From venkyphysicsiitm at gmail.com Wed Jan 14 22:09:35 2015 From: venkyphysicsiitm at gmail.com (venkatesh chandragiri) Date: Thu, 15 Jan 2015 02:39:35 +0530 Subject: [xcrysden] primitive cell for PHON Message-ID: Dear Sir, I am planing to carryout phonon calculations using PHON package. For this, I need to generate the primitive structure of the given material which is going to fed into PHON program. In wien2k, one could able to generate the structure file by giving atomic co-ordinates and space group. In xcrysden, one could press F3 and F4 to toggle between the primitive and conventional cell types. After this, I have extracted the case.struct from xcrysden when it is showing primitive cell mode. Later, I have uploaded this case.struct into another package called VESTA to check the actual primitive cell. This case.struct results a structure looks like conventional cell with FCC type with space group 1 (actual space group, 225 was not shown). In PHON code, I have to give the primitive cell of the given material in a POSCAR format (this is the structure file in VASP program). For this, I have used same VESTA package to save this primitive cell data into VASP format (POSCAR file). But, the program VESTA saved it as 16 number of co-ordinates with a cubic type (not a 4 co-ordinates with FCC type). The phonon calculations will take much more time if i could use this 16 numbered POSCAR and the time consumption may be greatly reduced, if i could use the 4 numbered FCC type POSCAR file. Hence, kindly suggest me the proper pathway to get the POSCAR of FCC type using wein2k-4 atomic primitive cell sturct generated by xcrysden. kindly, find the attached struct files in the various formats for your reference. My compound was Fe2VAl with a 225 space group, F m-3m symmetry Fe (0.25,0.25,0.25) V (0.5,0.5,0.5) Al (0,0,0) I need your suggestions to proceed further, thanking you and looking for your help. Sincerely, venkatesh chandragiri C/o. Prof. V. Srinivas, Dept. of Physics IIT Madras, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150115/be65d389/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Fe2VAl_SG_primitive.struct Type: application/octet-stream Size: 1151 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20150115/be65d389/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Fe2VAl_SG_primitive.vasp Type: application/octet-stream Size: 1216 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20150115/be65d389/attachment-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Fe2VAl_SG_primitive.vesta Type: application/octet-stream Size: 4683 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20150115/be65d389/attachment-0002.obj From tone.kokalj at ijs.si Fri Jan 16 21:01:58 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 16 Jan 2015 21:01:58 +0100 Subject: [xcrysden] primitive cell for PHON In-Reply-To: References: Message-ID: <1421438518.1116.39.camel@ijs.si> On Thu, 2015-01-15 at 02:39 +0530, venkatesh chandragiri wrote: > The phonon calculations will take much more time if i could use this > 16 numbered POSCAR and the time consumption may be greatly reduced, if > i could use the 4 numbered FCC type POSCAR file. Hence, kindly suggest > me the proper pathway to get the POSCAR of FCC type using wein2k-4 > atomic primitive cell sturct generated by xcrysden. kindly, find the > attached struct files in the various formats for your reference. Consider using the following trick: 1) display structure with xcrysden 2) change to primitive cell mode 3) change to "translational assymetric unit" mode 3) click the "Atoms Info" button at the left-bottom 4) select the Crystal-Primitive coordinates on "Atoms Info" window and select all the atoms (now you obtained the crystal coordinates for all the atoms in the primitive unit cell) 5) the primitive-lattice vectors may be obtained by saving the display structure as XSF file (PRIMCOORD sectiond) 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 venkyphysicsiitm at gmail.com Sun Jan 18 13:25:53 2015 From: venkyphysicsiitm at gmail.com (venkatesh chandragiri) Date: Sun, 18 Jan 