From lazycle at gmail.com Fri Jan 3 05:29:05 2014 From: lazycle at gmail.com (Yu Xie) Date: Thu, 2 Jan 2014 23:29:05 -0500 Subject: [xcrysden] xcrysden doesn't show isosurface Message-ID: Dear users, I'm using Xcrysden 1.5.53 on MAC OS X 10.9 to view the ELFCAR generated by VASP. I've converted the ELFCAR to .xsf formate. The crystal structure was showed perfectly. But there is no isosurface for the electron localization function. I'm pretty sure that the lightning is on. Does anyone has the same experience and happen to know how to solve it? Your response is appreciated. Best regards, Yu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140102/0bd5e084/attachment.htm From hadi.arefi at tyndall.ie Fri Jan 3 15:04:57 2014 From: hadi.arefi at tyndall.ie (Hadi Arefi) Date: Fri, 3 Jan 2014 14:04:57 +0000 Subject: [xcrysden] xcrysden doesn't show isosurface In-Reply-To: References: Message-ID: <9B517AB3CFA7E649800F39802E6668C220F7EA73@MAILBOXSERVER.tyndall.ie> Have you tried look at the following links? http://www.xcrysden.org/doc/density.html http://www.xcrysden.org/doc/isocontrol.html From: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] On Behalf Of Yu Xie Sent: 03 January 2014 04:29 To: xcrysden at democritos.it Subject: [xcrysden] xcrysden doesn't show isosurface Dear users, I'm using Xcrysden 1.5.53 on MAC OS X 10.9 to view the ELFCAR generated by VASP. I've converted the ELFCAR to .xsf formate. The crystal structure was showed perfectly. But there is no isosurface for the electron localization function. I'm pretty sure that the lightning is on. Does anyone has the same experience and happen to know how to solve it? Your response is appreciated. Best regards, Yu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140103/48e1f975/attachment.htm From lazycle at gmail.com Fri Jan 3 23:18:07 2014 From: lazycle at gmail.com (Yu Xie) Date: Fri, 3 Jan 2014 17:18:07 -0500 Subject: [xcrysden] xcrysden doesn't show isosurface Message-ID: Dear Dr. Hadi, Thanks for your tips! Now I can get the isosurface! Best regards, Yu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140103/0f6775f3/attachment.htm From hamidrezabalangi at yahoo.com Wed Jan 8 15:05:59 2014 From: hamidrezabalangi at yahoo.com (Hamidreza Balangi) Date: Wed, 8 Jan 2014 06:05:59 -0800 (PST) Subject: [xcrysden] charge density In-Reply-To: <1389189842.45240.YahooMailNeo@web141206.mail.bf1.yahoo.com> References: <1389189842.45240.YahooMailNeo@web141206.mail.bf1.yahoo.com> Message-ID: <1389189959.39926.YahooMailNeo@web141204.mail.bf1.yahoo.com> Hello, I have used denchar program and generated .XSF file including data blocks of RHOof SIESTA by mulliken. But when I open it using Xcrysden I always see the atoms only and Data Grid section in tools does not show me the density plots. Your helps are appreciated. best regards hamidreza balangi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140108/07faf49f/attachment.htm From c00jsh00 at nchc.narl.org.tw Fri Jan 10 02:57:12 2014 From: c00jsh00 at nchc.narl.org.tw (c00jsh00 at nchc.narl.org.tw) Date: Fri, 10 Jan 2014 09:57:12 +0800 (CST) Subject: [xcrysden] libX11.so xcb_lib_lock undefined Message-ID: <1389319031.21872.c00jsh00@nchc.narl.org.tw> Hi, Our installation of Xcrysden-1.5.53 on SuSE 11 is not working, I got an error TCL_LIBRARY=/pkg/chem/xcrysden/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/pkg/chem/xcrysden XCRYSDEN_SCRATCH=/work/chem /pkg/chem/xcrysden/bin/xcrys: symbol lookup error: /usr/lib64/libX11.so.6: undefined symbol: xcb_xlib_lock for shared and semi-shared version. I also tried to install it from the source, I got compilation errors: ... gcc -O2 -pipe -Wl,--export-dynamic tkAppInit.o -L/pkg/chem/workdir/xcrysden-1.5.53/external/src/tk8.5.11/unix -ltk8.5 \ -L/pkg/chem/workdir/xcrysden-1.5.53/external/src/tcl8.5.11/unix -ltcl8.5 -L/usr/lib64 -lX11 -ldl -lieee -lm -Wl,-rpath,/pkg/chem/workdir/xcrysden-1.5.53/external/lib -o wish /usr/lib64/libX11.so: undefined reference to `xcb_xlib_lock' /usr/lib64/libX11.so: undefined reference to `xcb_xlib_unlock' /usr/lib64/libX11.so: undefined reference to `xcb_get_request_sent' ... Any suggestion to avoid this problem? Thank you. Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High Performance Computing Hsinchu, Taiwan, ROC From mohammedlawal08 at yahoo.com Fri Jan 10 05:06:33 2014 From: mohammedlawal08 at yahoo.com (Lawal Mohammed) Date: Thu, 9 Jan 2014 20:06:33 -0800 (PST) Subject: [xcrysden] Need help Message-ID: <1389326793.77321.YahooMailNeo@web125702.mail.ne1.yahoo.com> Dear Developers and Users, I am using Wien2k, I got this error zero vector was submitted for normal, when executing xc_isospacesel center2D -normal {x y z}...... when I try to calculate density with xcrysden. Can anybody help me to resolve this? Lawal -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140109/02aa8d4b/attachment.htm From tone.kokalj at ijs.si Fri Jan 10 08:58:32 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 10 Jan 2014 08:58:32 +0100 Subject: [xcrysden] libX11.so xcb_lib_lock undefined In-Reply-To: <1389319031.21872.c00jsh00@nchc.narl.org.tw> References: <1389319031.21872.c00jsh00@nchc.narl.org.tw> Message-ID: <1389340712.9965.2.camel@catalyst.ijs.si> On Fri, 2014-01-10 at 09:57 +0800, c00jsh00 at nchc.narl.org.tw wrote: > Hi, > > Our installation of Xcrysden-1.5.53 on SuSE 11 is not working, I got > an error > TCL_LIBRARY=/pkg/chem/xcrysden/external/lib/tcl8.5 > XCRYSDEN_TOPDIR=/pkg/chem/xcrysden > XCRYSDEN_SCRATCH=/work/chem > > /pkg/chem/xcrysden/bin/xcrys: symbol lookup error: /usr/lib64/libX11.so.6: undefined symbol: xcb_xlib_lock > > for shared and semi-shared version. I also tried to install it from the source, > I got compilation errors: > > ... > gcc -O2 -pipe -Wl,--export-dynamic tkAppInit.o -L/pkg/chem/workdir/xcrysden-1.5.53/external/src/tk8.5.11/unix -ltk8.5 \ > -L/pkg/chem/workdir/xcrysden-1.5.53/external/src/tcl8.5.11/unix -ltcl8.5 -L/usr/lib64 -lX11 -ldl -lieee -lm -Wl,-rpath,/pkg/chem/workdir/xcrysden-1.5.53/external/lib -o wish > /usr/lib64/libX11.so: undefined reference to `xcb_xlib_lock' > /usr/lib64/libX11.so: undefined reference to `xcb_xlib_unlock' > /usr/lib64/libX11.so: undefined reference to `xcb_get_request_sent' > ... There seems to be an issue on SuSE wrt xcb_xlib_loc. See this email and its corresponding thread, perhaps you may find some useful info: http://marc.info/?l=freedesktop-xcb&m=127122726310143&w=2 Regards, -- 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 Jan 10 09:12:01 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 10 Jan 2014 09:12:01 +0100 Subject: [xcrysden] Need help In-Reply-To: <1389326793.77321.YahooMailNeo@web125702.mail.ne1.yahoo.com> References: <1389326793.77321.YahooMailNeo@web125702.mail.ne1.yahoo.com> Message-ID: <1389341521.9965.8.camel@catalyst.ijs.si> On Thu, 2014-01-09 at 20:06 -0800, Lawal Mohammed wrote: > Dear Developers and Users, > I am using Wien2k, I got this error > > zero vector was submitted for normal, when executing xc_isospacesel > center2D -normal {x y z}...... > when I try to calculate density with xcrysden. Can anybody help me to > resolve this? This message provide way insufficient information. You should provide more thorough description of what you did to obtain this error. I believe that the error occurred before you tried to calculate the density, i.e., during the selection of rectangular/parallelepiped 2D region for the 2D density grid. The error