From member at linkedin.com Wed Jan 2 20:33:44 2013 From: member at linkedin.com (Ajit Vallabhaneni via LinkedIn) Date: Wed, 2 Jan 2013 19:33:44 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn?= Message-ID: <780571018.39903223.1357155224486.JavaMail.app@ela4-app2311.prod> LinkedIn ------------ Ajit Vallabhaneni solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de Ajit Vallabhaneni http://www.linkedin.com/e/-fe5rcs-hbgv6h7c-2e/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I305446936_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnPoPejoQd3kMcQALdRpbjmZye7ELcPoOe3gPejkOc34LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=1GpCHBrDtR95A1 Visualizar perfil de Ajit Vallabhaneni http://www.linkedin.com/e/-fe5rcs-hbgv6h7c-2e/rso/184682876/F7Ed/name/128644874_I305446936_125/?hs=false&tok=1DfPIQVEBR95A1 ------------------------------------------ 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-hbgv6h7c-2e/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=0VKMm4fktR95A1 (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/20130102/f425bcee/attachment.htm From trambui1985 at gmail.com Wed Jan 2 21:51:46 2013 From: trambui1985 at gmail.com (Tram Bui) Date: Wed, 2 Jan 2013 13:51:46 -0700 Subject: [xcrysden] building an interfacial structure using xcrysden Message-ID: Dear Xcrysden Users, I'm planning to build a structure that contain an interface of hzp-Zr [0001] and fcc-ZrH [111]. I want to run some calculations for this interfacial energy. However, I really don't know how to start. So I write to the forum hopefully getting some suggestions from anyone that has had experience building such interface through Xcrysden. I'd really appreciate all the help! Regards, Tram -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130102/9079bf53/attachment.htm From usnat59 at gmail.com Thu Jan 3 09:47:02 2013 From: usnat59 at gmail.com (Usnatdin Ernazarov) Date: Thu, 3 Jan 2013 09:47:02 +0100 Subject: [xcrysden] Fwd: Printed figure is tilted and doubled In-Reply-To: References: Message-ID: Hi, I am using xcrysden-1.5.53-bin-cygwin. I have plotted electron localization function. On the screen there is one figure, which is not tilted. However, the figure printed into a file of *.png or other formats is not the same as it is on the screen. Namely, it has been doubled and is tilted . Is there any tric(s) to get the same figure as that on the screen? Thanks. Usnatdin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130103/b75cb70b/attachment.htm From usnat59 at gmail.com Thu Jan 3 09:55:32 2013 From: usnat59 at gmail.com (Usnatdin Ernazarov) Date: Thu, 3 Jan 2013 09:55:32 +0100 Subject: [xcrysden] Vizualization of charge density from calculations by VASP for a particular plane of a crystal Message-ID: *My question is related to the one entitled "*Help regarding cutting planes and crystals*" by *Arvind Ajoy *(*2009-06-08). ** *Is it possible to vizualize charge density for particular plane of a crystal if the results are obtained from calculations by VASP ? * Best regards Usnatdin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130103/34be0f62/attachment-0001.htm From usnat59 at gmail.com Thu Jan 3 10:29:21 2013 From: usnat59 at gmail.com (Usnatdin Ernazarov) Date: Thu, 3 Jan 2013 10:29:21 +0100 Subject: [xcrysden] Vizualization of charge density from calculations by VASP for a particular plane of a crystal In-Reply-To: References: Message-ID: *My question is related to the one entitled "*Help regarding cutting planes and crystals*" by *Arvind Ajoy *(*2009-06-08). *Is it possible to vizualize charge density for particular plane of a crystal if the results are obtained from calculations by VASP ?* *Usnatdin* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130103/99fe35c8/attachment.htm From tone.kokalj at ijs.si Thu Jan 3 18:01:46 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 03 Jan 2013 18:01:46 +0100 Subject: [xcrysden] building an interfacial structure using xcrysden In-Reply-To: References: Message-ID: <1357232506.17842.15.camel@catalyst.ijs.si> On Wed, 2013-01-02 at 13:51 -0700, Tram Bui wrote: > Dear Xcrysden Users, > > I'm planning to build a structure that contain an interface of > hzp-Zr [0001] and fcc-ZrH [111]. I want to run some calculations for > this interfacial energy. However, I really don't know how to start. So > I write to the forum hopefully getting some suggestions from anyone > that has had experience building such interface through Xcrysden. xcrysden cannot build structures but merely visualizes them, unless you have the CRYSTAL program, http://www.crystal.unito.it/ (in that case it can use some of crystal functionality and offers some structure building capability). The main tips for the structure building would be the following: 1) one first need to well understand the structure of a given system 2) then a structure can be build by assembling bits together, say, one by one; here some small user-built auxiliary scripts/programs can be much beneficial (an example would be a simple script for building a supercells). In you particular case, the basic building block would be the two hcp(0001) (A-B-A-B- stacking) and three fcc(111) layers (A-B-C-A-B-C- stacking), which can be then "multiplied" to a particular supercell size and stacked together. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Thu Jan 3 18:02:46 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 03 Jan 2013 18:02:46 +0100 Subject: [xcrysden] Fwd: Printed figure is tilted and doubled In-Reply-To: References: Message-ID: <1357232566.17842.16.camel@catalyst.ijs.si> On Thu, 2013-01-03 at 09:47 +0100, Usnatdin Ernazarov wrote: > Hi, > I am using xcrysden-1.5.53-bin-cygwin. I have plotted electron > localization function. On the screen there is one figure, which is not > tilted. However, the figure printed into a file of *.png or other > formats is not the same as it is on the screen. Namely, it has been > doubled and is tilted . Is there any tric(s) to get the same figure as > that on the screen? Could you provide an example of such a figure? 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 3 18:07:57 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 03 Jan 2013 18:07:57 +0100 Subject: [xcrysden] Vizualization of charge density from calculations by VASP for a particular plane of a crystal In-Reply-To: References: Message-ID: <1357232877.17842.20.camel@catalyst.ijs.si> On Thu, 2013-01-03 at 09:55 +0100, Usnatdin Ernazarov wrote: > My question is related to the one entitled "Help regarding cutting > planes and crystals" by Arvind Ajoy (2009-06-08). > > Is it possible to vizualize charge density for particular plane of a > crystal if the results are obtained from calculations by VASP ? In general there are two possibilities (which are not equivalent): (1) calculate the charge density for the whole crystal cell and then you can display the charge density on any basal AB, AC, or BC plane by xcrysden (2) for an arbitrary plane you need to specially calculate the charge density on that plane (requires some small auxiliary calculation to get the plane right), in your case by VASP program I believe there are VASP --> XSF converters. You will need the charge density in XSF format to display it by xcrysden. 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 usnat59 at gmail.com Fri Jan 4 13:16:21 2013 From: usnat59 at gmail.com (Usnatdin Ernazarov) Date: Fri, 4 Jan 2013 13:16:21 +0100 Subject: [xcrysden] Fwd: Printed figure is tilted and doubled In-Reply-To: References: <1357232566.17842.16.camel@catalyst.ijs.si> Message-ID: Here is the example of the figure printed into a file , which is not the same as it is on the screen. Usnat > Could you provide an example of such a figure? >> Regards, >> -- >> Anton Kokalj >> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia >> (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130104/7213e515/attachment.htm From eng_rageh at yahoo.com Sat Jan 5 07:50:20 2013 From: eng_rageh at yahoo.com (rageh attia) Date: Fri, 4 Jan 2013 22:50:20 -0800 (PST) Subject: [xcrysden] question Message-ID: <1357368620.5521.YahooMailClassic@web140703.mail.bf1.yahoo.com> Hello all ??????????? I am a new user of XCrySDen and i want to use it to visualize CRYSTAL09 . I have?CRYSTAL09 for windows platform and i tried to install??XCrySDen on windows but it did't work .So I made my friend to download and install the one for linex platform (upontu) but when I try to run the code the File- ->CRYSTAL92/98/03/06 was inactive .Please any one guide me what to do. ????????????????????????????????????????????????????????????????????????????????????????????????????????????? Regards ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130104/d80f30ee/attachment.htm From usnat59 at gmail.com Sat Jan 5 14:05:22 2013 From: usnat59 at gmail.com (Usnatdin Ernazarov) Date: Sat, 5 Jan 2013 14:05:22 +0100 Subject: [xcrysden] example of doubled and tilted figure Message-ID: Here is the example of the figure saved by xcrysden, which is not the same as it is on the screen. Usnat -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130105/3bfc4488/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: elf.png Type: image/png Size: 21866 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20130105/3bfc4488/attachment-0001.png From wyxphy at yahoo.com.cn Tue Jan 8 01:31:22 2013 From: wyxphy at yahoo.com.cn (Yuanxu Wang) Date: Tue, 8 Jan 2013 08:31:22 +0800 (CST) Subject: [xcrysden] can not open saved xcrysden script files (version 1.5.53) Message-ID: <1357605082.58502.YahooMailClassic@web15307.mail.cnb.yahoo.com> Dear users, I installed semishared xcrysden (version 1.5.53). After I? modified structure (labels et al.), I saved it as xcrysden script file. Then I open it by using "xcrysden? -s o.xcrysden". Xcrysden is closed suddenly. Error message is below: ?Running on platform : unix ?? Operating system : Linux Package ImageMagick's convert: /usr/bin/convert Package ImageMagick's import: /usr/bin/import Package Xwd: /usr/bin/xwd Executing: /home/wyx/xcrysden-1.5.53-bin-semishared/bin/ftnunit Error in startup script: child killed: segmentation violation ??? while executing "exec $system(BINDIR)/xsf2xsf $filedir $filedir.raw" ??? ("eval" body line 1) ??? invoked from within "eval {exec $system(BINDIR)/xsf2xsf $filedir $filedir.raw} $xcMisc(reduce_to)" ??? (procedure "xsfOpen" line 26) ??? invoked from within "xsfOpen $filedir .mesa" ??? (procedure "parseComLinArg" line 64) ??? invoked from within "parseComLinArg $args" ??? (procedure "::scripting::open" line 2) ??? invoked from within "::scripting::open --xsf $system(SCRDIR)/xc_xsf.