2015 17:55:53 +0530 Subject: [xcrysden] primitive cell for PHON Message-ID: Dear Sir, thank you for your helpful reply. I have done as suggested by you. The obtained file has been attached here. Now, I want to understand the lattice vector's format in this file. In this file, the primitive cell have 4 lattice points with a lattice parameter of "a/1.414". The primitive cell is rhombohedral type as conventional cell was FCC type. Typically, the lattice vectors of FCC primitive cell is written as (0, 0.5, 0.5), (0.5,0,0.5) and (0.5,0.5,0). But, the lattice vectors of this file is different. Here, the first lattice vector is made to coincide with the X-axis of the conventional lattice and hence, the remaining two lattice vectors are adjusted according to this. However, I want to confirm whether, I got accurate lattice vectors or not. So, kindly provide me, if you have any kind of mathematical support or references to know how to generate these lattice vectors for a FCC conventional lattice. thanking you and looking forward to your response Regards, venkatesh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150118/9a46ec0c/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Fe2VAl_SG_primitive2_P1.vasp Type: application/octet-stream Size: 489 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20150118/9a46ec0c/attachment.obj From victoria-povilus at uiowa.edu Wed Jan 28 05:27:48 2015 From: victoria-povilus at uiowa.edu (Kortan, Victoria R) Date: Wed, 28 Jan 2015 04:27:48 +0000 Subject: [xcrysden] xcrysden-1.5.60 not opening .struct files Message-ID: Dear xcrysden users, I have installed xcrysden-1.5.60 using fink, and am running OSX-10.10. I have tried to open a WIEN2k .struct file both using the GUI and command line: "xcrysden --wien_struct Si216.struct". Either way I get an error (I have copied it to the bottom of this e-mail). Previously I was using xcrysden-1.5.24 and OSX-10.6.8 to successfully to open the same file. I am at a loss and not sure what to do. Thank you for any guidance/ideas, ~Victoria Kortan Error Message: Error in startup script: error renaming "Si216}.xcr": no such file or directory while executing "file rename -force ${filehead}.xcr $system(SCRDIR)/xc_str2xcr.$system(PID)" (procedure "wnOpenSFile" line 50) invoked from within "wnOpenSFile $file" (procedure "parseComLinArg" line 174) invoked from within "parseComLinArg [lrange $argv 2 end]" invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/sw/share/xcrysden-1.5.60/Tcl/xcInit.tcl" line 609) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150128/f17fc514/attachment.htm From martin at ruby.chemie.uni-freiburg.de Wed Jan 28 12:03:52 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Wed, 28 Jan 2015 12:03:52 +0100 (CET) Subject: [xcrysden] xcrysden-1.5.60 not opening .struct files In-Reply-To: Message-ID: <20150128110352.676F1801B3@ruby.chemie.uni-freiburg.de> > Error in startup script: error renaming "Si216}.xcr": no such file or directory The "proc FileHead" in Tcl/auxil.tcl appears to return a brace that was not in the original filename. At first glance it is not clear to me why that procedure is not simply written as proc FileHead file { set filehead [file rootname $file] regsub -all { } $filehead \. filehead return $filehead } So if you feel adventurous you could try modifying that part of auxil.tcl accordingly. Hope this helps Martin -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From tone.kokalj at ijs.si Wed Jan 28 12:33:09 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 28 Jan 2015 12:33:09 +0100 Subject: [xcrysden] xcrysden-1.5.60 not opening .struct files In-Reply-To: <20150128110352.676F1801B3@ruby.chemie.uni-freiburg.de> References: <20150128110352.676F1801B3@ruby.chemie.uni-freiburg.de> Message-ID: <1422444789.1582.42.camel@ijs.si> On Wed, 2015-01-28 at 12:03 +0100, Martin Kroeker wrote: > > Error in startup script: error renaming "Si216}.xcr": no such file or directory > The "proc FileHead" in Tcl/auxil.tcl appears to return a brace that was not in the > original filename. At first glance it is not clear to me why