanks for your reply first. I have tried to run it in the command line.But I have a question about it.When I have done what has been listed in the pop-up window.How can I got the fermi-surface with the current xcrysden? It still has the same ERROR message while clicking the "render fermi surface".Or this is a waste of time, I should get a version which matches. I get the Wien2k version 2008.1, which version of XCrysDen shall I use? Thanks again. Have a nice day! Pan Deng Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091207/d76585ae/attachment.htm From panda.deng.pan at gmail.com Mon Dec 7 14:52:56 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 7 Dec 2009 21:52:56 +0800 Subject: [xcrysden] Problem in Ploting Fermi-Surface In-Reply-To: References: <4B1CD1AD.9040505@theochem.tuwien.ac.at> Message-ID: Dear All, My Wien2k version is 08.1. I want to know which xcrysden version is compatible.With goole I just find 1.6 pre-release.If I need 1.6 version, could someone tell me how find it. Thanks a lot. Pan Deng Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091207/c760ee6a/attachment.htm From pblaha at theochem.tuwien.ac.at Mon Dec 7 14:57:26 2009 From: pblaha at theochem.tuwien.ac.at (Peter Blaha) Date: Mon, 07 Dec 2009 14:57:26 +0100 Subject: [xcrysden] Problem in Ploting Fermi-Surface In-Reply-To: References: <4B1CD1AD.9040505@theochem.tuwien.ac.at> Message-ID: <4B1D09C6.7040805@theochem.tuwien.ac.at> If I remember correctly, for WIEN2k_08.1 you would need an OLDER Xcrysden version. Even more, I would recommend to upgrade WIEN2k ! Or run: x kgen x lapw1 x lapw2 -fermi and get EF from case.scf2 Then use xcrysden and FS-plotting, but put in EF by hand. ?? schrieb: > Dear Blaha, > > Thanks for your reply first. > I have tried to run it in the command line.But I have a question > about it.When I have done what has been listed in the pop-up window.How > can I got the fermi-surface with the current xcrysden? It still has the > same ERROR message while clicking the "render fermi surface".Or this is > a waste of time, I should get a version which matches. > I get the Wien2k version 2008.1, which version of XCrysDen shall > I use? > Thanks again. > > Have a nice day! > > > Pan Deng > Nanjing University > > > ------------------------------------------------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- P.Blaha -------------------------------------------------------------------------- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/ -------------------------------------------------------------------------- From panda.deng.pan at gmail.com Mon Dec 7 15:16:16 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 7 Dec 2009 22:16:16 +0800 Subject: [xcrysden] Problem in Ploting Fermi-Surface In-Reply-To: <4B1D09C6.7040805@theochem.tuwien.ac.at> References: <4B1CD1AD.9040505@theochem.tuwien.ac.at> <4B1D09C6.7040805@theochem.tuwien.ac.at> Message-ID: Mr Blaha Thanks for your patience. I felt terrible when I don't know what's wrong. Pan Deng Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091207/679f65e0/attachment.htm From ppzang at gmail.com Tue Dec 8 04:43:16 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Tue, 8 Dec 2009 11:43:16 +0800 Subject: [xcrysden] Problem in starting XCrysDen Message-ID: Weeks ago I have installed the XCrysDen successfully and used it for several times. But this we something happened. When I started the XCrysDen, an error occurs which is "/home/Zangcp/software/XCrySDen-1.5.17-bin-semishared/xcrysden: line 211: 3792 ??? ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null" I have re-installed XCrysDen for several times, but the same problem is reported each time. What can I do? My os is fedora 11 and the vision of XCrysDen is " XCrySDen-1.5.17-bin-semishared". -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091208/ddea9075/attachment.htm From paulatto at sissa.it Tue Dec 8 10:08:35 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 08 Dec 2009 10:08:35 +0100 Subject: [xcrysden] Problem in starting XCrysDen In-Reply-To: References: Message-ID: Replying to message "[xcrysden] Problem in starting XCrysDen" from Chenpeng Zang (08/12/09): > ??? Dear Chepepeng Zang, you could have translated the error message for us... anyway, babelfish says it is a SEGFAUL, which may depend on the system you're trying to plot. Can you provide more information? 