complains about a zero vector, which probably implies that you clicked three collinear atoms. Regards, -- 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 Jan 10 09:16:30 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 10 Jan 2014 09:16:30 +0100 Subject: [xcrysden] charge density In-Reply-To: <1389189959.39926.YahooMailNeo@web141204.mail.bf1.yahoo.com> References: <1389189842.45240.YahooMailNeo@web141206.mail.bf1.yahoo.com> <1389189959.39926.YahooMailNeo@web141204.mail.bf1.yahoo.com> Message-ID: <1389341790.9965.12.camel@catalyst.ijs.si> On Wed, 2014-01-08 at 06:05 -0800, Hamidreza Balangi wrote: > Hello, > > I have used denchar program and generated .XSF file including data > blocks of > RHOof SIESTA by mulliken. But when I open it using Xcrysden I always > see the atoms > only and Data Grid section in tools does not show me the density > plots. What do you mean by "Data Grid section in tools does not show me the density plots"? Does it imply that the menu is inactive? If not, then read these: http://www.xcrysden.org/doc/density.html http://www.xcrysden.org/doc/isocontrol.html http://www.xcrysden.org/doc/plane1control.html Note the "lighting" mode should be switched on (radiobutton on the right toolbox) to see the density plots! Regards, -- 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 member at linkedin.com Fri Jan 10 23:59:11 2014 From: member at linkedin.com (baaouague khaled via LinkedIn) Date: Fri, 10 Jan 2014 22:59:11 +0000 (UTC) Subject: [xcrysden] Join my network on LinkedIn Message-ID: <1799504864.7569290.1389394751475.JavaMail.app@ela4-app0046.prod> LinkedIn ------------ baaouague khaled requested to add you as a connection on LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Accept invitation from baaouague khaled http://www.linkedin.com/e/-fe5rcs-hqa1rffq-51/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I526424080_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnP0Uc3gOd3oOdkALjkB2ciR3iQcLdzsNc3wRcPASdj4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=0nojjY6MZzlS41 View profile of baaouague khaled http://www.linkedin.com/e/-fe5rcs-hqa1rffq-51/rso/197724472/oED1/name/128644874_I526424080_125/?hs=false&tok=1eFidf7edzlS41 ------------------------------------------ You are receiving Invitation emails. This email was intended for Andr? Pereira XCrysden. Learn why this is included: http://www.linkedin.com/e/-fe5rcs-hqa1rffq-51/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=17S1jWbutzlS41 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140110/b6fdd8d3/attachment-0001.htm From ngangbam.singh5 at gmail.com Tue Jan 14 11:30:15 2014 From: ngangbam.singh5 at gmail.com (beda singh) Date: Tue, 14 Jan 2014 16:00:15 +0530 Subject: [xcrysden] Data grid is inactive Message-ID: Dear Xcrysden Users, I am trying to see the isosurface using the rho2xsf of siesta Utility. But when I open the XSF file the datagrid do not show the OK and cancel button. Therefore can not see the isosurface. I am using xcrysden 1.5.24. I also tried to to install xcrysden 1.5.53 assuming the latest version may solve the problem but could not install it. Please help -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140114/244c0962/attachment.htm From yzunt at yahoo.com Tue Jan 14 12:19:18 2014 From: yzunt at yahoo.com (Yusuf Zuntu) Date: Tue, 14 Jan 2014 03:19:18 -0800 (PST) Subject: [xcrysden] Boron atom is bigger than Nitrogen in the structure visualization Message-ID: <1389698358.88638.YahooMailNeo@web140701.mail.bf1.yahoo.com> Please may I know how to fix this problem. In my armchair hydrogen-terminated boron nitride nanoribbons structure visualization in XcrysDen, boron atom is bigger than nitrogen atom. This is not suppose to be since