that > procedure is not simply written as > > proc FileHead file { > set filehead [file rootname $file] > regsub -all { } $filehead \. filehead > > return $filehead > } It should be simply written as: proc FileHead file { return [file rootname $file] } I presume I was not aware of "file rootname" command at the time this proc was written (which was long-long ago). Anyway this does not explain the weird behaviour observed by Victoria. This proc run w/o problems for two decades without any such report. I believe the problem lies elsewhere. Check if the ./bin/str2xcr binary is functional, i.e., if you have a given structu file, say file.struct, then run as: $XCRYSDEN_TOPDIR/bin/str2xcr file (where XCRYSDEN_TOPDIR is the path to your xcrysden root directory) This should create an XSF file named as "file.xcr". 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 martin at ruby.chemie.uni-freiburg.de Wed Jan 28 13:17:21 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Wed, 28 Jan 2015 13:17:21 +0100 (CET) Subject: [xcrysden] xcrysden-1.5.60 not opening .struct files In-Reply-To: <1422444789.1582.42.camel@ijs.si> Message-ID: <20150128121721.B0C71801B3@ruby.chemie.uni-freiburg.de> > On Wed, 2015-01-28 at 12:03 +0100, Martin Kroeker wrote: > > > Error in startup script: error renaming "Si216}.xcr": no such file or directory > > The "proc FileHead" in Tcl/auxil.tcl appears to return a brace that was not in the > > original filename. At first glance it is not clear to me why that > > procedure is not simply written as > > > > proc FileHead file { > > set filehead [file rootname $file] > > regsub -all { } $filehead \. filehead > > > > return $filehead > > } > > It should be simply written as: > > proc FileHead file { > return [file rootname $file] > } > Thanks, I was unsure if the replacement of blanks in the filename by dots was actually used anywhere so I left it in. > the weird behaviour observed by Victoria. This proc run w/o problems for > two decades without any such report. I believe the problem lies > elsewhere. Check if the ./bin/str2xcr binary is functional, i.e., if you > have a given structu file, say file.struct, then run as: I'd say that is unlikely to be the root cause of the problem, as "filehead" is determined before calling str2xcr. Could it be a double dot in the original filename, something like Si216..struct ? I could imagine that the "tcl list mangling" in the original FileHead proc might fall over when the list created by "split" contains empty elements "{}". Hmmm... seeing that the result of "proc FileHead" is not used much anywhere else, would it be conceivable that this part of wnOpen.tcl has been happily creating (temporary) xcr files with an extraneous brace in them for decades, and only now str2xcr refuses to create them (or the underlying file system / operating system / shell does not allow a stray closing brace in filenames) ?? -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From tone.kokalj at ijs.si Wed Jan 28 14:11:23 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 28 Jan 2015 14:11:23 +0100 Subject: [xcrysden] xcrysden-1.5.60 not opening .struct files In-Reply-To: <20150128121721.B0C71801B3@ruby.chemie.uni-freiburg.de> References: <20150128121721.B0C71801B3@ruby.chemie.uni-freiburg.de> Message-ID: <1422450683.1582.53.camel@ijs.si> On Wed, 2015-01-28 at 13:17 +0100, Martin Kroeker wrote: > I'd say that is unlikely to be the root cause of the problem, as "filehead" > is determined before calling str2xcr. > Could it be a double dot in the original filename, something like > Si216..struct ? I could imagine that the "tcl list mangling" in the > original FileHead proc might fall over when the list created by "split" > contains empty elements "{}". > Hmmm... seeing that the result of "proc FileHead" is not used much anywhere > else, would it be conceivable that this part of wnOpen.tcl has been happily > creating (temporary) xcr files with an extraneous brace in them for decades, and > only now str2xcr refuses to create them (or the underlying file system / > operating system / shell does not allow a stray closing brace in filenames) ?? This is absolutely correct; the old FileHead does return the "file.