$system(PID)" ??? (file "/home/wyx/OsN2-1/elf/O/o.xcrysden" line 94) ??? invoked from within "source [gunzipFile $scriptFile]" ??? ("uplevel" body line 4) ??? invoked from within "uplevel \#0 { ??????? cd $system(PWD) ??????? SetWatchCursor ??????? source [gunzipFile $scriptFile] ??????? ResetCursor ??? }" ??? (procedure "scripting::source" line 7) ??? invoked from within "scripting::source $filedir???????????????? " ??? (procedure "parseComLinArg" line 247) ??? invoked from within "parseComLinArg [lrange $argv 2 end]" ??? invoked from within "if { [llength $argv] > 2 } { ??? parseComLinArg [lrange $argv 2 end] } else { ??? ViewMol . }" ??? (file "/home/wyx/xcrysden-1.5.53-bin-semishared/Tcl/xcInit.tcl" line 609) Thank you! Yuanxu WANG -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130108/051ef441/attachment.htm From tone.kokalj at ijs.si Thu Jan 10 13:47:54 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 10 Jan 2013 13:47:54 +0100 Subject: [xcrysden] example of doubled and tilted figure In-Reply-To: References: Message-ID: <1357822074.14916.14.camel@catalyst.ijs.si> On Sat, 2013-01-05 at 14:05 +0100, Usnatdin Ernazarov wrote: > Here is the example of the figure saved by xcrysden, which is not the > same as it is on the screen. I suspect it may be the problem of the program used to convert image into PNG format; the default that xcrysden uses is the ImageMagick's convert program. Check for the xcrysden startup output, line looking as: Package ImageMagick's convert: /usr/bin/convert To verify if this is the case save the image in PPM format; this is native format that xcrysden uses. If the PPM saved figure is OK, then the hypothesis is correct. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Thu Jan 10 13:53:26 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 10 Jan 2013 13:53:26 +0100 Subject: [xcrysden] question In-Reply-To: <1357368620.5521.YahooMailClassic@web140703.mail.bf1.yahoo.com> References: <1357368620.5521.YahooMailClassic@web140703.mail.bf1.yahoo.com> Message-ID: <1357822406.14916.19.camel@catalyst.ijs.si> On Fri, 2013-01-04 at 22:50 -0800, rageh attia wrote: > Hello all > I am a new user of XCrySDen and i want to use it to > visualize CRYSTAL09 . I have CRYSTAL09 for windows platform and i > tried to install XCrySDen on windows but it did't work .So I made my > friend to download and install the one for linex platform (upontu) > but when I try to run the code the File- ->CRYSTAL92/98/03/06 was > inactive .Please any one guide me what to do. xcrysden cannot directly run on windows but requires the Cygwin (and even so its functionality is limited). Why don't you also use the Linux version of CRYSTAL09 and customize xcrysden accordingly ( http://www.xcrysden.org/doc/custom.html )? Then you will be to use xcrysden's extension for CRYSTAL. 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 10 13:55:02 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 10 Jan 2013 13:55:02 +0100 Subject: [xcrysden] can not open saved xcrysden script files (version 1.5.53) In-Reply-To: <1357605082.58502.YahooMailClassic@web15307.mail.cnb.yahoo.com> References: <1357605082.58502.YahooMailClassic@web15307.mail.cnb.yahoo.com> Message-ID: <1357822502.14916.21.camel@catalyst.ijs.si> On Tue, 2013-01-08 at 08:31 +0800, Yuanxu Wang wrote: > Dear users, > > I installed semishared xcrysden (version 1.5.53). After I modified > structure (labels et al.), I saved it as xcrysden script file. Then I > open it by using "xcrysden -s o.xcrysden". Xcrysden is closed > suddenly. > Does it happen with all the scripts or with just the particulate one you are mentioning? If the latter applies, please send me the script. 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 wyxphy at yahoo.com.cn Fri Jan 11 04:00:36 2013 From: wyxphy at yahoo.com.cn (wangyx) Date: Fri, 11 Jan 2013 11:00:36 +0800 Subject: [xcrysden] can not open saved xcrysden script files (version 1.5.53) In-Reply-To: <1357822502.14916.21.camel@catalyst.ijs.si> References: <1357605082.58502.YahooMailClassic@web15307.mail.cnb.yahoo.com> <1357822502.14916.21.camel@catalyst.ijs.si> Message-ID: <12351202.DFsD0fCaKi@wyxphy> Dear Dr. Anton Kokalj, Thank you! It happens for all cases. The attached file is the script file. Yuanxu WANG ? 2013?1?10? ??? 13:55:02?Tone Kokalj ??? > On Tue, 2013-01-08 at 08:31 +0800, Yuanxu Wang wrote: > > Dear users, > > > > I installed semishared xcrysden (version 1.5.53). After I modified > > structure (labels et al.), I saved it as xcrysden script file. Then I > > open it by using "xcrysden -s o.xcrysden". Xcrysden is closed > > suddenly. > > Does it happen with all the scripts or with just the particulate one you > are mentioning? If the latter applies, please send me the script. > > Regards, -------------- next part -------------- # ------------------------------------------------------------------------ # This is the script saved via the XCRYSDEN "File-->Save Current State # and Structure" menu. This feature saves the currently displayed # structure. When it will be loaded again it will recall all the # display parameters, such as orientation, zoom, perspective, ... # # Execute this script as: xcrysden --script this_file_name # # File created by wyx on wyxphy.site # File creation date: Xxx Xxx XX XX:XX:XX CEST 20XX # ------------------------------------------------------------------------ # ======================================================================== # # # # STRUCTURE-PART OF THE FILE # # # # ======================================================================== # # ------------------------------------------------------------------------ # BEGIN: XSF structure data # ------------------------------------------------------------------------ # Store the content of the XSF file in the xsfStructure variable set xsfStructure { CRYSTAL PRIMVEC 8.2960630000 0.0377060000 0.0000000000 0.0450170000 9.9085740000 0.0000000000 0.0000000000 0.0000000000 5.4472440000 CONVVEC 8.2960630000 0.0377060000 0.0000000000 0.0450170000 9.9085740000 0.0000000000 0.0000000000 0.0000000000 5.4472440000 PRIMCOORD 48 1 1 0.0460680000 9.8989490000 5.3609320000 1 0.0460680000 9.8989490000 2.8099340000 1 8.3137110000 4.9831420000 5.4238050000 1 8.3137110000 4.9831420000 2.7470610000 1 4.1497620000 0.0345160000 0.0878150000 1 4.1497620000 0.0345160000 2.6358070000 1 4.1923010000 4.9933230000 0.1184830000 1 4.1923010000 4.9933230000 2.6051390000 1 2.0457120000 2.4877870000 1.3618110000 1 2.0755590000 2.4873090000 4.0854330000 1 2.0834160000 7.4485640000 1.3618110000 1 2.1792890000 7.4810230000 4.0854330000 1 6.2559490000 2.4924470000 1.3618110000 1 6.1933730000 2.5106610000 4.0854330000 1 6.3025400000 7.4541160000 1.3618110000 1 6.2293300000 7.4616010000 4.0854330000 2 0.5266650000 1.9921530000 0.0047390000 2 0.5266650000 1.9921530000 2.7188830000 2 0.5764820000 6.9571460000 0.0023040000 2 0.5764820000 6.9571460000 2.7213180000 2 4.6632180000 2.0371410000 5.4465140000 2 4.6632180000 2.0371410000 2.7243520000 2 4.7476670000 7.0014000000 0.0198120000 2 4.7476670000 7.0014000000 2.7038100000 2 3.6174250000 2.9895170000 0.0136620000 2 3.6174250000 2.9895170000 2.7099600000 2 3.6676720000 7.9394320000 0.0142830000 2 3.6676720000 7.9394320000 2.7093390000 2 7.7383540000 2.9680090000 0.0149690000 2 7.7383540000 2.9680090000 2.7086530000 2 7.8211950000 7.9381160000 5.4350810000 2 7.8211950000 7.9381160000 2.7357860000 2 1.5405250000 4.4924610000 1.3618110000 2 1.2373380000 4.1992320000 4.0854330000 2 1.5407560000 9.4480340000 1.3618110000 2 1.6492370000 9.4433950000 4.0854330000 2 5.7389230000 4.4897940000 1.3618110000 2 5.6817180000 4.5198940000 4.0854330000 2 5.7907140000 9.4583540000 1.3618110000 2 5.6853070000 9.4692890000 4.0854330000 2 2.5494030000 0.4859600000 1.3618110000 2 2.6635080000 0.4629070000 4.0854330000 2 2.6016160000 5.4541350000 1.3618110000 2 6.8125540000 0.4839340000 1.3618110000 2 6.6975560000 0.4986310000 4.0854330000 2 6.7960880000 5.4345470000 1.3618110000 2 6.7415230000 5.4650540000 4.0854330000 3 2.9729780000 5.6158930000 4.0854330000 } # END of defintion of xsfStructure variable WriteFile $system(SCRDIR)/xc_xsf.$system(PID) $xsfStructure w ::scripting::open --xsf $system(SCRDIR)/xc_xsf.$system(PID) # ------------------------------------------------------------------------ # END: XSF structure data # ------------------------------------------------------------------------ # ======================================================================== # # # # STATE-PART OF THE FILE # # # # ======================================================================== # # ------------------------------------------------------------------------ # definition of xcMisc array # ------------------------------------------------------------------------ array set xcMisc {ImageMagick.import /usr/bin/import reduce_to {} rescale_image_list {up down left right center rotXY rotXZ rotYZ rotAB rotAC rotBC wireframes_2d pointlines_2d pipeballs_2d ballsticks2_2d ballsticks1_2d spacefills_2d spacefills_3d ballsticks_3d pipeballs_3d sticks_3d dm_wire dm_solid dm_anaglyph dm_stereo dm_smooth dm_flat rep_unit rep_asym} resolution 1920x1200 gif_encoder convert status_init_label {Building GUI ...