atomic number of nitrogen atom is more than the atomic of atomic number of boron atom. Thank you for anticipated positive response to enable fix this problem. Yusuf Zuntu. Postgraduate Student UPM -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140114/f352122b/attachment.htm From mangoldc at mpip-mainz.mpg.de Thu Jan 16 13:09:52 2014 From: mangoldc at mpip-mainz.mpg.de (Claudia Mangold) Date: Thu, 16 Jan 2014 13:09:52 +0100 Subject: [xcrysden] problems with visualisation of QE input file Message-ID: <52D7CC10.80304@mpip-mainz.mpg.de> Dear xcrysden developer(s), I use xcrysden to visualise QE input and output and I mam very happy with it. Thanks a lot for providing this program for free to the community. So far I only discovered one problem of which I am not 100% sure if it is a bug or a misunderstanding from my side: In QE input files you can specify CELL_PARAMETERS and ATOMIC_POSITIONS in angstrom and in bohr. However, the visualisation with xcrysden works only properly with CELL_PARAMETERS specified in bohr. If I use angstrom then the cell is visualised wrongly. This doesnt affect the ATOMIC_POSITIONS: If I specify them in angstrom, it works. Is this a known problem? I use Version: xcrysden 1.5.53 I would be happy, if you could help me to solve this problem Best wishes, Claudia Mangold -- --------------------------------------- Claudia Mangold Postdoctoral fellow MPI for Polymer Research Ackermannweg 10 55128 Mainz Tel.: +49 6131 379-481 --------------------------------------- From tone.kokalj at ijs.si Thu Jan 16 13:33:20 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 16 Jan 2014 13:33:20 +0100 Subject: [xcrysden] problems with visualisation of QE input file In-Reply-To: <52D7CC10.80304@mpip-mainz.mpg.de> References: <52D7CC10.80304@mpip-mainz.mpg.de> Message-ID: <1389875600.9965.38.camel@catalyst.ijs.si> On Thu, 2014-01-16 at 13:09 +0100, Claudia Mangold wrote: > Dear xcrysden developer(s), > > I use xcrysden to visualise QE input and output and I mam very happy > with it. Thanks a lot for providing this program for free to the > community. So far I only discovered one problem of which I am not 100% > sure if it is a bug or a misunderstanding from my side: Actually it is the backward incompatibility (xcrysden does not yet understand correctly the new QE's syntax of CELL_PARAMETERS bohr | angstroms but implicitly assumes "alat" units for CELL_PARAMETERS. > In QE input files you can specify > > CELL_PARAMETERS and ATOMIC_POSITIONS in angstrom and in bohr. However, > the visualisation with xcrysden works only properly with CELL_PARAMETERS > specified in bohr. As said above, it ignores both "bohr" and "angstrom", but when celldm(1) or A (i.e. lattice parameter, aka "alat") is not specified, then it assumes alat=1 bohr, which implies that CELL_PARAMETERS are actually in bohr units. This issue will be fixed in a new release. Regards, -- 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 masoodyousaf1 at yahoo.com Thu Jan 16 13:42:20 2014 From: masoodyousaf1 at yahoo.com (Masood Yousaf) Date: Thu, 16 Jan 2014 04:42:20 -0800 (PST) Subject: [xcrysden] How to quantify charge density (as a single value of charge density) along certain Bond length Via Xcrystalden Message-ID: <1389876140.81260.YahooMailNeo@web141505.mail.bf1.yahoo.com> Dear Fellows I know how to calculate contour charge density plots for certain planes. I want to quantify the charge density (as a single value of charge density) in between two species i.e., along the bond length. Kindly suggest a way to quantify the charge density.? Thank You Best wishes Masood Universiti Tecknologi Malaysia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140116/d05ce130/attachment.htm From tone.kokalj