{}" for the double dotted "file..ext", while "file rootname file..ext" returns "file."; I have correct the old proc. However, if I do a double dotted example I obtain a slightly different error, i.e.: xcrysden --wien_struct al2o3..struct returns: Error in startup script: error renaming "al2o3.{}.xcr": no such file or directory (the file al2o3..struct must of course exist or else xcrysden complains "file does not exist") 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 victoria-povilus at uiowa.edu Wed Jan 28 19:01:02 2015 From: victoria-povilus at uiowa.edu (Kortan, Victoria R) Date: Wed, 28 Jan 2015 18:01:02 +0000 Subject: [xcrysden] xcrysden-1.5.60 not opening .struct files In-Reply-To: <1422450683.1582.53.camel@ijs.si> References: <20150128121721.B0C71801B3@ruby.chemie.uni-freiburg.de>, <1422450683.1582.53.camel@ijs.si> Message-ID: Victory! I edited /sw/share/xcrysden-1.5.60/Tcl/auxil.tcl to change FileHead as suggested: proc FileHead file { set filehead [file rootname $file] regsub -all { } $filehead \. filehead return $filehead } And I can now successfully visualize my .struct files. Thank you very much! ~Victoria ________________________________________ From: xcrysden-bounces at democritos.it [xcrysden-bounces at democritos.it] on behalf of Tone Kokalj [tone.kokalj at ijs.si] Sent: Wednesday, January 28, 2015 7:11 AM To: xcrysden at democritos.it Subject: Re: [xcrysden] xcrysden-1.5.60 not opening .struct files On Wed, 2015-01-28 at 13:17 +0100, Martin Kroeker wrote: > I'd say that is unlikely to be the root cause of the problem, as "filehead" > is determined before calling str2xcr. > Could it be a double dot in the original filename, something like > Si216..struct ? I could imagine that the "tcl list mangling" in the > original FileHead proc might fall over when the list created by "split" > contains empty elements "{}". > Hmmm... seeing that the result of "proc FileHead" is not used much anywhere > else, would it be conceivable that this part of wnOpen.tcl has been happily > creating (temporary) xcr files with an extraneous brace in them for decades, and > only now str2xcr refuses to create them (or the underlying file system / > operating system / shell does not allow a stray closing brace in filenames) ?? This is absolutely correct; the old FileHead does return the "file.{}" for the double dotted "file..ext", while "file rootname file..ext" returns "file."; I have correct the old proc. However, if I do a double dotted example I obtain a slightly different error, i.e.: xcrysden --wien_struct al2o3..struct returns: Error in startup script: error renaming "al2o3.{}.xcr": no such file or directory (the file al2o3..struct must of course exist or else xcrysden complains "file does not exist") 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 pascal.boulet at univ-amu.fr Wed Jan 28 22:43:48 2015 From: pascal.boulet at univ-amu.fr (Pascal Boulet) Date: Wed, 28 Jan 2015 22:43:48 +0100 Subject: [xcrysden] XCrySDen windows fail to show up Message-ID: <56D411A6-2D95-4369-9FDD-0ED63134FA73@univ-amu.fr> Dear all, I have installed XCrySDen v. 1.5.24 (semi-shared) on my MAC OS Darwin laptop. I have solved a couple of library-related issues but now I facing a problem with X11 (I guess). I have installed XQuartz. The error message is: Executing: /usr/local/XCrySDen-1.5.24-bin-semishared/bin/ftnunit X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 560 Current serial number in output stream: 561 I have seen a similar message in the XCrySDen mailing-list that dates back to 2012, but there seems to be no answer to this question. Does anyone have encountered this before? Thank you in advance for your help, Best regards Pascal Boulet -- pascal.boulet at univ-amu.fr Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen F-13397 Marseille Cedex 20 Tel.: +33 413.55.18.10 Fax: +33 413.55.18.50 http://allos.up.univ-mrs.fr/pascal/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150128/2a7769e9/attachment.htm From martin at ruby.chemie.uni-freiburg.de Thu Jan 29 00:23:07 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Thu, 29 Jan 2015 00:23:07 +0100 (CET) Subject: [xcrysden] XCrySDen windows fail to show up In-Reply-To: <56D411A6-2D95-4369-9FDD-0ED63134FA73@univ-amu.fr> Message-ID: <20150128232307.CC89E801B3@ruby.chemie.uni-freiburg.de> I think this was something with xcrysden insisting on some particular opengl feature (or was it color depth) for no particular reason. Any chance you could try a more recent version that may already contain a fix for this problem ? 