} wm_rootYshift 0 debug 0 convert /usr/bin/convert titlefile /home/wyx/xcrys_tmp/xc_9999/p.xsf xwd /usr/bin/xwd resolution_ratio1 1.0 resolutionX 1920 resolution_ratio2 1.0 wm_rootXshift 0 resolutionY 1200 ImageMagick.convert /usr/bin/convert} # ------------------------------------------------------------------------ # display "waiting" toplevel and watch-cursor # ------------------------------------------------------------------------ set wait_window [DisplayUpdateWidget "Reconstructing" "Reconstructing the structure and display parameters. Please wait"] SetWatchCursor set xcCursor(dont_update) 1 # ------------------------------------------------------------------------ # size of the main window fonts # ------------------------------------------------------------------------ wm geometry . 1920x1136 # ------------------------------------------------------------------------ # BEGIN: create fonts # ------------------------------------------------------------------------ saveState:fontCreate font10 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font1 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font11 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font2 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font12 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font3 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font13 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font4 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkDefaultFont -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkMenuFont -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font14 -family {DejaVu Sans Mono} -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font5 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font15 -family {Nimbus Roman No9 L} -size 47 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font6 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font7 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkHeadingFont -family Arial -size -12 -weight bold -slant roman -underline 0 -overstrike 0 saveState:fontCreate font8 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate font9 -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkTooltipFont -family Arial -size -10 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkTextFont -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkCaptionFont -family Arial -size -14 -weight bold -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkSmallCaptionFont -family Arial -size -10 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkFixedFont -family {DejaVu Sans Mono} -size -12 -weight normal -slant roman -underline 0 -overstrike 0 saveState:fontCreate TkIconFont -family Arial -size -12 -weight normal -slant roman -underline 0 -overstrike 0 # ------------------------------------------------------------------------ # END: create fonts # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # BEGIN: take care of display-mode # ------------------------------------------------------------------------ set translationStep 0.05 set rotstep 10 set light On Lighting On array set mode2D {PL Off SF Off WF Off BS1 Off PB Off BS2 Off} array set mode3D {space Off sticks On pipe Off balls On} array set dispmode {mode3D_name BS mode3D Preset mode3D_f2_packinfo {-in .ctrl.c.f.fr3 -anchor center -expand 1 -fill x -ipadx 0 -ipady 0 -padx 0 -pady 0 -side top} style 3D mode3D_ModeFrame .ctrl.c.f.fr3.2.a0} saveState:displayMode set style3D(draw) solid; Style3D draw solid set style3D(shade) smooth; Style3D shade smooth set viewer(rot_zoom_button_mode) Discrete; Viewer:rotZoomButtonMode # ------------------------------------------------------------------------ # END: take care of display-mode # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # Number of Units Drawn # ------------------------------------------------------------------------ set nxdir 1 set nydir 1 set nzdir 1 # ------------------------------------------------------------------------ # BEGIN: Atomic-Labels/Fonts # ------------------------------------------------------------------------ array set atomLabel {globalFont {-*-Nimbus Roman No9 L-medium-r-*-*-47-*-*-*-*-*-*-*} lastfont font15 atomFont.brightID 3 fontBrowser {Simple Font Browser} globalFont.darkID 2 globalFont.brightColor {1.0 1.0 1.0} atomFont.label {} atomFont.do_display 1 atomFont.darkColor {0.0 0.0 0.0} atomFont.entry .atom_label.nb.fatomLabel.atom.e1 atomFont {} atomFont.id {} globalFont.brightID 1 atomTypes.do_not_display {} atomFont.darkID 4 atomFont.brightColor {1.0 1.0 1.0} globalFont.do_display 1 atomIDs.do_not_display {} globalFont.darkColor {0.0 0.0 0.0}} set t [ModAtomLabels] .mesa xc_setfont {-*-Nimbus Roman No9 L-medium-r-*-*-47-*-*-*-*-*-*-*} {1.0 1.0 1.0} {0.0 0.0 0.0} ModAtomLabels:advancedCheckButton default ModAtomLabels:advancedCheckButton custom ModAtomLabels:advancedCloseUpdate dummy update CancelProc $t # ------------------------------------------------------------------------ # END: Atomic-Labels/Fonts # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # BEGIN: Various colors # ------------------------------------------------------------------------ xc_newvalue .mesa 8 0 0.770000 1.000000 0.420000 xc_newvalue .mesa 8 1 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 2 0.950000 0.950000 0.950000 xc_newvalue .mesa 8 3 0.950000 0.950000 0.950000 xc_newvalue .mesa 8 4 0.707900 0.707900 0.707900 xc_newvalue .mesa 8 5 0.707900 0.707900 0.707900 xc_newvalue .mesa 8 6 0.950000 0.950000 0.000000 xc_newvalue .mesa 8 7 0.644500 0.804700 0.856900 xc_newvalue .mesa 8 8 0.700000 0.000000 0.000000 xc_newvalue .mesa 8 9 0.834500 0.950000 0.950000 xc_newvalue .mesa 8 10 0.950000 0.950000 0.950000 xc_newvalue .mesa 8 11 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 12 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 13 0.950000 0.000000 0.950000 xc_newvalue .mesa 8 14 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 15 0.950000 0.950000 0.000000 xc_newvalue .mesa 8 16 0.950000 0.950000 0.450000 xc_newvalue .mesa 8 17 0.710000 1.000000 0.000000 xc_newvalue .mesa 8 18 0.950000 0.950000 0.950000 xc_newvalue .mesa 8 19 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 20 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 21 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 22 0.600000 0.600000 0.600000 xc_newvalue .mesa 8 23 0.644500 0.804700 0.856900 xc_newvalue .mesa 8 24 0.644500 0.804700 0.856900 xc_newvalue .mesa 8 25 0.644500 0.804700 0.856900 xc_newvalue .mesa 8 26 0.950000 0.000000 0.000000 xc_newvalue .mesa 8 27 0.644500 0.804700 0.856900 xc_newvalue .mesa 8 28 0.644500 0.804700 0.856900 xc_newvalue .mesa 8 29 0.820000 0.450000 0.140000 xc_newvalue .mesa 8 30 0.950000 0.000000 0.950000 xc_newvalue .mesa 8 31 0.950000 0.000000 0.950000 xc_newvalue .mesa 8 32 0.950000 0.000000 0.950000 xc_newvalue .mesa 8 33 0.950000 0.950000 0.000000 xc_newvalue .mesa 8 34 0.950000 0.950000 0.000000 xc_newvalue .mesa 8 35 0.950000 0.000000 0.000000 xc_newvalue .mesa 8 36 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 37 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 38 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 39 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 40 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 41 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 42 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 43 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 44 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 45 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 46 1.000000 1.000000 1.000000 xc_newvalue .mesa 8 47 1.000000 1.000000 1.000000 xc_newvalue .mesa 8 48 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 49 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 50 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 51 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 52 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 53 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 54 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 55 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 56 0.000000 0.950000 0.950000 xc_newvalue .mesa 8 57 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 58 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 59 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 60 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 61 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 62 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 63 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 64 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 65 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 66 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 67 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 68 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 69 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 70 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 71 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 72 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 73 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 74 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 75 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 76 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 77 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 78 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 79 1.000000 0.850000 0.000000 xc_newvalue .mesa 8 80 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 81 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 82 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 83 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 84 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 85 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 86 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 87 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 88 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 89 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 90 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 91 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 92 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 93 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 94 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 95 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 