at ijs.si Thu Jan 16 13:46:05 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 16 Jan 2014 13:46:05 +0100 Subject: [xcrysden] Boron atom is bigger than Nitrogen in the structure visualization In-Reply-To: <1389698358.88638.YahooMailNeo@web140701.mail.bf1.yahoo.com> References: <1389698358.88638.YahooMailNeo@web140701.mail.bf1.yahoo.com> Message-ID: <1389876365.9965.49.camel@catalyst.ijs.si> On Tue, 2014-01-14 at 03:19 -0800, Yusuf Zuntu wrote: > Please may I know how to fix this problem. In my armchair > hydrogen-terminated boron nitride nanoribbons structure visualization > in XcrysDen, boron atom is bigger than nitrogen atom. Which is the way it should be, because the size of plotted "balls" in xcrysden is proportional with covalent radii. > This is not suppose to be since atomic number of nitrogen atom is more > than the atomic of atomic number of boron atom. Is it? Well, atomic number of N > B, but ... See: https://www.webelements.com/periodicity/covalent_radius/ and try to answer to yourself why it is the other way around, i.e., r_B > r_N. Anyway you can change the display radius via: Modify-->Atomic Radii menu (e.g., if you want to base the size of the balls on the ionic radius instead). Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Thu Jan 16 13:49:18 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 16 Jan 2014 13:49:18 +0100 Subject: [xcrysden] Data grid is inactive In-Reply-To: References: Message-ID: <1389876558.9965.51.camel@catalyst.ijs.si> On Tue, 2014-01-14 at 16:00 +0530, beda singh wrote: > Dear Xcrysden Users, > > I am trying to see the isosurface using the rho2xsf of siesta Utility. > But when I open the XSF file the datagrid do not show the OK and > cancel button. What happens if you try to enlarge the pertinent window? > I also tried to to install xcrysden 1.5.53 assuming the latest > version may solve the problem but could not install it. What was the problem? Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Thu Jan 16 13:57:17 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 16 Jan 2014 13:57:17 +0100 Subject: [xcrysden] How to quantify charge density (as a single value of charge density) along certain Bond length Via Xcrystalden In-Reply-To: <1389876140.81260.YahooMailNeo@web141505.mail.bf1.yahoo.com> References: <1389876140.81260.YahooMailNeo@web141505.mail.bf1.yahoo.com> Message-ID: <1389877037.9965.58.camel@catalyst.ijs.si> On Thu, 2014-01-16 at 04:42 -0800, Masood Yousaf wrote: > Dear Fellows > > I know how to calculate contour charge density plots for certain > planes. I want to quantify the charge density (as a single value of > charge density) in between two species i.e., along the bond length. > Kindly suggest a way to quantify the charge density. Not sure what you really mean, but if you would like to know what is roughly a value of charge density in some region, then a few options may be useful. E.g., for contours/colorplane plot, set the "Range" (click the "Ranges" tab) and the number of isolines, and then display the thermometer. For more details refer to: http://www.xcrysden.org/doc/plane1control.html Regards, -- 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 yzunt at yahoo.com Thu Jan 16 14:18:58 2014 From: yzunt at yahoo.com (Yusuf Zuntu) Date: Thu, 16 Jan 2014 05:18:58 -0800 (PST) Subject: [xcrysden] Boron atom is bigger than Nitrogen in the structure visualization In-Reply-To: <1389876365.9965.49.camel@catalyst.ijs.si> References: <1389698358.88638.YahooMailNeo@web140701.mail.bf1.yahoo.com> <1389876365.9965.49.camel@catalyst.ijs.si> Message-ID: <1389878338.695.YahooMailNeo@web140705.mail.bf1.yahoo.com> Dear prof Kokalj, Thank you very much On Thursday, January 16, 2014 8:46 PM, Tone Kokalj