From member at linkedin.com Thu May 2 04:45:48 2013 From: member at linkedin.com (Bin Shao via LinkedIn) Date: Thu, 2 May 2013 02:45:48 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn?= Message-ID: <1267808833.11267620.1367462748587.JavaMail.app@ela4-bed77.prod> LinkedIn ------------ Bin Shao solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de Bin Shao http://www.linkedin.com/e/-fe5rcs-hg7c0hot-1z/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I373712130_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnP0Pcj8NdPcTcQALpjBcdlpBgB4LcPcQdzgQc38Vcz4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=0_Atx6qaG5MRI1 Visualizar perfil de Bin Shao http://www.linkedin.com/e/-fe5rcs-hg7c0hot-1z/rso/118072233/syDA/name/128644874_I373712130_125/?hs=false&tok=0TYL9OK3C5MRI1 ------------------------------------------ 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-hg7c0hot-1z/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=2jg8sOLXC5MRI1 (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/20130502/8ba1c3e3/attachment.htm From vjain045 at gmail.com Thu May 2 12:49:26 2013 From: vjain045 at gmail.com (vishal jain) Date: Thu, 2 May 2013 16:19:26 +0530 Subject: [xcrysden] Installation Problem Message-ID: Dear All I have to install xcrysden to ubuntu 11.04 using xcrysden_1.5.53-1_i386.deb file but it shows the error message dependency is not satisfiable: libc6(>=2.15) How to i install in ubuntu 11.01 since (IBM R51 laptop i cannot install ubuntu 12.04) Thanks and regards Vishal Jain -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130502/d7884fe1/attachment.htm From tone.kokalj at ijs.si Mon May 13 12:42:06 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 13 May 2013 12:42:06 +0200 Subject: [xcrysden] Installation Problem In-Reply-To: References: Message-ID: <1368441726.4509.5.camel@catalyst.ijs.si> On Thu, 2013-05-02 at 16:19 +0530, vishal jain wrote: > Dear All > > > I have to install xcrysden to ubuntu 11.04 using > xcrysden_1.5.53-1_i386.deb file but it shows the error message > dependency is not satisfiable: libc6(>=2.15) .. which implies your ubuntu is too old and you have unresolved dependecies. You may either (i) upgrade your ubuntu or (ii) compile xcrysden from sources, i.e.: http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz 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 yves.limoge at cea.fr Wed May 15 11:06:03 2013 From: yves.limoge at cea.fr (Yves Limoge) Date: Wed, 15 May 2013 11:06:03 +0200 Subject: [xcrysden] centering plots Message-ID: <51934FFB.9020802@cea.fr> Y. Limoge Xcrysden community Plotting structures and isosurfaces relatives to defects in solids, I would like i) to center xcysden plots on a given atom (defect), ii) to enlight the defect and surounding atoms but shadowing the others, bot for a better visibility of the structure. Is this possible, and how ? Thanks youy for any advice. Y. Limoge From tone.kokalj at ijs.si Tue May 21 12:28:47 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 21 May 2013 12:28:47 +0200 Subject: [xcrysden] centering plots In-Reply-To: <51934FFB.9020802@cea.fr> References: <51934FFB.9020802@cea.fr> Message-ID: <1369132127.25205.7.camel@catalyst.ijs.si> On Wed, 2013-05-15 at 11:06 +0200, Yves Limoge wrote: > Y. Limoge Xcrysden community > > Plotting structures and isosurfaces relatives to defects in solids, I would like i) to > center xcysden plots on a given atom (defect), ii) to enlight the defect and surounding > atoms but shadowing the others, bot for a better visibility of the structure. > Is this possible, and how ? There is no automatic way of doing these, but they can be done more or less manually. As for the item-(ii), it can be achieved manually by a trick, which goes as follows: i) identify which atoms you would like to enhance visually ii) substitute all the other atoms in the XSF file by other atom types; For example: say that we have ZnS, and you want to stress only a few of Zn and S atoms; substitute all the others, say, by Se an Ga iii) modify/reduce the display radii of Se and Ga (menu: Modify->Atomic Radius) and modify their colors (Modify->Atomic color); by using a "smart" radii/color modification you can achieve rather good "enhancement"; In addition to that you can also do some post-processing image manipulation, e.g., with gimp. 