96 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 97 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 98 0.750000 0.750000 0.750000 xc_newvalue .mesa 8 99 0.931400 0.875500 0.801000 xc_newvalue .mesa 8 100 0.931400 0.875500 0.801000 xc_newvalue .mesa 26 1.000000 1.000000 1.000000 1.0 xc_newvalue .mesa 17 0.880000 1.000000 0.670000 # ------------------------------------------------------------------------ # END: Various colors # ------------------------------------------------------------------------ xc_newvalue .mesa 0 # ------------------------------------------------------------------------ # Various parameters # ------------------------------------------------------------------------ xc_newvalue .mesa 13 1.050000000000000 xc_newvalue .mesa 6 0.400000000000000 xc_newvalue .mesa 7 0.600000000000000 xc_newvalue .mesa 9 1.000000000000000 xc_newvalue .mesa 10 1.000000000000000 xc_newvalue .mesa 18 1.000000000000000 xc_newvalue .mesa 10010 1.000000000000000 xc_newvalue .mesa 10009 1.000000000000000 xc_newvalue .mesa 11 6.000000000000000 xc_newvalue .mesa 19 0.100000000000000 xc_newvalue .mesa 24 30.000000000000000 xc_newvalue .mesa 28 3.000000000000000 xc_newvalue .mesa 29 2.500000000000000 xc_newvalue .mesa 10029 1.000000000000000 xc_newvalue .mesa 23 0.000000 0.000000 0.000000 1.000000 # ------------------------------------------------------------------------ # Various displays (i.e. checkbuttons of DISPLAY menu) # ------------------------------------------------------------------------ array set check {pseudoDens 0 perspective 0 labels 1 depthcuing 0 crds 0 wigner 0 antialias 0 Hbonds 0 forces 0 frames 1 unibond 0 perpective 0} CrdSist AtomLabels CrysFrames Unibond forceVectors .mesa Hbonds .mesa WignerSeitz Perspective # ------------------------------------------------------------------------ # Various displays (i.e. radiobuttons DISPLAY menu) # ------------------------------------------------------------------------ array set radio {space {SpaceFill based on covalent radii} .mesa,bg #000000 cellmode conv frames rods unitrep cell hexamode parapipedal ball {Balls based on covalent radii}} CellMode 1 DispFramesAs xc_newvalue .mesa 2 # ------------------------------------------------------------------------ # BEGIN: Wigner-Seitz Cell # ------------------------------------------------------------------------ set check(wigner) 1 WignerSeitz array set ws {rcc 9 rpcc 11 transparent 0 pc 1 ic 6 bc 3 rc 7 hcc 10 not_config_yet 1 selected_pos_color #33ff66 normal_pos_color #ef0000 fc 5 can_disable_color #eeeeee hc 8 ac 2 cc 4 color #55eeff} array set wsp {sel,10 0 sel,11 0 sel,12 0 sel,13 0 sel,14 0 sel,15 0 sel,16 0 sel,0 0 sel,17 0 sel,1 0 sel,18 0 sel,2 0 sel,19 0 sel,20 0 sel,3 0 sel,21 0 sel,4 0 sel,22 0 sel,5 0 sel,23 0 sel,6 0 sel,24 0 sel,7 0 sel,25 0 sel,8 0 sel,26 0 sel,9 0 sel,27 0 sel,28 0 sel,29 0 sel,30 0 sel,31 0 sel,32 0 sel,33 0 sel,34 0 sel,35 0 sel,36 0 sel,37 0 sel,38 0 sel,39 0 sel,40 0 sel,41 0 sel,42 0 sel,43 0 sel,44 0 sel,45 0 sel,46 0 sel,47 0 sel,48 0 sel,49 0} array set wsc {sel,10 0 sel,11 0 sel,12 0 sel,13 0 sel,14 0 sel,15 0 sel,16 0 sel,0 0 sel,17 0 sel,1 0 sel,18 0 sel,2 0 sel,19 0 sel,20 0 sel,3 0 sel,21 0 sel,4 0 sel,22 0 sel,5 0 sel,23 0 sel,6 0 sel,24 0 sel,7 0 sel,25 0 sel,8 0 sel,26 0 sel,9 0 sel,27 0 sel,28 0 sel,29 0 sel,30 0 sel,31 0 sel,32 0 sel,33 0 sel,34 0 sel,35 0 sel,36 0 sel,37 0 sel,38 0 sel,39 0 sel,40 0 sel,41 0 sel,42 0 sel,43 0 sel,44 0 sel,45 0 sel,46 0 sel,47 0 sel,48 0 sel,49 0} SetWignerSeitzInit; update; SetWignerSeitz_OK test; SetWignerSeitz_Cancel .wgnset # ------------------------------------------------------------------------ # END: Wigner-Seitz Cell # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # BEGIN: Atomic radii # ------------------------------------------------------------------------ xc_newvalue .mesa 4 0 0.532000 xc_newvalue .mesa 4 1 0.532000 xc_newvalue .mesa 4 2 0.532000 xc_newvalue .mesa 4 3 1.722000 xc_newvalue .mesa 4 4 1.246000 xc_newvalue .mesa 4 5 1.274000 xc_newvalue .mesa 4 6 1.078000 xc_newvalue .mesa 4 7 1.050000 xc_newvalue .mesa 4 8 1.022000 xc_newvalue .mesa 4 9 0.994000 xc_newvalue .mesa 4 10 0.994000 xc_newvalue .mesa 4 11 2.240000 xc_newvalue .mesa 4 12 1.960000 xc_newvalue .mesa 4 13 1.750000 xc_newvalue .mesa 4 14 1.554000 xc_newvalue .mesa 4 15 1.400000 xc_newvalue .mesa 4 16 1.456000 xc_newvalue .mesa 4 17 1.386000 xc_newvalue .mesa 4 18 1.372000 xc_newvalue .mesa 4 19 2.982000 xc_newvalue .mesa 4 20 2.436000 xc_newvalue .mesa 4 21 2.240000 xc_newvalue .mesa 4 22 1.960000 xc_newvalue .mesa 4 23 1.890000 xc_newvalue .mesa 4 24 1.960000 xc_newvalue .mesa 4 25 1.960000 xc_newvalue .mesa 4 26 1.960000 xc_newvalue .mesa 4 27 1.890000 xc_newvalue .mesa 4 28 1.890000 xc_newvalue .mesa 4 29 1.890000 xc_newvalue .mesa 4 30 1.890000 xc_newvalue .mesa 4 31 1.820000 xc_newvalue .mesa 4 32 1.750000 xc_newvalue .mesa 4 33 1.610000 xc_newvalue .mesa 4 34 1.610000 xc_newvalue .mesa 4 35 1.596000 xc_newvalue .mesa 4 36 1.568000 xc_newvalue .mesa 4 37 3.080000 xc_newvalue .mesa 4 38 2.800000 xc_newvalue .mesa 4 39 2.590000 xc_newvalue .mesa 4 40 2.170000 xc_newvalue .mesa 4 41 2.030000 xc_newvalue .mesa 4 42 2.030000 xc_newvalue .mesa 4 43 1.890000 xc_newvalue .mesa 4 44 1.820000 xc_newvalue .mesa 4 45 1.890000 xc_newvalue .mesa 4 46 1.960000 xc_newvalue .mesa 4 47 2.240000 xc_newvalue .mesa 4 48 2.170000 xc_newvalue .mesa 4 49 2.170000 xc_newvalue .mesa 4 50 1.974000 xc_newvalue .mesa 4 51 2.030000 xc_newvalue .mesa 4 52 1.960000 xc_newvalue .mesa 4 53 1.960000 xc_newvalue .mesa 4 54 1.834000 xc_newvalue .mesa 4 55 3.640000 xc_newvalue .mesa 4 56 2.800000 xc_newvalue .mesa 4 57 2.450000 xc_newvalue .mesa 4 58 2.170000 xc_newvalue .mesa 4 59 2.170000 xc_newvalue .mesa 4 60 2.170000 xc_newvalue .mesa 4 61 2.170000 xc_newvalue .mesa 4 62 2.170000 xc_newvalue .mesa 4 63 2.170000 xc_newvalue .mesa 4 64 2.170000 xc_newvalue .mesa 4 65 2.170000 xc_newvalue .mesa 4 66 2.170000 xc_newvalue .mesa 4 67 2.170000 xc_newvalue .mesa 4 68 2.170000 xc_newvalue .mesa 4 69 2.170000 xc_newvalue .mesa 4 70 2.170000 xc_newvalue .mesa 4 71 2.170000 xc_newvalue .mesa 4 72 2.170000 xc_newvalue .mesa 4 73 2.030000 xc_newvalue .mesa 4 74 1.890000 xc_newvalue .mesa 4 75 1.890000 xc_newvalue .mesa 4 76 1.820000 xc_newvalue .mesa 4 77 1.890000 xc_newvalue .mesa 4 78 1.890000 xc_newvalue .mesa 4 79 1.890000 xc_newvalue .mesa 4 80 2.100000 xc_newvalue .mesa 4 81 2.660000 xc_newvalue .mesa 4 82 2.520000 xc_newvalue .mesa 4 83 2.240000 xc_newvalue .mesa 4 84 2.170000 xc_newvalue .mesa 4 85 2.170000 xc_newvalue .mesa 4 86 2.170000 xc_newvalue .mesa 4 87 3.920000 xc_newvalue .mesa 4 88 2.016000 xc_newvalue .mesa 4 89 2.730000 xc_newvalue .mesa 4 90 2.170000 xc_newvalue .mesa 4 91 2.170000 xc_newvalue .mesa 4 92 2.170000 xc_newvalue .mesa 4 93 2.170000 xc_newvalue .mesa 4 94 2.170000 xc_newvalue .mesa 4 95 2.170000 xc_newvalue .mesa 4 96 2.170000 xc_newvalue .mesa 4 97 2.170000 xc_newvalue .mesa 4 98 2.170000 xc_newvalue .mesa 4 99 2.170000 xc_newvalue .mesa 4 100 2.170000 xc_newvalue .mesa 10004 0 0.000000 xc_newvalue .mesa 10004 1 0.399000 xc_newvalue .mesa 10004 2 0.399000 xc_newvalue .mesa 10004 3 1.291500 xc_newvalue .mesa 10004 4 0.934500 xc_newvalue .mesa 10004 5 0.955500 xc_newvalue .mesa 10004 6 0.808500 xc_newvalue .mesa 10004 7 0.787500 xc_newvalue .mesa 10004 8 0.766500 xc_newvalue .mesa 10004 9 0.745500 xc_newvalue .mesa 10004 10 0.745500 xc_newvalue .mesa 10004 11 1.680000 xc_newvalue .mesa 10004 12 1.470000 xc_newvalue .mesa 10004 13 1.312500 xc_newvalue .mesa 10004 14 1.165500 xc_newvalue .mesa 10004 15 1.050000 xc_newvalue .mesa 10004 16 1.092000 xc_newvalue .mesa 10004 17 1.039500 xc_newvalue .mesa 10004 18 1.029000 xc_newvalue .mesa 10004 19 2.236500 xc_newvalue .mesa 10004 20 1.827000 xc_newvalue .mesa 10004 21 1.680000 xc_newvalue .mesa 10004 22 1.470000 xc_newvalue .mesa 10004 23 1.417500 xc_newvalue .mesa 10004 24 1.470000 xc_newvalue .mesa 10004 25 1.470000 xc_newvalue .mesa 10004 26 1.470000 xc_newvalue .mesa 10004 27 1.417500 xc_newvalue .mesa 10004 28 1.417500 xc_newvalue .mesa 10004 29 1.417500 xc_newvalue .mesa 10004 30 1.417500 xc_newvalue .mesa 10004 31 1.365000 xc_newvalue .mesa 10004 32 1.312500 xc_newvalue .mesa 10004 33 1.207500 xc_newvalue .mesa 10004 34 1.207500 xc_newvalue .mesa 10004 35 1.197000 xc_newvalue .mesa 10004 36 1.176000 xc_newvalue .mesa 10004 37 2.310000 xc_newvalue .mesa 10004 38 2.100000 xc_newvalue .mesa 10004 39 1.942500 xc_newvalue .mesa 10004 40 1.627500 xc_newvalue .mesa 10004 41 1.522500 xc_newvalue .mesa 10004 42 1.522500 xc_newvalue .mesa 10004 43 1.417500 xc_newvalue .mesa 10004 44 1.365000 xc_newvalue .mesa 10004 45 1.417500 xc_newvalue .mesa 10004 46 1.470000 xc_newvalue .mesa 10004 47 1.680000 xc_newvalue .mesa 10004 48 1.627500 xc_newvalue .mesa 10004 49 1.627500 xc_newvalue .mesa 10004 50 1.480500 xc_newvalue .mesa 10004 51 1.522500 xc_newvalue .mesa 10004 52 1.470000 xc_newvalue .mesa 10004 53 1.470000 xc_newvalue .mesa 10004 54 1.375500 xc_newvalue .mesa 10004 55 2.730000 xc_newvalue .mesa 10004 56 2.100000 xc_newvalue .mesa 10004 57 1.837500 xc_newvalue .mesa 10004 58 1.627500 xc_newvalue .mesa 10004 59 1.627500 xc_newvalue .mesa 10004 60 1.627500 xc_newvalue .mesa 10004 61 1.627500 xc_newvalue .mesa 10004 62 1.627500 xc_newvalue .mesa 10004 63 1.627500 xc_newvalue .mesa 10004 64 1.627500 xc_newvalue .mesa 10004 65 1.627500 xc_newvalue .mesa 10004 66 1.627500 xc_newvalue .mesa 10004 67 1.627500 xc_newvalue .mesa 10004 68 1.627500 xc_newvalue .mesa 10004 69 1.627500 xc_newvalue .mesa 10004 70 1.627500 xc_newvalue .mesa 10004 71 1.627500 xc_newvalue .mesa 10004 72 1.627500 xc_newvalue .mesa 10004 73 1.522500 xc_newvalue .mesa 10004 74 1.417500 xc_newvalue .mesa 10004 75 1.417500 xc_newvalue .mesa 10004 76 1.365000 xc_newvalue .mesa 10004 77 1.417500 xc_newvalue .mesa 10004 78 1.417500 xc_newvalue .mesa 10004 79 1.417500 xc_newvalue .mesa 10004 80 1.575000 xc_newvalue .mesa 10004 81 1.995000 xc_newvalue .mesa 10004 82 1.890000 xc_newvalue .mesa 10004 83 1.680000 xc_newvalue .mesa 10004 84 1.627500 xc_newvalue .mesa 10004 85 1.627500 xc_newvalue .mesa 10004 86 1.627500 xc_newvalue .mesa 10004 87 2.940000 xc_newvalue .mesa 10004 88 1.512000 xc_newvalue .mesa 10004 89 2.047500 xc_newvalue .mesa 10004 90 1.627500 xc_newvalue .mesa 10004 91 1.627500 xc_newvalue .mesa 10004 92 1.627500 xc_newvalue .mesa 10004 93 1.627500 xc_newvalue .mesa 10004 94 1.627500 xc_newvalue .mesa 10004 95 1.627500 xc_newvalue .mesa 10004 96 1.627500 xc_newvalue .mesa 10004 97 1.627500 xc_newvalue .mesa 10004 98 1.627500 xc_newvalue .mesa 10004 99 1.627500 xc_newvalue .mesa 10004 100 1.627500 # ------------------------------------------------------------------------ # END: Atomic radii # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # load appropriate color-scheme # ------------------------------------------------------------------------ array set colSh {slab_dir -z slabrange_min 0.00 slabrange_max 1.00 scheme atomic slab_colbas monochrome dist_r 1.0 dist_coltyp combined dist_alpha 0.65 dist_x 0.0 slab_fractional 1 slab_coltyp combined dist_y 0.0 dist_z 0.0 slab_alpha 0.65 dist_colbas monochrome} ColorSchemeUpdate .mesa # ------------------------------------------------------------------------ # BEGIN: Isosurface colors/transparency ... # ------------------------------------------------------------------------ xc_setGLparam material -what isosurf pos front \ -shininess 0.000000 \ -specular {0.000000 0.000000 0.000000 0.000000} \ -ambient {0.000000 0.000000 0.000000 0.000000} \ -diffuse {0.000000 0.000000 0.000000 0.000000} \ -emission {0.000000 0.000000 0.000000 0.000000} xc_setGLparam material -what isosurf pos back \ -shininess 0.000000 \ -specular {0.000000 0.000000 0.000000 0.000000} \ -ambient {0.000000 0.000000 0.000000 0.000000} \ -diffuse {0.000000 0.000000 0.000000 0.000000} \ -emission {0.000000 0.000000 0.000000 0.000000} xc_setGLparam material -what isosurf neg front \ -shininess 0.000000 \ -specular {0.000000 0.000000 0.000000 0.000000} \ -ambient {0.000000 0.000000 0.000000 0.000000} \ -diffuse {0.000000 0.000000 0.000000 0.000000} \ -emission {0.000000 0.000000 0.000000 0.000000} xc_setGLparam material -what isosurf neg back \ -shininess 0.000000 \ -specular {0.000000 0.000000 0.000000 0.000000} \ -ambient {0.000000 0.000000 0.000000 0.000000} \ -diffuse {0.000000 0.000000 0.000000 0.000000} \ -emission {0.000000 0.000000 0.000000 0.000000} xc_setGLparam material -what isosurf one front \ -shininess 0.000000 \ -specular {0.000000 0.000000 0.000000 0.000000} \ -ambient {0.000000 0.000000 0.000000 0.000000} \ -diffuse {0.000000 0.000000 0.000000 0.000000} \ -emission {0.000000 0.000000 0.000000 0.000000} xc_setGLparam material -what isosurf one back \ -shininess 0.000000 \ -specular {0.000000 0.000000 0.000000 0.000000} \ -ambient {0.000000 0.000000 0.000000 0.000000} \ -diffuse {0.000000 0.000000 0.000000 0.000000} \ -emission {0.000000 0.000000 0.000000 0.000000} xc_setGLparam blendfunc -what isosurf -sfunc GL_SRC_ALPHA -dfunc GL_ONE_MINUS_SRC_ALPHA # ------------------------------------------------------------------------ # END: Isosurface colors/transparency ... # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # rotation matrix and zooming factor, and translation displacements # ------------------------------------------------------------------------ xc_rotationmatrix set 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 xc_translparam set 0.000000000000000e+00 0.000000000000000e+00 1.881373293927946e+00 # this is used to force the update of display .mesa cry_toglzoom 0.0 # ------------------------------------------------------------------------ # Anti-Aliasing & Depth-Cuing & PseudoDensity (these are time consuming) # ------------------------------------------------------------------------ DepthCuing; PseudoDensity; AntiAlias # ------------------------------------------------------------------------ # reset cursor # ------------------------------------------------------------------------ set xcCursor(dont_update) 0 ResetCursor destroy $wait_window From tone.kokalj at ijs.si Fri Jan 11 15:58:19 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 11 Jan 2013 15:58:19 +0100 Subject: [xcrysden] can not open saved xcrysden script files (version 1.5.53) In-Reply-To: <12351202.DFsD0fCaKi@wyxphy> References: <1357605082.58502.YahooMailClassic@web15307.mail.cnb.yahoo.com> <1357822502.14916.21.camel@catalyst.ijs.si> <12351202.DFsD0fCaKi@wyxphy> Message-ID: <1357916299.8205.63.camel@catalyst.ijs.si> On Fri, 2013-01-11 at 11:00 +0800, wangyx wrote: > Dear Dr. Anton Kokalj, > > Thank you! > It happens for all cases. > > The attached file is the script file. The file works without any problem on my side. The really funny thing is that according to your first email the error seems to occur while parsing the XSF file, which this happens for almost every case whatsoever. So the question is: can you load any file at all? 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 dstrubbe at civet.berkeley.edu Fri Jan 11 19:46:02 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Fri, 11 Jan 2013 13:46:02 -0500 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS Message-ID: Dear XCrySDen users, I would like to report my experience getting XCrySDen 1.5.53 to work on MacOS 10.8, regarding the mesa and tcl/tk libraries. I found that the macports versions of mesa do not work (dies with an X-Window error, as has been mentioned on this list before), but mesa built with Fink does work successfully (and of course the fink port of xcrysden is reported to be working). This may be a matter simply of version numbers as opposed to the build, because macports has 8.0.4 (and earlier 7.11.2, which I couldn't get to work either) whereas fink has mesa 7.0.2 (released Nov 2007!). I built mesa 7.0.2 by hand and that worked too. Incidentally, I checked that linking against libGLU and libGL from /usr/bin/X11R6 also gives the same error as the macports mesa versions. Using macports builds of Tcl and Tk, I also found that the 8.5.12 versions work but the 8.5.13 and 8.6.0 ones do not for me. tcl 8.5.13 failed at runtime with this error, which looks like a problem in the macport installation: Application initialization failed: Can't find a usable init.tcl in the following directories: /opt/local/lib/tcl8.5 /Users/dstrubbe/Software/xcrysden-1.5.53_macportslibs/lib/tcl8.5 /Users/dstrubbe/Software/lib/tcl8.5 /Users/dstrubbe/Software/xcrysden-1.5.53_macportslibs/library /Users/dstrubbe/Software/library /Users/dstrubbe/Software/tcl8.5.12/library /Users/dstrubbe/tcl8.5.12/library /opt/local/lib/tcl8.5/init.tcl: version conflict for package "Tcl": have 8.5.12, need exactly 8.5.13 version conflict for package "Tcl": have 8.5.12, need exactly 8.5.13 With 8.6.0, the compilation fails with these errors: xcAppInit.c: In function 'XC_OpenStrCmd': xcAppInit.c:786:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:798:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:798:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:805:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:805:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:811:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:811:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:821:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:821:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:838:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:838:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_DisplayMode2DCmd': xcAppInit.c:942:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:948:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:948:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:960:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:960:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1016:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1016:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_RotateCb': xcAppInit.c:1050:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1089:8: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1130:8: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1220:8: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_TranslateCb': xcAppInit.c:1384:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1413:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1413:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_CloseStrCmd': xcAppInit.c:1450:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1456:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1456:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1463:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_DisplayMode3DCmd': xcAppInit.c:1557:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1563:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1563:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1578:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1594:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1594:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_DrawStyle3DCmd': xcAppInit.c:1712:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1718:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1718:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1760:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1760:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_ShadeModel3DCmd': xcAppInit.c:1787:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1793:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1793:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1813:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1813:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_PointSizeCmd': xcAppInit.c:1837:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1843:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1843:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1849:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1849:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_ResetVarCmd': xcAppInit.c:1882:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