wrote: On Tue, 2014-01-14 at 03:19 -0800, Yusuf Zuntu wrote: > Please may I know how to fix this problem. In my armchair > hydrogen-terminated boron nitride nanoribbons structure visualization > in XcrysDen, boron atom is bigger than nitrogen atom. Which is the way it should be, because the size of plotted "balls" in xcrysden is proportional with covalent radii. > This is not suppose to be since atomic number of nitrogen atom is more > than the atomic of atomic number of boron atom. Is it? Well, atomic number of N > B, but ... See: https://www.webelements.com/periodicity/covalent_radius/ and try to answer to yourself why it is the other way around, i.e., r_B > r_N. Anyway you can change the display radius via: Modify-->Atomic Radii menu (e.g., if you want to base the size of the balls on the ionic radius instead). Regards, -- 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/20140116/96894786/attachment-0001.htm From georg.eickerling at physik.uni-augsburg.de Thu Jan 16 14:59:47 2014 From: georg.eickerling at physik.uni-augsburg.de (Georg Eickerling) Date: Thu, 16 Jan 2014 14:59:47 +0100 Subject: [xcrysden] How to quantify charge density (as a single value of charge density) along certain Bond length Via Xcrystalden In-Reply-To: <1389876140.81260.YahooMailNeo@web141505.mail.bf1.yahoo.com> References: <1389876140.81260.YahooMailNeo@web141505.mail.bf1.yahoo.com> Message-ID: <20140116145947.2c072b54@poseidon.cpm> Hi again, I guess the answers here will be the same than on the Wien2K list: Use QTAIM! cheers Georg Am Thu, 16 Jan 2014 04:42:20 -0800 (PST) schrieb Masood Yousaf : > Dear Fellows > > I know how to calculate contour charge density plots > for certain planes. I want to quantify the charge density (as a > single value of charge density) in between two species i.e., along > the bond length. Kindly suggest a way to quantify the charge > density.? > > > Thank You > Best wishes > Masood > Universiti Tecknologi Malaysia -- ============================ Dr. Georg Eickerling Universitaet Augsburg Institut fuer Physik Lehrstuhl fuer Chemische Physik und Materialwissenschaften Universitaetsstr. 1 86159 Augsburg E-Mail: georg.eickerling at physik.uni-augsburg.de Phone: +49-821-598-3362 FAX: +49-821-598-3227 WWW: http://www.physik.uni-augsburg.de/cpm/ ===================================================== -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 490 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20140116/c8c08d65/attachment.pgp From masoodyousaf1 at yahoo.com Thu Jan 16 15:54:52 2014 From: masoodyousaf1 at yahoo.com (Masood Yousaf) Date: Thu, 16 Jan 2014 06:54:52 -0800 (PST) Subject: [xcrysden] How to quantify charge density (as a single value of charge density) along certain Bond length Via Xcrystalden In-Reply-To: <20140116145947.2c072b54@poseidon.cpm> References: <1389876140.81260.YahooMailNeo@web141505.mail.bf1.yahoo.com> <20140116145947.2c072b54@poseidon.cpm> Message-ID: <1389884092.62784.YahooMailNeo@web141506.mail.bf1.yahoo.com> Thank You Dr. Kokalj and Dr. Eickerling Best wishes Masood On Thursday, January 16, 2014 7:12 PM, Georg Eickerling wrote: Hi again, I guess the answers here will be the same than on the Wien2K list: Use QTAIM! cheers Georg Am Thu, 16 Jan 2014 04:42:20 -0800 (PST) schrieb Masood Yousaf : > Dear Fellows > > I know how to calculate contour charge density plots >? for certain planes. I want to quantify the charge density (as a > single value of charge density) in between two species i.e., along > the bond length. Kindly suggest a way to quantify the charge > density.? > > > Thank You > Best wishes > Masood > Universiti Tecknologi Malaysia -- ============================ Dr. Georg Eickerling Universitaet Augsburg Institut fuer Physik Lehrstuhl fuer Chemische Physik und Materialwissenschaften Universitaetsstr. 