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 yves.limoge at cea.fr Tue May 21 14:47:45 2013 From: yves.limoge at cea.fr (Yves Limoge) Date: Tue, 21 May 2013 14:47:45 +0200 Subject: [xcrysden] centering plots In-Reply-To: <1369132127.25205.7.camel@catalyst.ijs.si> References: <51934FFB.9020802@cea.fr> <1369132127.25205.7.camel@catalyst.ijs.si> Message-ID: <519B6CF1.8040306@cea.fr> Le 21/05/2013 12:28, Tone Kokalj a ?crit : > On Wed, 2013-05-15 at 11:06 +0200, Yves Limoge wrote: >> Y. Limoge Xcrysden community >> >> Plotting structures and isosurfaces relatives to defects in solids, I would like i) to >> center xcysden plots on a given atom (defect), ii) to enlight the defect and surounding >> atoms but shadowing the others, bot for a better visibility of the structure. >> Is this possible, and how ? > > There is no automatic way of doing these, but they can be done more or > less manually. > > As for the item-(ii), it can be achieved manually by a trick, which goes > as follows: > > i) identify which atoms you would like to enhance visually > ii) substitute all the other atoms in the XSF file by other atom types; > For example: say that we have ZnS, and you want to stress only a few of > Zn and S atoms; substitute all the others, say, by Se an Ga > iii) modify/reduce the display radii of Se and Ga (menu: Modify->Atomic > Radius) and modify their colors (Modify->Atomic color); by using a > "smart" radii/color modification you can achieve rather good > "enhancement"; > > In addition to that you can also do some post-processing image > manipulation, e.g., with gimp. > > Regards, Y. Limoge M. T. KOKALJ Saclay ce 21 mais 2013 Dear Sir I will try the solution you propose for the enlightment of the defect ans surrounding. Thanks for the solution. As concern the centering on a given atom of the plot, I already did this operation with a small fortan program working on simple data giving the position of the atoms coming from pw and producing an input file for xbs, a much simple visualization tools. I wonder if I could do the job on the much elaborated xsf files xcrysden uses ? Do you think it is possible ? Sincerely yours. Y. Limoge From yuanyue.liu.microman at gmail.com Mon May 27 00:04:58 2013 From: yuanyue.liu.microman at gmail.com (Yuanyue Liu) Date: Sun, 26 May 2013 17:04:58 -0500 Subject: [xcrysden] fail to visualize the Fermi surface Message-ID: Dear XcrysDen users: I encounter a problem when visualizing the Fermi surface. XcrysDen can read the attached bxsf file, but after selecting the bands to plot, it crashes. I also attach the output file with error messages. Could someone help me with this issue? Thanks in advance. Yuanyue -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130526/55b1fc6f/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Bands_FS.bxsf Type: application/octet-stream Size: 10305 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20130526/55b1fc6f/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: output Type: application/octet-stream Size: 9577 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20130526/55b1fc6f/attachment-0001.obj From tone.kokalj at ijs.si Thu May 30 08:54:44 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 30 May 2013 08:54:44 +0200 Subject: [xcrysden] fail to visualize the Fermi surface In-Reply-To: References: Message-ID: <1369896884.12998.17.camel@catalyst.ijs.si> On Sun, 2013-05-26 at 17:04 -0500, Yuanyue Liu wrote: > Dear XcrysDen users: > > I encounter a problem when visualizing the Fermi surface. XcrysDen can > read the attached bxsf file, but after selecting the bands to plot, it > crashes. I also attach the output file with error messages. Could > someone help me with this issue? Thanks in advance. The problem is likely that your system is probably a 2D system and you assigned only 2 mesh-points along the 3rd direction. The problem is that xcrysden expects the real 3D mesh and only 2 points in 3rd direction are not sufficient (I will insert a check in the code that will warn about this). Please use more points in 3rd direction and let me know if it works. Note that xcrysden will not plot "loops" for 2D Fermi surfaces, but rather "cylinders" ..., because it works-only-for/expects-the 3D system. 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 fedele.stabile at fis.unical.it Thu May 30 11:55:58 2013 From: fedele.stabile at fis.unical.it (Fedele Stabile) Date: Thu, 30 May 2013 11:55:58 +0200 Subject: [xcrysden] XcrysDen - CRYSTAL configuration Help Message-ID: <1369907758.4448.78.camel@tango.fis.unical.it> Hello, may I have help to install XCrysDen and be able to use Crystal Inputs? I just installed xcrysden-1.5.53-bin-semishared and CRYSTAL09.v.2.0.1 Now I have problems configuring xcrysden: I created through xvConfigure.sh a file for custom definitions in which there is the name of the executable of crystal, but it doesn't work: xcrysden doesn't recognize crystal. Do I have to indicate instead runcry09 (in utils09 folder) which contains also variable environment definitions? Best regards, Fedele From fedele.stabile at fis.unical.it Thu May 30 11:53:54 2013 From: fedele.stabile at fis.unical.it (Fedele Stabile) Date: Thu, 30 May 2013 11:53:54 +0200 