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/ From ppzang at gmail.com Tue Dec 8 15:41:37 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Tue, 8 Dec 2009 22:41:37 +0800 Subject: [xcrysden] Problem in starting XCrysDen In-Reply-To: References: Message-ID: Dear Lorenzo Paulatto, Thank you for your replying! To start the XCrysDen, I just use the command "xcrysden". I have used XCrysDen to plot some charge density in crystal with xsf formed file. I did my calculation with VASP, and transplanted the VASP's file CHACAR into xsf formed file, with a tool called v2xsf. If you kind people needs more information, just tell me. By the way, what is SEGFAUL? and babelfish? is it a name of some gay? best wishes! 2009/12/8 Lorenzo Paulatto > Replying to message "[xcrysden] Problem in starting XCrysDen" from > Chenpeng Zang (08/12/09): > > ??? > > Dear Chepepeng Zang, > you could have translated the error message for us... anyway, babelfish > says it is a SEGFAUL, which may depend on the system you're trying to > plot. Can you provide more information? > > 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/ > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091208/322ee62b/attachment.htm From henrik.lofas at fysik.uu.se Fri Dec 18 11:15:36 2009 From: henrik.lofas at fysik.uu.se (=?ISO-8859-1?B?SGVucmlrIEz2ZuVz?=) Date: Fri, 18 Dec 2009 11:15:36 +0100 Subject: [xcrysden] Multiple 3D-grids? Message-ID: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> Hi, I have an .XSF file with a 3D-grid containing two subblocks(real and imag wavefcn), is it any way to plot those separately, and not added together as XCrysden seems to do? Best Regards Henrik -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091218/8e9290b3/attachment.htm From paulatto at sissa.it Fri Dec 18 11:17:13 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 18 Dec 2009 11:17:13 +0100 Subject: [xcrysden] Multiple 3D-grids? In-Reply-To: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> References: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> Message-ID: Replying to message "[xcrysden] Multiple 3D-grids?" from Henrik L?f?s (18/12/09): > I have an .XSF file with a 3D-grid containing two subblocks(real and imag > wavefcn), is it any way to plot those separately, and not added together > as XCrysden seems to do? Dear Henrik, it is unfortunately impossible with the current (and past) version of XCrysDen. 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/ From tone.kokalj at ijs.si Fri Dec 18 11:38:27 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 18 Dec 2009 11:38:27 +0100 Subject: [xcrysden] Multiple 3D-grids? In-Reply-To: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> References: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> Message-ID: <1261132707.21830.10.camel@walk.ijs.si> On Fri, 2009-12-18 at 11:15 +0100, Henrik L?f?s wrote: > Hi, > > > I have an .XSF file with a 3D-grid containing two subblocks(real and > imag wavefcn), is it any way to plot those separately, What do you mean by separately? If you want to plot the 1st and then the 2nd, there is no problem, you plot one at a time. However, if you want to plot the two (superimposed) at the same time, this is not possible with xcrysden. But why would you like to plot real and imag part of the wave-function? (is there any sense in doing it; wouldn't its square modulus be more appropriate) 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 henrik.lofas at fysik.uu.se Fri Dec 18 12:12:59 2009 From: henrik.lofas at fysik.uu.se (=?ISO-8859-1?B?SGVucmlrIEz2ZuVz?=) Date: Fri, 18 Dec 2009 12:12:59 +0100 Subject: [xcrysden] Multiple 3D-grids? In-Reply-To: <1261132707.21830.10.camel@walk.ijs.si> References: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> <1261132707.21830.10.camel@walk.ijs.si> Message-ID: <15432db0912180312h761474f9j2c76cd7015c26181@mail.gmail.com> Hi, Thanks for the fast reply. Yes, I would to like have them superimposed. What I want to plot is the transmission eigenchannels, which can be seen as travelling waves hence, both real and imag part separately are interesting, see for example http://link.aps.org/doi/10.1103/PhysRevB.76.115117 Regards Henrik 2009/12/18 Tone Kokalj > On Fri, 2009-12-18 at 11:15 +0100, Henrik L?f?s wrote: > > Hi, > > > > > > I have an .XSF file with a 3D-grid containing two subblocks(real and > > imag wavefcn), is it any way to plot those separately, > > What do you mean by separately? If you want to plot the 1st > and then the 2nd, there is no problem, you plot one at a time. > > However, if you want to plot the two (superimposed) at the same time, > this is not possible with xcrysden. > > But why would you like to plot real and imag part of the wave-function? > (is there any sense in doing it; wouldn't its square modulus be more > appropriate) > > Regards, Tone > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091218/3a562ab8/attachment.htm From paulatto at sissa.it Fri Dec 18 12:18:39 