1 86159 Augsburg E-Mail:??? georg.eickerling at physik.uni-augsburg.de Phone:??? +49-821-598-3362 FAX:??? +49-821-598-3227 WWW:??? http://www.physik.uni-augsburg.de/cpm/ ===================================================== _______________________________________________ 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/20140116/e34fcafb/attachment.htm From gopakumargeetha at gmail.com Fri Jan 17 01:37:14 2014 From: gopakumargeetha at gmail.com (Geetha Gopakumar) Date: Fri, 17 Jan 2014 09:37:14 +0900 Subject: [xcrysden] Installation of crysden in MAC Message-ID: Hello all, I am trying to install Crysden software in MAC 10.8 (i386-apple-darwin12.5.0. I downloaded crysden Mac OS version and did as per the advice given in the website. Running ./xcConfigure.sh While running crysden it gives error Bad CPU type Someone can help me how to go about???? Best! Geetha From amar.b.007 at gmail.com Sat Jan 18 17:20:52 2014 From: amar.b.007 at gmail.com (Dr. Amar Bahadur) Date: Sat, 18 Jan 2014 21:50:52 +0530 Subject: [xcrysden] reg: conversion .xyz into .xsf Message-ID: Dear all, How can I convert .xyz file into .xsf file? ========================================== Amar Bahadur Email: amar.b.007 at gmail.com Mob.-+91-9451431428 ========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140118/0c6e9b8f/attachment.htm From member at linkedin.com Fri Jan 24 15:07:36 2014 From: member at linkedin.com (Peram Reddy via LinkedIn) Date: Fri, 24 Jan 2014 14:07:36 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn=2E?= Message-ID: <205827324.902196.1390572456808.JavaMail.app@ela4-app3607.prod> LinkedIn ------------ Peram Reddy solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de Peram Reddy http://www.linkedin.com/e/-fe5rcs-hqtixqoa-60/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I534495831_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnP4Pe3kVd3gPdkALlRZgsjxAskkLd38Md30PczARej4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=2kk9nQf-cfF641 Visualizar perfil de Peram Reddy http://www.linkedin.com/e/-fe5rcs-hqtixqoa-60/rso/154018473/XxwE/name/128644874_I534495831_125/?hs=false&tok=3dnwyTITkfF641 ------------------------------------------ Voc? est? recebendo e-mails de convites. Este e-mail era para Andr? Pereira XCrysden. Saiba por que isto est? inclu?do: http://www.linkedin.com/e/-fe5rcs-hqtixqoa-60/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=2001NGiukfF641 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043 - EUA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140124/0577df6c/attachment.htm From tone.kokalj at ijs.si Mon Jan 27 11:37:44 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 27 Jan 2014 11:37:44 +0100 Subject: [xcrysden] Installation of crysden in MAC In-Reply-To: References: Message-ID: <1390819064.5008.8.camel@catalyst.ijs.si> On Fri, 2014-01-17 at 09:37 +0900, Geetha Gopakumar wrote: > Hello all, > > I am trying to install Crysden software in MAC 10.8 (i386-apple-darwin12.5.0. > > I downloaded crysden Mac OS version and did as per the advice given > in the website. > > Running ./xcConfigure.sh > > While running crysden it gives error > > Bad CPU type I am not a mac user, but as far as I know different macs have different CPUs and seems the one on the website is not compatible with your mac. Have you tried the fink version of xcrysden? http://pdb.finkproject.org/pdb/package.php/xcrysden Also try to browse the xcrysden mailing list about the issues with mac. http://lmgtfy.com/?q=mac+xcrysden+site%3Ademocritos.it Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Mon Jan 27 11:43:27 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 