1888:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1888:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1894:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1894:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_NewValueCmd': xcAppInit.c:1923:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1929:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1929:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1935:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1935:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1941:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1941:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1952:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1952:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1957:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1957:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1972:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1972:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1988:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1988:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1993:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:1993:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_GetDefaultCmd': xcAppInit.c:2026:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2031:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2031:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2036:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2036:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_GetValueCmd': xcAppInit.c:2109:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2114:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2114:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2119:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2119:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2167:2: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2167:2: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2176:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2176:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2188:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2188:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2203:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2203:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2219:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2219:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_UpdateStrCmd': xcAppInit.c:2299:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2309:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2309:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2315:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2315:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2335:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2335:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_SwapBufferCmd': xcAppInit.c:2386:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2392:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2392:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_DisplayCmd': xcAppInit.c:2421:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2427:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2427:5: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_Dump2EpsCb': xcAppInit.c:2450:11: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2456:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2456:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_RotationMatrixCmd': xcAppInit.c:2503:2: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2503:2: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2509:6: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2509:6: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2524:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2524:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c: In function 'XC_TranslParamCmd': xcAppInit.c:2553:2: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2553:2: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2559:6: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2559:6: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2571:7: error: 'Tcl_Interp' has no member named 'result' xcAppInit.c:2571:7: error: 'Tcl_Interp' has no member named 'result' make[2]: *** [xcAppInit.o] Error 1 make[1]: *** [compile] Error 2 make: *** [src-C] Error 2 David Strubbe MIT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130111/8c6e6e28/attachment.htm From wyxphy at yahoo.com.cn Mon Jan 14 13:38:14 2013 From: wyxphy at yahoo.com.cn (Yuanxu Wang) Date: Mon, 14 Jan 2013 20:38:14 +0800 (CST) Subject: [xcrysden] can not open saved xcrysden script files (version 1.5.53) In-Reply-To: <1357916299.8205.63.camel@catalyst.ijs.si> Message-ID: <1358167094.15328.YahooMailClassic@web15305.mail.cnb.yahoo.com> yes, i can load xsf file without problem. Only script file has this problem. --- 13?1?11????, Tone Kokalj ??? ???: Tone Kokalj ??: Re: [xcrysden] can not open saved xcrysden script files (version 1.5.53) ???: xcrysden at democritos.it ??: 2013?1?11?,??,??11:58 On Fri, 2013-01-11 at 11:00 +0800, wangyx wrote: > Dear Dr. Anton Kokalj, > > Thank you! > It happens for all cases. > > The attached file is the script file. The file works without any problem on my side. The really funny thing is that according to your first email the error seems to occur while parsing the XSF file, which this happens for almost every case whatsoever. So the question is: can you load any file at all? 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/20130114/8d546a8c/attachment.htm From carmen_quimica at hotmail.com Tue Jan 15 13:49:46 2013 From: carmen_quimica at hotmail.com (Carmen Souza) Date: Tue, 15 Jan 2013 12:49:46 +0000 Subject: [xcrysden] Crystal09 and XCrysDen Message-ID: Dear Users, I am having some problems with the visualization of Crystal09 files in the XCrysDen program. Anyone have a solution? Thank you. Carmen Regina de Souza -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130115/9858745f/attachment.htm From tone.kokalj at ijs.si Tue Jan 15 17:42:54 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 15 Jan 2013 17:42:54 +0100 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: References: Message-ID: <1358268174.4537.13.camel@catalyst.ijs.si> On Fri, 2013-01-11 at 13:46 -0500, David Strubbe wrote: > Application initialization failed: Can't find a usable init.tcl in the > following directories: > > /opt/local/lib/tcl8.5 /Users/dstrubbe/Software/xcrysden-1.5.53_macportslibs/lib/tcl8.5 /Users/dstrubbe/Software/lib/tcl8.5 /Users/dstrubbe/Software/xcrysden-1.5.53_macportslibs/library /Users/dstrubbe/Software/library /Users/dstrubbe/Software/tcl8.5.12/library /Users/dstrubbe/tcl8.5.12/library > > /opt/local/lib/tcl8.5/init.tcl: version conflict for package "Tcl": > have 8.5.12, need exactly 8.5.13 > version conflict for package "Tcl": have 8.5.12, need exactly 8.5.13 This is due to, say, incomplete or inconsistent installation of Tcl 8.5.13. As the message suggests, it cannot locate the matching init.tcl file. Set the TCL_LIBRARY shell environmental variable to point to the directory that contain the Tcl's system library of Tcl scripts. The one of /opt/local/lib/tcl8.5/ obviously corresponds to version 8.5.12. > > With 8.6.0, the compilation fails with these errors: > > xcAppInit.c: In function 'XC_OpenStrCmd': > xcAppInit.c:786:11: error: 'Tcl_Interp' has no member named 'result' There are some backward incompatibilities with the new Tcl8.6. Browsing Tcl documentation, one finds the workaround by defining the USE_INTERP_RESULT macro (e.g. defining the -DUSE_INTERP_RESULT for Make.sys's CFLAGS). Best 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 Tue Jan 15 17:43:42 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 15 Jan 2013 17:43:42 +0100 Subject: [xcrysden] Crystal09 and XCrysDen In-Reply-To: References: Message-ID: <1358268222.4537.14.camel@catalyst.ijs.si> On Tue, 2013-01-15 at 12:49 +0000, Carmen Souza wrote: > > Dear Users, > I am having some problems with the visualization of Crystal09 files in > the XCrysDen program. Anyone have a solution? I guess nobody does nor will have, unless you provide more information/description of 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 Tue Jan 15 17:44:49 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 15 Jan 2013 17:44:49 +0100 Subject: [xcrysden] can not open saved xcrysden script files (version 1.5.53) In-Reply-To: <1358167094.15328.YahooMailClassic@web15305.mail.cnb.yahoo.com> References: <1358167094.15328.YahooMailClassic@web15305.mail.cnb.yahoo.com> Message-ID: <1358268289.4537.15.camel@catalyst.ijs.si> On Mon, 2013-01-14 at 20:38 +0800, Yuanxu Wang wrote: > yes, i can load xsf file without problem. Only script file has this > problem. This is really strange. I have never encountered such kind of problem, hence I also don't the solution. 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 dstrubbe at civet.berkeley.edu Wed Jan 16 21:02:36 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Wed, 16 Jan 2013 15:02:36 -0500 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: <1358268174.4537.13.camel@catalyst.ijs.si> References: <1358268174.4537.13.camel@catalyst.ijs.si> Message-ID: Dear Tone, Including the C flag you mentioned, I can now compile with tcl/tk 8.6.0 (despite a huge number of warnings of the form writeXSF.c:128:5: warning: 'result' is deprecated (declared at /opt/local/include/tcl.h:507); however the program crashes while trying to open the X11 window with a segmentation fault, and shows this info in a window about sending a report to Apple. Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000 VM Regions Near 0: --> __TEXT 000000010dd16000-000000010ddde000 [ 800K] r-x/rwx SM=COW /Users/USER/* Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libX11.6.dylib 0x000000010e6a692d _XInternAtom + 84 1 libX11.6.dylib 0x000000010e6a682f XInternAtom + 76 2 libGL.1.dylib 0x000000010e543538 choose_x_visual + 56 3 libGL.1.dylib 0x000000010e543292 choose_visual + 978 4 libGL.1.dylib 0x000000010e54114f Fake_glXChooseVisual + 143 5 xcrys 0x000000010dda8041 Togl_CreateWindow + 1709 6 libtk8.6.dylib 0x000000010e07f50d Tk_MakeWindowExist + 125 7 xcrys 0x000000010dda78c2 Togl_Cmd + 1301 8 libtcl8.6.dylib 0x000000010e1cc059 TclInvokeStringCommand + 121 9 libtcl8.6.dylib 0x000000010e1cda79 TclNREvalObjv + 1657 10 libtcl8.6.dylib 0x000000010e236b07 TEBCresume + 12887 11 libtcl8.6.dylib 0x000000010e1cdae8 TclNRRunCallbacks + 88 12 libtcl8.6.dylib 0x000000010e1ce706 TclEvalEx + 1734 13 libtcl8.6.dylib 0x000000010e25f3fd Tcl_FSEvalFileEx + 621 14 libtk8.6.dylib 0x000000010e0707cd Tk_MainEx + 1453 15 xcrys 0x000000010dd18089 main + 66 16 libdyld.dylib 0x00007fff8f7d47e1 start + 1 On Tue, Jan 15, 2013 at 11:42 AM, Tone Kokalj wrote: > On Fri, 2013-01-11 at 13:46 -0500, David Strubbe wrote: > > Application initialization failed: Can't find a usable init.tcl in the > > following directories: > > > > /opt/local/lib/tcl8.5 > /Users/dstrubbe/Software/xcrysden-1.5.53_macportslibs/lib/tcl8.5 > /Users/dstrubbe/Software/lib/tcl8.5 > /Users/dstrubbe/Software/xcrysden-1.5.53_macportslibs/library > /Users/dstrubbe/Software/library /Users/dstrubbe/Software/tcl8.5.12/library > /Users/dstrubbe/tcl8.5.12/library > > > > /opt/local/lib/tcl8.5/init.tcl: version conflict for package "Tcl": > > have 8.5.12, need exactly 8.5.13 > > version conflict for package "Tcl": have 8.5.12, need exactly 8.5.13 > > This is due to, say, incomplete or inconsistent installation of Tcl > 8.5.13. As the message suggests, it cannot locate the matching init.tcl > file. Set the TCL_LIBRARY shell environmental variable to point to the > directory that contain the Tcl's system library of Tcl scripts. The one > of /opt/local/lib/tcl8.5/ obviously corresponds to version 8.5.12. > > > > > With 8.6.0, the compilation fails with these errors: > > > > xcAppInit.c: In function 'XC_OpenStrCmd': > > xcAppInit.c:786:11: error: 'Tcl_Interp' has no member named 'result' > > There are some backward incompatibilities with the new Tcl8.6. Browsing > Tcl documentation, one finds the workaround by defining the > USE_INTERP_RESULT macro (e.g. defining the -DUSE_INTERP_RESULT for > Make.sys's CFLAGS). > > Best 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/20130116/9b713e63/attachment.htm From jxzhu at lanl.gov Fri Jan 18 17:15:27 2013 From: jxzhu at lanl.gov (Zhu, Jianxin) Date: Fri, 18 Jan 2013 16:15:27 +0000 Subject: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX In-Reply-To: Message-ID: <1A9F0F275F0DE54BA1FBF55D068937C72D228CE9@ECS-EXG-P-MB05.win.lanl.gov> Hi Tone and Xcrysden users, I spent long time on putting in customized labels etc on a structure (imported from wien2k), and then clicked "Save Current State and Structure" trying to save what I have made. Unfortunately, the Xcrysden program simply crashed. The problem happens to the program installed on all Mac OSX machines (OS 10.6.8 and 10.7.2) I can have access. The xcrysden version is 1.5.24. The error is --- ? sInfo(dim) = 3; periodic(dim) = 3 saving colSh ... saving datagrid ... saving rotations/translations ... /Users/jxzhu/XCrySDen/xcrysden: line 227: 66513 Abort trap ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH "$@" > /dev/null I have also given a try with a test case.struct on linux clusters installed with xcrysden 1.5.21, the above problem does not occur. But when I reopened it with the command "xcrysden ?s case.xcrysden", the displayed picture has bonds missing. Is it possible that this problem is related to the fact the structure is imported from wien2k structure file? On Mac, I am now trying to update the program to 1.5.53 but not sure whether it will make any difference. I appreciate if you have any suggestions. Thanks, Jianxin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130118/58d7c106/attachment.htm From tone.kokalj at ijs.si Fri Jan 18 17:58:46 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 18 Jan 2013 17:58:46 +0100 Subject: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX In-Reply-To: <1A9F0F275F0DE54BA1FBF55D068937C72D228CE9@ECS-EXG-P-MB05.win.lanl.gov> References: <1A9F0F275F0DE54BA1FBF55D068937C72D228CE9@ECS-EXG-P-MB05.win.lanl.gov> Message-ID: <1358528326.3779.52.camel@catalyst.ijs.si> On Fri, 2013-01-18 at 16:15 +0000, Zhu, Jianxin wrote: > Hi Tone and Xcrysden users, > > > I spent long time on putting in customized labels etc on a structure > (imported from wien2k), and then clicked "Save Current State and > Structure" trying to save what I have made. > Unfortunately, the Xcrysden program simply crashed. I am sorry for the loss. I don't know why it crashed. > Is it possible that this problem is related to the fact the structure > is imported from wien2k structure file? No, it is not related to that at all. > > On Mac, I am now trying to update the program to 1.5.53 but not sure > whether it will make any difference. Let me know if the problem persists in the new version. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Fri Jan 18 18:04:50 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 18 Jan 2013 18:04:50 +0100 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: References: <1358268174.4537.13.camel@catalyst.ijs.si> Message-ID: <1358528690.3779.57.camel@catalyst.ijs.si> On Wed, 2013-01-16 at 15:02 -0500, David Strubbe wrote: > Dear Tone, > > > Including the C flag you mentioned, I can now compile with tcl/tk > 8.6.0 (despite a huge number of warnings of the form > writeXSF.c:128:5: warning: 'result' is deprecated (declared > at /opt/local/include/tcl.h:507); Ok, this is some progress, but apparently small, because of the crash. > > however the program crashes while trying to open the X11 window with a > segmentation fault, ... Does it work if you do the same kind of compilation, but with the Tcl8.5. Namely, the failure seems to be related to choosing the correct visual, hence it may be unrelated to Tcl. But if this is so than it will crash also if compiled with Tcl8.5. 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 dstrubbe at civet.berkeley.edu Fri Jan 18 18:59:47 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Fri, 18 Jan 2013 12:59:47 -0500 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: <1358528690.3779.57.camel@catalyst.ijs.si> References: <1358268174.4537.13.camel@catalyst.ijs.si> <1358528690.3779.57.camel@catalyst.ijs.si> Message-ID: > Does it work if you do the same kind of compilation, but with the > Tcl8.5. Namely, the failure seems to be related to choosing the correct > visual, hence it may be unrelated to Tcl. But if this is so than it will > crash also if compiled with Tcl8.5. > > As I mentioned originally, the program compiles and runs fine for me with Tcl and Tk 8.5.12. Also, I checked that the same is true if I use the cflag -DUSE_INTERP_RESULT. Is this what you are asking? David -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130118/035f59d8/attachment.htm From jxzhu at lanl.gov Fri Jan 18 19:33:58 2013 From: jxzhu at lanl.gov (Zhu, Jianxin) Date: Fri, 18 Jan 2013 18:33:58 +0000 Subject: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX In-Reply-To: <1358528326.3779.52.camel@catalyst.ijs.si> Message-ID: <1A9F0F275F0DE54BA1FBF55D068937C72D228E1D@ECS-EXG-P-MB05.win.lanl.gov> Dear Tone, I did update the program to 1.5.53 on one of my MacOSX machines and the problem remains. Attached below is the output to screen after I click "Save Current State and Structure". The output is essentially the same as that from 1.5.24. Best regards, Jianxin .... Version: 1.5.53 Please report bugs to: tone.kokalj at ijs.si TERMS OF USE: ------------- XCRYSDEN is released under the GNU General Public License. Whenever graphics generated by XCRYSDEN are used in scientific publications, it shall be greatly appreciated to include an explicit reference. The preferred form is the following: [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003. Code available from http://www.xcrysden.org/. XCRYSDEN_TOPDIR=/sw/share/xcrysden-1.5.53 XCRYSDEN_SCRATCH=/Users/jxzhu/XCryScratch Running on platform : unix Operating system : Darwin Package ImageMagick's convert: /opt/local/bin/convert Package ImageMagick's import: /opt/local/bin/import Package Whirlgif: /opt/local/bin/whirlgif Package Ppmtompeg: /sw/bin/ppmtompeg Package Xwd: /usr/X11/bin/xwd Executing: /sw/lib/xcrysden-1.5.53/ftnunit Executing: /sw/lib/xcrysden-1.5.53/gengeom 0 1 21 1 1 1 1 /Users/jxzhu/XCryScratch/xc_25418/xc_gengeom.25418 /Users/jxzhu/XCryScratch/xc_25418/xc_str2xcr.25418 Executing: /sw/lib/xcrysden-1.5.53/gengeom 2 1 21 5 1 1 1 /Users/jxzhu/XCryScratch/xc_25418/xc_struc.25418 /Users/jxzhu/XCryScratch/xc_25418/xc_str2xcr.25418 reading PRIMCOORD reading CONVCOORD Number of Atoms: 27 Number of Frames: 12 natoms: 27 , ndel: 0 Filtered number of atoms: 27 Estimated number of bonds = 108 sInfo(dim) = 3; periodic(dim) = 3 saving colSh ... saving datagrid ... saving rotations/translations ... /sw/share/xcrysden-1.5.53/xcrysden: line 233: 25418 Abort trap: 6 ${XCRYSDEN_XCRYS_DIR}/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH "$@" > /dev/null -----Original Message----- From: Tone Kokalj Organization: J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Reply-To: , XCrySDen mailing list Date: Fri, 18 Jan 2013 17:58:46 +0100 To: Subject: Re: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX >On Fri, 2013-01-18 at 16:15 +0000, Zhu, Jianxin wrote: >> Hi Tone and Xcrysden users, >> >> >> I spent long time on putting in customized labels etc on a structure >> (imported from wien2k), and then clicked "Save Current State and >> Structure" trying to save what I have made. >> Unfortunately, the Xcrysden program simply crashed. > >I am sorry for the loss. I don't know why it crashed. > >> Is it possible that this problem is related to the fact the structure >> is imported from wien2k structure file? > >No, it is not related to that at all. > >> >> On Mac, I am now trying to update the program to 1.5.53 but not sure >> whether it will make any difference. > >Let me know if the problem persists in the new version. > >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 From tone.kokalj at ijs.si Thu Jan 24 18:49:41 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 24 Jan 2013 18:49:41 +0100 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: References: <1358268174.4537.13.camel@catalyst.ijs.si> <1358528690.3779.57.camel@catalyst.ijs.si> Message-ID: <1359049781.19990.25.camel@catalyst.ijs.si> On Fri, 2013-01-18 at 12:59 -0500, David Strubbe wrote: > As I mentioned originally, the program compiles and runs fine for me > with Tcl and Tk 8.5.12. Also, I checked that the same is true if I use > the cflag -DUSE_INTERP_RESULT. Is this what you are asking? More or less. This indicates that other fixes besides -DUSE_INTERP_RESULT are needed. I guess that due to backward incompatibility of Tcl/Tk8.6 with the 8.5 and older versions some code adjustment will probably be necessary. 