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 18 Dec 2009 12:18:39 +0100 Subject: [xcrysden] Multiple 3D-grids? In-Reply-To: <15432db0912180312h761474f9j2c76cd7015c26181@mail.gmail.com> References: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> <1261132707.21830.10.camel@walk.ijs.si> <15432db0912180312h761474f9j2c76cd7015c26181@mail.gmail.com> Message-ID: Replying to message "Re: [xcrysden] Multiple 3D-grids?" from Henrik L?f?s (18/12/09): > Yes, I would to like have them superimposed. What I want to plot is the > transmission eigenchannels, which can be seen as travelling waves hence, > both real and imag part separately are interesting, see for example > http://link.aps.org/doi/10.1103/PhysRevB.76.115117 Dear Henrik, I could never find a software that does both multiple grids and non-simple-cubic cells. It may still exist, but I could not find it. On ther other hand, if your unit cell *is* simple cubic you can use gOpenMol (which I think was used for the pictures in that paper) and/or vmd. Otherwise, you can try with XCrysDen + gimp, plot the different datagrids and then compose them by hand; its painful, but it works. 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/ From tone.kokalj at ijs.si Fri Dec 18 12:39:54 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 18 Dec 2009 12:39:54 +0100 Subject: [xcrysden] Multiple 3D-grids? In-Reply-To: References: <15432db0912180215rac07948ode31bd4ce8cb5e73@mail.gmail.com> <1261132707.21830.10.camel@walk.ijs.si> <15432db0912180312h761474f9j2c76cd7015c26181@mail.gmail.com> Message-ID: <1261136394.21830.27.camel@walk.ijs.si> On Fri, 2009-12-18 at 12:18 +0100, Lorenzo Paulatto wrote: > Replying to message "Re: [xcrysden] Multiple 3D-grids?" from Henrik L?f?s > (18/12/09): > > Yes, I would to like have them superimposed. What I want to plot is the > > transmission eigenchannels, which can be seen as travelling waves hence, > > both real and imag part separately are interesting, see for example > > http://link.aps.org/doi/10.1103/PhysRevB.76.115117 > > Dear Henrik, > I could never find a software that does both multiple grids and > non-simple-cubic cells. It may still exist, but I could not find it. On > ther other hand, if your unit cell *is* simple cubic you can use gOpenMol > (which I think was used for the pictures in that paper) and/or vmd. > Otherwise, you can try with XCrysDen + gimp, plot the different datagrids > and then compose them by hand; its painful, but it works. Lorenzo is right. You cannot do plot like the Fig.3 in that paper. But you can use the gimp for the assembly, and in same cases it may not be that painful. However if the two surfaces "penetrate one into the other" like a chain the result may not be very good. Nevertheless, here is the recipe. 1. Plot first, say the real part, (you can do two positive and negative simultaneous plot. 2. save he xcrysden script, i.e., menu File-->Save Current State and Structure (this is important for having the two pictures displayed in a completely the same way) 3. edit the so-saved script, i.e., replace the first structure part of the file with something like: ::scripting::open -r my_dim --xsf my_second_grid.xsf (where my_dim is the dimension of your structure: 0=molecule, 1=polymer, 2=slab,3=crystal, i.e. it's a periodic dimensionality) 4. load so edited script with: xcrysden -s my_script.xcrysden and plot it accordingly Then you need some image manipulation program. This is the most tedious part. I've seen people doing "miracles" with gimp ... You may make both plots (layers) a bit transparent for better superposition. Good luck! 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 panda.deng.pan at gmail.com Sat Dec 26 17:33:10 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Sun, 27 Dec 2009 00:33:10 +0800 Subject: [xcrysden] 2D fermi-surface Message-ID: Dear All, Since I have plotted the 3D fermi surface.But I want to survey some detail in a specify plane such as xy-plane.Beside to zoom in.Is ther any way to get the the projection of 3D fermi surface onto the the plane which is needed. Have a nice day Pan Deng Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091227/f9e03750/attachment.htm From mohnish.iitk at gmail.com Sun Dec 27 08:10:44 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 27 Dec 2009 12:40:44 +0530 Subject: [xcrysden] problem in making monoclinic cell Message-ID: Dear xcrysden users, I am using PWSCF for BaTiO3 thin films calculation, I just wanted to visualize the (110) surface of the same by xcrysden. I am pasting the input PWSCF file for the same, the problem is my system is monoclinic but xcrysden is showing it to be cubic, may be I am doing