Subject: [xcrysden] XcrysDen - CRYSTAL configuration Help Message-ID: <1369907634.4448.77.camel@tango.fis.unical.it> Hello, may I have help to install XCrysDen and be able to use Crystal Inputs? I just installed xcrysden-1.5.53-bin-semishared and CRYSTAL09.v.2.0.1 Now I have problems configuring xcrysden: I created through xvConfigure.sh a file for custom definitions in which there is the name of the executable of crystal, but it doesn't work: xcrysden doesn't recognize crystal. Do I have to indicate instead runcry09 (in utils09 folder) which contains also variable environment definitions? Best regards, Fedele From tone.kokalj at ijs.si Thu May 30 14:48:06 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 30 May 2013 14:48:06 +0200 Subject: [xcrysden] XcrysDen - CRYSTAL configuration Help In-Reply-To: <1369907634.4448.77.camel@tango.fis.unical.it> References: <1369907634.4448.77.camel@tango.fis.unical.it> Message-ID: <1369918086.30793.3.camel@catalyst.ijs.si> On Thu, 2013-05-30 at 11:53 +0200, Fedele Stabile wrote: > Hello, > may I have help to install XCrysDen and be able to use Crystal Inputs? > > I just installed xcrysden-1.5.53-bin-semishared and CRYSTAL09.v.2.0.1 > > Now I have problems configuring xcrysden: > I created through xvConfigure.sh a file for custom definitions in which > there is the name of the executable of crystal, but it doesn't work: > xcrysden doesn't recognize crystal. > Do I have to indicate instead runcry09 (in utils09 folder) which > contains also variable environment definitions? Please consult this document: http://www.xcrysden.org/doc/custom.html and if you will still face problems, then email me your ~/.xcrysden/custom-definitions file. 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 fedele.stabile at fis.unical.it Thu May 30 16:28:35 2013 From: fedele.stabile at fis.unical.it (Fedele Stabile) Date: Thu, 30 May 2013 16:28:35 +0200 Subject: [xcrysden] XcrysDen - CRYSTAL configuration Help In-Reply-To: <1369918086.30793.3.camel@catalyst.ijs.si> References: <1369907634.4448.77.camel@tango.fis.unical.it> <1369918086.30793.3.camel@catalyst.ijs.si> Message-ID: <1369924115.4448.82.camel@tango.fis.unical.it> This is my custom-definitions file: set system(c95_exist) 1 ------------------------------------------------------------------------ # CRYSTAL modules ------------------------------------------------------------------------ set system(c95_crystal) /apps/CRYSTAL09.v.2/bin/Linux-ifort_XE_openmpi-1.6_emt64/v2_0_1/crystal set system(c95_properties) /apps/CRYSTAL09.v.2/bin/Linux-ifort_XE_openmpi-1.6_emt64/v2_0_1/properties I'm not able to see any Crystal input file. Fedele Il giorno gio, 30/05/2013 alle 14.48 +0200, Tone Kokalj ha scritto: > On Thu, 2013-05-30 at 11:53 +0200, Fedele Stabile wrote: > > Hello, > > may I have help to install XCrysDen and be able to use Crystal Inputs? > > > > I just installed xcrysden-1.5.53-bin-semishared and CRYSTAL09.v.2.0.1 > > > > Now I have problems configuring xcrysden: > > I created through xvConfigure.sh a file for custom definitions in which > > there is the name of the executable of crystal, but it doesn't work: > > xcrysden doesn't recognize crystal. > > Do I have to indicate instead runcry09 (in utils09 folder) which > > contains also variable environment definitions? > > Please consult this document: > > http://www.xcrysden.org/doc/custom.html > > and if you will still face problems, then email me your > ~/.xcrysden/custom-definitions file. > > Regards, From tone.kokalj at ijs.si Fri May 31 09:10:47 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 31 May 2013 09:10:47 +0200 Subject: [xcrysden] XcrysDen - CRYSTAL configuration Help In-Reply-To: <1369924115.4448.82.camel@tango.fis.unical.it> References: <1369907634.4448.77.camel@tango.fis.unical.it> <1369918086.30793.3.camel@catalyst.ijs.si> <1369924115.4448.82.camel@tango.fis.unical.it> Message-ID: <1369984247.16587.6.camel@catalyst.ijs.si> On Thu, 2013-05-30 at 16:28 +0200, Fedele Stabile wrote: > This is my custom-definitions file: > > set system(c95_exist) 1 > ------------------------------------------------------------------------ > # CRYSTAL modules > ------------------------------------------------------------------------ > > set system(c95_crystal) /apps/CRYSTAL09.v.2/bin/Linux-ifort_XE_openmpi-1.6_emt64/v2_0_1/crystal > set system(c95_properties) /apps/CRYSTAL09.v.2/bin/Linux-ifort_XE_openmpi-1.6_emt64/v2_0_1/properties This looks OK. Did you verified that the specified path is correct and that "crystal" and "properties" binaries have executable permissions. If the answer to all these question is yes, then you should describe in more details the cause that prevents the viewing of Crystal inputs. 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