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 24 19:32:40 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 24 Jan 2013 19:32:40 +0100 Subject: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX In-Reply-To: <1A9F0F275F0DE54BA1FBF55D068937C72D228E1D@ECS-EXG-P-MB05.win.lanl.gov> References: <1A9F0F275F0DE54BA1FBF55D068937C72D228E1D@ECS-EXG-P-MB05.win.lanl.gov> Message-ID: <1359052360.19990.32.camel@catalyst.ijs.si> On Fri, 2013-01-18 at 18:33 +0000, Zhu, Jianxin wrote: > Dear Tone, > > I did update the program to 1.5.53 on one of my MacOSX machines and the > problem remains. > Attached below is the output to screen after I click "Save Current State > and Structure". > The output is essentially the same as that from 1.5.24. Well, this may be due to a bug in the code. Please put the file xcAppInit.c (attached in a separate email) into the subdirectory C/ (for 1.5.53 version only) and recompile with debugging option "-g" (edit CFLAGS in Make.sys). If it still crashes then run as "xcrysden -d" and upon crash write "where" in the gdb prompt (perhaps gdb will give some useful info). 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 jxzhu at lanl.gov Thu Jan 24 22:32:04 2013 From: jxzhu at lanl.gov (Zhu, Jianxin) Date: Thu, 24 Jan 2013 21:32:04 +0000 Subject: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX In-Reply-To: <1359052360.19990.32.camel@catalyst.ijs.si> Message-ID: <1A9F0F275F0DE54BA1FBF55D068937C72D238469@ECS-EXG-P-MB06.win.lanl.gov> Dear Tone, Thanks for the revised xcAppInit.c file for Mac OSX. Since I originally built xcrysden 1.5.53 from Fink, I simply don't know how to put in this file there. As such I just built a standalone program directly from the xcrysden 1.5.53 source package (with all libraries from Fink) on my Mac OSX machine. With your new xcAppInit.c, the reported issue is gone. And when I execute "xcrysden -s TiC.xcrysden" and the program takes the pictures back fully and completely. On the other hand, as I reported before, although I don't have crash issue with the program (same version of 1.5.53) on my linux cluster when I do XCrysden "Save Current State and Structure", the execution of "xcrysden -s TiC.xcrysden" does not give me back a complete picture. In a separate message, I will attach one picture for your perusal. I wish you have a solution to it. BTW: I tried using this new file to replace the one on my linux clusters. The compilation fails. Thanks, Jianxin -----Original Message----- From: Tone Kokalj Organization: J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Reply-To: , XCrySDen mailing list Date: Thu, 24 Jan 2013 19:32:40 +0100 To: Subject: Re: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX >On Fri, 2013-01-18 at 18:33 +0000, Zhu, Jianxin wrote: >> Dear Tone, >> >> I did update the program to 1.5.53 on one of my MacOSX machines and the >> problem remains. >> Attached below is the output to screen after I click "Save Current State >> and Structure". >> The output is essentially the same as that from 1.5.24. > >Well, this may be due to a bug in the code. Please put the file >xcAppInit.c (attached in a separate email) into the subdirectory C/ (for >1.5.53 version only) and recompile with debugging option "-g" (edit >CFLAGS in Make.sys). If it still crashes then run as "xcrysden -d" and >upon crash write "where" in the gdb prompt (perhaps gdb will give some >useful info). > >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 From member at linkedin.com Mon Jan 28 16:28:43 2013 From: member at linkedin.com (Eduardo Menendez Proupin via LinkedIn) Date: Mon, 28 Jan 2013 15:28:43 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn?= Message-ID: <269582940.16711444.1359386923796.JavaMail.app@ela4-app2313.prod> LinkedIn ------------ Eduardo Menendez Proupin solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de Eduardo Menendez Proupin http://www.linkedin.com/e/-fe5rcs-hchrvjey-27/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I318242362_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnP8ScP8QczwNcQALjnx9rSFKrjwLdzgVd38Ne3gTc34LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=3ZNCkGcw_0JlA1 Visualizar perfil de Eduardo Menendez Proupin http://www.linkedin.com/e/-fe5rcs-hchrvjey-27/rso/70754723/BDT1/name/128644874_I318242362_125/?hs=false&tok=21i1hz_pf0JlA1 ------------------------------------------ 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-hchrvjey-27/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=0A_mqNRc30JlA1 (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/20130128/a77a65de/attachment.htm From tone.kokalj at ijs.si Tue Jan 29 14:35:06 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 29 Jan 2013 14:35:06 +0100 Subject: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX In-Reply-To: <1A9F0F275F0DE54BA1FBF55D068937C72D238469@ECS-EXG-P-MB06.win.lanl.gov> References: <1A9F0F275F0DE54BA1FBF55D068937C72D238469@ECS-EXG-P-MB06.win.lanl.gov> Message-ID: <1359466506.23142.7.camel@catalyst.ijs.si> On Thu, 2013-01-24 at 21:32 +0000, Zhu, Jianxin wrote: > With your new xcAppInit.c, the reported issue is gone. And when I execute > "xcrysden -s TiC.xcrysden" and the program takes the pictures back fully > and completely. Very good. Hence this bug has been solved! > On the other hand, as I reported before, although I don't have crash issue > with the program (same version of 1.5.53) on my linux cluster when I do > XCrysden "Save Current State and Structure", the execution of "xcrysden -s > TiC.xcrysden" does not give me back a complete picture. In a separate > message, I will attach one picture for your perusal. > I wish you have a solution to it. This is a very funny manifestation of the roundoff problem. It happens from time to time (and it has been reported several times). In your "incomplete" picture you will notice that some atoms at the "border" are missing (these are periodic replicas). If you multiply the structure (menu: Modify-->Number of Units drawn), then those atoms will appear there. However, this roundoff problem is annoying and I could get rid of it by reducing the precision in your TiC.xcrysden structure part of the file, i.e.: set xsfStructure { CRYSTAL PRIMVEC 2.23385 2.23385 0.00000 2.23385 0.00000 2.23385 0.00000 2.23385 2.23385 CONVVEC 4.46770 0.00000 0.00000 0.00000 4.46770 0.00000 0.00000 0.00000 4.46770 PRIMCOORD 2 1 22 0.00000 0.0000000000 0.0000000000 6 2.23385 0.0000000000 0.0000000000 } 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 jxzhu at lanl.gov Thu Jan 31 23:26:53 2013 From: jxzhu at lanl.gov (Zhu, Jianxin) Date: Thu, 31 Jan 2013 22:26:53 +0000 Subject: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX In-Reply-To: <1359466506.23142.7.camel@catalyst.ijs.si> Message-ID: <1A9F0F275F0DE54BA1FBF55D068937C72D555B0E@ECS-EXG-P-MB05.win.lanl.gov> Dear Tone, Sorry for the delay in reply. Motivated by your point on roundoff/resolution issue, I looked back into the wien2k structure file and found that the TiC.struct file, which was giving me incomplete picture on my cluster, has a different number of digits (for lattice constants) from the one giving me a complete picture on my macbook pro. After I corrected the digits, the program just gave me back a complete picture. By this, I would say the program (1.5.53) works great! Thank you very much for going through this issue with me. Best regards, Jianxin -----Original Message----- From: Tone Kokalj Organization: J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Reply-To: , XCrySDen mailing list Date: Tue, 29 Jan 2013 14:35:06 +0100 To: Subject: Re: [xcrysden] XCrysden "Save Current State and Structure" on Mac OSX >On Thu, 2013-01-24 at 21:32 +0000, Zhu, Jianxin wrote: >> With your new xcAppInit.c, the reported issue is gone. And when I >>execute >> "xcrysden -s TiC.xcrysden" and the program takes the pictures back fully >> and completely. > >Very good. Hence this bug has been solved! > >> On the other hand, as I reported before, although I don't have crash >>issue >> with the program (same version of 1.5.53) on my linux cluster when I do >> XCrysden "Save Current State and Structure", the execution of "xcrysden >>-s >> TiC.xcrysden" does not give me back a complete picture. In a separate >> message, I will attach one picture for your perusal. >> I wish you have a solution to it. > >This is a very funny manifestation of the roundoff problem. It happens >from time to time (and it has been reported several times). In your >"incomplete" picture you will notice that some atoms at the "border" are >missing (these are periodic replicas). If you multiply the structure >(menu: Modify-->Number of Units drawn), then those atoms will appear >there. However, this roundoff problem is annoying and I could get rid of >it by reducing the precision in your TiC.xcrysden structure part of the >file, i.e.: > >set xsfStructure { >CRYSTAL >PRIMVEC > 2.23385 2.23385 0.00000 > 2.23385 0.00000 2.23385 > 0.00000 2.23385 2.23385 >CONVVEC > 4.46770 0.00000 0.00000 > 0.00000 4.46770 0.00000 > 0.00000 0.00000 4.46770 >PRIMCOORD >2 1 > 22 0.00000 0.0000000000 0.0000000000 > 6 2.23385 0.0000000000 0.0000000000 >} > >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