From w2agz at pacbell.net Sun Nov 4 20:23:50 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Sun, 4 Nov 2007 11:23:50 -0800 Subject: [xcrysden] CIF & XSF Message-ID: <019601c81f18$3c681770$b5384650$@net> To All: Is there a script available that extracts/converts the appropriate contents of a cif file into xsf input for XCrysDen? I confess I haven't even looked to see if this is possible, but I strongly suspect it would be. Given the wide acceptance of the cif protocol, I'm kind of surprised if no one has attempted such, but I could find no reference to "cif" in the past two years of the XCrysDen archives, nor a "Google hit" on cif + xcrysden. Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20071104/0c52cd32/attachment.htm From tone.kokalj at ijs.si Mon Nov 5 12:41:04 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 05 Nov 2007 12:41:04 +0100 Subject: [xcrysden] CIF & XSF In-Reply-To: <019601c81f18$3c681770$b5384650$@net> References: <019601c81f18$3c681770$b5384650$@net> Message-ID: <1194262864.2602.7.camel@localhost.localdomain> On Sun, 2007-11-04 at 11:23 -0800, Paul M. Grant wrote: > To All: > > > > Is there a script available that extracts/converts the appropriate > contents of a cif file into xsf input for XCrysDen? Not that I would know. When I need it I do it manually. I extract the structural information from CIF and convert it accordingly. Here are a few tips: The CIF files contain only the non-equivalent atoms. To generate the other equivalent atoms, you may use the utilities of Bilbao Crystallographic Server. I suppose this utility should do the job: http://www.cryst.ehu.es/cryst/wpassign.html Then you will have all atomic positions in crystal-coordinates. To pass from them to Cartesian (in Angstrom units) is simplel (write a simple script or fortran program for conversion). Regards, Tone From w2agz at pacbell.net Tue Nov 6 01:26:26 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Mon, 5 Nov 2007 16:26:26 -0800 Subject: [xcrysden] CIF & XSF In-Reply-To: <1194262864.2602.7.camel@localhost.localdomain> References: <019601c81f18$3c681770$b5384650$@net> <1194262864.2602.7.camel@localhost.localdomain> Message-ID: <001b01c8200b$abec0540$03c40fc0$@net> Thanks, Tone. I completely forgot about the Bilboa site. I actually have several of their other tables stored locally, and overlooked the Wyckoff utility. -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] On Behalf Of Tone Kokalj Sent: Monday, November 05, 2007 3:41 AM To: XCrySDen mailing list Subject: Re: [xcrysden] CIF & XSF On Sun, 2007-11-04 at 11:23 -0800, Paul M. Grant wrote: > To All: > > > > Is there a script available that extracts/converts the appropriate > contents of a cif file into xsf input for XCrysDen? Not that I would know. When I need it I do it manually. I extract the structural information from CIF and convert it accordingly. Here are a few tips: The CIF files contain only the non-equivalent atoms. To generate the other equivalent atoms, you may use the utilities of Bilbao Crystallographic Server. I suppose this utility should do the job: http://www.cryst.ehu.es/cryst/wpassign.html Then you will have all atomic positions in crystal-coordinates. To pass from them to Cartesian (in Angstrom units) is simplel (write a simple script or fortran program for conversion). Regards, Tone _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From zubaexy at gmail.com Fri Nov 9 15:52:07 2007 From: zubaexy at gmail.com (zubaer) Date: Fri, 9 Nov 2007 08:52:07 -0600 Subject: [xcrysden] XCrySDen installation for Windows Message-ID: <51ec861d0711090652h7e42134awb57356f704ca7e6b@mail.gmail.com> Hi, I am a very new user of XCrySDen. I am having problems in XCrySDen installation for Windows. I am using compiled binary. When I open cygwin I see its home directory as C:\Documents and Settings\myname\ I see "XCrysDen" directory here and it has all the files like (bin, Awk, contrib etc...). I have pasted xcConfigure files at ..\hossain2\ When in the cygwin window I type ./xcConfigure it shows $ ./xcConfigure ./xcConfigure: line 39: cd: /cygdrive/c/Documents: No such file or directory ./xcConfigure: line 70: /cygdrive/c/Documents: No such file or directory I dont know how could I solve this problem. To note I installed Tcl also. And set path variables as suggested in the installation instructions. Is it necessary to rename the folder 'XCrySDen' as '.xcrysden'? I am sorry if I am asking stupid questions. I appreciate any help in this regard. Thanks, Zubaer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20071109/3568370c/attachment.htm From tone.kokalj at ijs.si Fri Nov 9 16:01:00 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 09 Nov 2007 16:01:00 +0100 Subject: [xcrysden] XCrySDen installation for Windows In-Reply-To: <51ec861d0711090652h7e42134awb57356f704ca7e6b@mail.gmail.com> References: <51ec861d0711090652h7e42134awb57356f704ca7e6b@mail.gmail.com> Message-ID: <1194620460.27078.29.camel@localhost.localdomain> On Fri, 2007-11-09 at 08:52 -0600, zubaer wrote: > Hi, > > I am a very new user of XCrySDen. I am having problems in XCrySDen > installation for Windows. I am using compiled binary. When I open > cygwin I see its home directory as > > C:\Documents and Settings\myname\ > > I see "XCrysDen" directory here and it has all the files like (bin, > Awk, contrib etc...). I have pasted xcConfigure files at ..