27 Jan 2014 11:43:27 +0100 Subject: [xcrysden] reg: conversion .xyz into .xsf In-Reply-To: References: Message-ID: <1390819407.5008.12.camel@catalyst.ijs.si> On Sat, 2014-01-18 at 21:50 +0530, Dr. Amar Bahadur wrote: > Dear all, > How can I convert .xyz file into .xsf file? You don't need to convert, just use: xcrysden --xyz file.xyz But if you want to convert, then you can do it manually by a text-editor; delete the first two lines of XYZ file and add an "ATOMS" first line. Example: water.xyz:: 3 Water molecule H -0.772 0.161 0.115 O -0.000 -0.322 -0.230 H 0.772 0.161 0.115 water.xsf:: ATOMS H -0.772 0.161 0.115 O -0.000 -0.322 -0.230 H 0.772 0.161 0.115 Regards, -- 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 hadi.arefi at tyndall.ie Mon Jan 27 18:30:38 2014 From: hadi.arefi at tyndall.ie (Hadi Arefi) Date: Mon, 27 Jan 2014 17:30:38 +0000 Subject: [xcrysden] custom-definition file Message-ID: <9B517AB3CFA7E649800F39802E6668C220F83E17@MAILBOXSERVER.tyndall.ie> Dear users, I tried to do some changes in the custom-definition file as mentioned in the below link: http://www.xcrysden.org/doc/custom.html#__toc__8 But even though I re-compiled the program, the changes are not included in the structures yet. I am using the source package of xcrysedn version 1.5.53. Any advised is highly appreciated. Best, Hadi. From tone.kokalj at ijs.si Tue Jan 28 10:45:18 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 28 Jan 2014 10:45:18 +0100 Subject: [xcrysden] custom-definition file In-Reply-To: <9B517AB3CFA7E649800F39802E6668C220F83E17@MAILBOXSERVER.tyndall.ie> References: <9B517AB3CFA7E649800F39802E6668C220F83E17@MAILBOXSERVER.tyndall.ie> Message-ID: <1390902318.29359.4.camel@catalyst.ijs.si> On Mon, 2014-01-27 at 17:30 +0000, Hadi Arefi wrote: > Dear users, > > I tried to do some changes in the custom-definition file as mentioned in the below link: > > http://www.xcrysden.org/doc/custom.html#__toc__8 > > But even though I re-compiled the program, the changes are not included in the structures yet. > I am using the source package of xcrysedn version 1.5.53. Recompiling xcrysden has no effect on ~/.xcrysden/custom-definitions, because the custom definitions work independent on the compilation. You should provide more information on what you are trying to achieve (current info is far insufficient to help). Regards, -- 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 hadi.arefi at tyndall.ie Tue Jan 28 11:00:34 2014 From: hadi.arefi at tyndall.ie (Hadi Arefi) Date: Tue, 28 Jan 2014 10:00:34 +0000 Subject: [xcrysden] custom-definition file In-Reply-To: <1390902318.29359.4.camel@catalyst.ijs.si> References: <9B517AB3CFA7E649800F39802E6668C220F83E17@MAILBOXSERVER.tyndall.ie>, <1390902318.29359.4.camel@catalyst.ijs.si> Message-ID: <4B7FFE04-D21F-46A0-A7CA-895B21A145AD@tyndall.ie> Thanks Antony for your answer, You are absolutely right! I was doing something wrong but it's working now. Best, Hadi. > On 28 Jan 2014, at 09:45, "Tone Kokalj" wrote: > >> On Mon, 2014-01-27 at 17:30 +0000, Hadi Arefi wrote: >> Dear users, >> >> I tried to do some changes in the custom-definition file as mentioned in the below link: >> >> http://www.xcrysden.org/doc/custom.html#__toc__8 >> >> But even though I re-compiled the program, the changes are not included in the structures yet. >> I am using the source package of xcrysedn version 1.5.53. > > Recompiling xcrysden has no effect on ~/.xcrysden/custom-definitions, > because the custom definitions work independent on the compilation. > > You should provide more information on what you are trying to achieve > (current info is far insufficient to help). > > Regards, > -- > 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