1.5.24 must be at least three years old, and in another message of today it was mentioned that the current 1.5.60 is available through the fink project at least. -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From martin at ruby.chemie.uni-freiburg.de Thu Jan 29 00:43:33 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Thu, 29 Jan 2015 00:43:33 +0100 (CET) Subject: [xcrysden] XCrySDen windows fail to show up In-Reply-To: <56D411A6-2D95-4369-9FDD-0ED63134FA73@univ-amu.fr> Message-ID: <20150128234333.4554B801B3@ruby.chemie.uni-freiburg.de> Also see thread "problem running on OS X 10.9" from November 2013 - there this problem was traced to incompatible (or broken) versions of the Mesa OpenGL library. The solution given there was to either install the "fink" versions of both xcrysden and mesa, or to use a specifically patched MacPorts version. You might want to see if the download links given in the thread still work. -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From pascal.boulet at univ-amu.fr Thu Jan 29 07:57:40 2015 From: pascal.boulet at univ-amu.fr (Pascal Boulet) Date: Thu, 29 Jan 2015 07:57:40 +0100 Subject: [xcrysden] XCrySDen Digest, Vol 83, Issue 5 In-Reply-To: References: Message-ID: <180BF0D0-518A-4287-96B0-E69660F6625D@univ-amu.fr> Thank you Martin for your prompt help. I?ll try to install a more recent version. Best regards Pascal Le 29 janv. 2015 ? 07:35, xcrysden-request at democritos.it a ?crit : > ------------------------------ > > Message: 7 > Date: Thu, 29 Jan 2015 00:23:07 +0100 (CET) > From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) > Subject: Re: [xcrysden] XCrySDen windows fail to show up > To: XCrySDen mailing list > Message-ID: <20150128232307.CC89E801B3 at ruby.chemie.uni-freiburg.de> > Content-Type: text/plain; charset="UTF-8" > > I think this was something with xcrysden insisting on some particular > opengl feature (or was it color depth) for no particular reason. > Any chance you could try a more recent version that may already > contain a fix for this problem ? 1.5.24 must be at least three years > old, and in another message of today it was mentioned that the current > 1.5.60 is available through the fink project at least. > > -- > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > c/o Prof.Dr. Caroline Roehr > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > > > ------------------------------ > > Message: 8 > Date: Thu, 29 Jan 2015 00:43:33 +0100 (CET) > From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) > Subject: Re: [xcrysden] XCrySDen windows fail to show up > To: XCrySDen mailing list > Message-ID: <20150128234333.4554B801B3 at ruby.chemie.uni-freiburg.de> > Content-Type: text/plain; charset="UTF-8" > > Also see thread "problem running on OS X 10.9" from November 2013 - > there this problem was traced to incompatible (or broken) versions > of the Mesa OpenGL library. The solution given there was to either > install the "fink" versions of both xcrysden and mesa, or to use a > specifically patched MacPorts version. You might want to see if the > download links given in the thread still work. > -- > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > c/o Prof.Dr. Caroline Roehr > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 83, Issue 5 > *************************************** Pascal Boulet -- pascal.boulet at univ-amu.fr Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen F-13397 Marseille Cedex 20 Tel.: +33 413.55.18.10 Fax: +33 413.55.18.50 http://allos.up.univ-mrs.fr/pascal/