\hossain2\ > When in the cygwin window I type ./xcConfigure it shows > > $ ./xcConfigure > ./xcConfigure: line 39: cd: /cygdrive/c/Documents: No such file or > directory > ./xcConfigure: line 70: /cygdrive/c/Documents: No such file or > directory This is due to a whitespace in the directory name for $HOME (i.e. home directory). This is not very smart. Please install cygwin under some different place then: C:\Documents and Settings\myname\ For example, the default C:\cygwin would be a good place. Regards, Tone From tommy91779 at hotmail.com Tue Nov 13 19:15:46 2007 From: tommy91779 at hotmail.com (Thomas Sadowski) Date: Tue, 13 Nov 2007 13:15:46 -0500 Subject: [xcrysden] Printing Images in Windows Message-ID: Hello all, I have successfully configured and rum xcrysden on my windows box through Cygwin. Problems arise when I attempt to print an image in a tiff or eps format. When I attempt to do so I get the following error: ERROR: while executing exec /bin/convert /home/Tom/XCrySDEN-1.4.1bin-shared/xcrys_temp/xc_1468/tmp.ppm C:/cygwin/home/Tom/XCrySDEN-1.4.1bin-shared/four_Shell_CdS.tiff When Clicking on ErrorInfo I get convert: unable to open image `/cygwin/home/Tom/XCrySDen-1.4.1bin-shared/four_Shell_CdS.tiff': No such file or directory. Cygwin installed my ImageMagic Package under /bin/convert. Has anyone come across this problem and discovered a work around?? Thanks in advance, Tom Sadowski University of Connecticut _________________________________________________________________ Climb to the top of the charts!? Play Star Shuffle:? the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_oct -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20071113/72043396/attachment.htm From tone.kokalj at ijs.si Mon Nov 19 15:19:07 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 19 Nov 2007 15:19:07 +0100 Subject: [xcrysden] Printing Images in Windows In-Reply-To: References: Message-ID: <1195481947.7411.14.camel@localhost.localdomain> On Tue, 2007-11-13 at 13:15 -0500, Thomas Sadowski wrote: > Hello all, > > > > I have successfully configured and rum xcrysden on my windows box > through Cygwin. Problems arise when I attempt to print an image in a > tiff or eps format. When I attempt to do so I get the following error: > > > > ERROR: while executing exec /bin/convert > /home/Tom/XCrySDEN-1.4.1bin-shared/xcrys_temp/xc_1468/tmp.ppm > C:/cygwin/home/Tom/XCrySDEN-1.4.1bin-shared/four_Shell_CdS.tiff > > When Clicking on ErrorInfo I get > > convert: unable to open image > `/cygwin/home/Tom/XCrySDen-1.4.1bin-shared/four_Shell_CdS.tiff': No > such file or directory. Seems like your /cygwin/home/Tom/XCrySDen-1.4.1bin-shared/ is write protected. Have you tried to save the file to some other directory? Tone From salguero at itp.uni-frankfurt.de Thu Nov 29 12:22:00 2007 From: salguero at itp.uni-frankfurt.de (Andrea Salguero) Date: Thu, 29 Nov 2007 12:22:00 +0100 Subject: [xcrysden] 2D charge density plot units Message-ID: <200711291222.01227.salguero@itp.uni-frankfurt.de> Dear Xcrysden users and developers I have made a 2D charge density plot and checking the xcrysden options one can include a thermometer in it, i know the thermometer is related to delta n(r), my question is, what are the units of it?, eV/A^2 or u.a/A^2?, where can one find it or deduce it from? Best Regards Andrea From tone.kokalj at ijs.si Thu Nov 29 13:17:38 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 29 Nov 2007 13:17:38 +0100 Subject: [xcrysden] 2D charge density plot units In-Reply-To: <200711291222.01227.salguero@itp.uni-frankfurt.de> References: <200711291222.01227.salguero@itp.uni-frankfurt.de> Message-ID: <1196338658.2824.22.camel@localhost.localdomain> On Thu, 2007-11-29 at 12:22 +0100, Andrea Salguero wrote: > Dear Xcrysden users and developers > I have made a 2D charge density plot and checking the xcrysden options one can > include a thermometer in it, i know the thermometer is related to delta n(r), > my question is, what are the units of it?, eV/A^2 or u.a/A^2?, where can one > find it or deduce it from? The termometer is related to the property you are plotting. The "\Delta n(r)" is just the default string, one can modify it by will. xcrysden makes no assumptions: it doesn't care about what property it displays nor about the units. It simply displays what is in the loaded file. This means that the units are those used in the loaded file ... (there is not conversion of units involved whatsoever). Regards, Tone