some mistake. Please anybody help me out to fix the problem. The calcualtin is for one layer. Sincere thanks in advance, Mohnish &control calculation = 'relax' prefix='BaTiO3' outdir='/home/rajpala/Desktop/BaTiO3' pseudo_dir="/home/rajpala/Desktop/BaTiO3" / &system ibrav=12,a =5.629,b=4.875,c=20,celldm(4)=0.577344716 ,nat=5, ntyp= 3, ecutwfc = 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'local-TF' mixing_beta = 0.7 conv_thr = 1.0d-6 / &IONS ion_dynamics='bfgs' trust_radius_min=1.D-4 / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS (crystal) Ba 0.5 0.5 0.070375 Ti 0.25 0.0 0.070375 O 0.0 0.0 0.0 O 0.5 0.0 0.0 O 0.0 0.5 0.070375 K_POINTS (automatic) 5 5 1 0 0 0 -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091227/93029e1b/attachment.htm From ppzang at gmail.com Sun Dec 27 16:23:30 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Sun, 27 Dec 2009 23:23:30 +0800 Subject: [xcrysden] problem in making monoclinic cell In-Reply-To: References: Message-ID: Dear Mohnish Pandey: Although I am not familiar with th PWSCF, I think, it might not be the xcrysden's fault. Whether your monoclinic system is similar to the cubic, for example a,b,c are just slightly different or the angle is near to 90, which would make the structure looks like cubic right? Best wishes Chenpeng 2009/12/27 mohnish pandey > Dear xcrysden users, > I am using PWSCF for BaTiO3 thin films > calculation, I just wanted to visualize the (110) surface of the same by > xcrysden. I am pasting the input PWSCF file for the same, the problem is my > system is monoclinic but xcrysden is showing it to be cubic, may be I am > doing some mistake. Please anybody help me out to fix the problem. The > calcualtin is for one layer. > > Sincere thanks in advance, > Mohnish > > &control > calculation = 'relax' > prefix='BaTiO3' > outdir='/home/rajpala/Desktop/BaTiO3' > pseudo_dir="/home/rajpala/Desktop/BaTiO3" > / > &system > ibrav=12,a =5.629,b=4.875,c=20,celldm(4)=0.577344716 ,nat=5, ntyp= 3, > ecutwfc = > 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' > / > &electrons > diagonalization='david' > mixing_mode = 'local-TF' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > &IONS > ion_dynamics='bfgs' > trust_radius_min=1.D-4 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ti 47.867 Ti.pbe-sp-van_ak.UPF > O 15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Ba 0.5 0.5 0.070375 > Ti 0.25 0.0 0.070375 > O 0.0 0.0 0.0 > O 0.5 0.0 0.0 > O 0.0 0.5 0.070375 > K_POINTS (automatic) > 5 5 1 0 0 0 > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091227/a73cb125/attachment.htm From testuser_2009 at yahoo.fr Tue Dec 29 14:54:04 2009 From: testuser_2009 at yahoo.fr (Testuser Name) Date: Tue, 29 Dec 2009 13:54:04 +0000 (GMT) Subject: [xcrysden] xcrysden in windows error Message-ID: <959168.18780.qm@web24001.mail.ird.yahoo.com> Dear all, When I running xcrysden (XCrySDen-1.4.1bin-shared) on the cygwin. and run FILE + ExCrysDen Examples+WIEN struct files a error message apear error copying "C:\XCrySDen-1.4.1bin-shared\tmp/xc_960/xc_struc.960" to "xc_struc.960": permission denied error copying "C:\XCrySDen-1.4.1bin-shared\tmp/xc_960/xc_struc.960" to "xc_struc.960": permission denied while executing "file copy -force $file $name" (procedure "gunzipXSF" line 10) invoked from within "gunzipXSF $file" (procedure "OpenStruct" line 24) invoked from within "OpenStruct .mesa $system(SCRDIR)/xc_struc.$system(PID)" (procedure "wnOpenSFile" line 71) invoked from within "wnOpenSFile $file" (menu invoke) what is the problem please -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091229/f6e79737/attachment.htm From zhuyingtao at mail.sdu.edu.cn Wed Dec 30 06:48:41 2009 From: zhuyingtao at mail.sdu.edu.cn (zhuyingtao) Date: Wed, 30 Dec 2009 13:48:41 +0800 Subject: [xcrysden] some problem with the xcrysden for crystal06 Message-ID: <462147913.12212@mail.sdu.edu.cn> Dear all, I use the lastst xcrysden for windows with the help of the cygwin, and want to dos2unix the crystal06 fort.34 because the error following: ==========================Error============================== invalid number: incomprehensible list input apparent state: unit 34 named fort.34 last format: list io lately reading sequential formatted external IO /cygdrive/c/home/user/xcrysden/scripts/launch.sh: line 5: 23364 Aborted ==========================Error end ========================== I think this error may cause by the dos style of the fort.34. I just want to know to how and where I can add the command "dos2unix fort.34" in the xcrysden code. thanks very much 2009-12-30 zhuyingtao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091230/e9bb795b/attachment.htm