From xcrysden@democritos.it Sat Jul 1 01:48:50 2006 From: xcrysden@democritos.it (Zhufeng Hou) Date: Fri, 30 Jun 2006 17:48:50 -0700 (PDT) Subject: [xcrysden] Re: XCrySDen digest, Vol 1 #100 - 2 msgs In-Reply-To: <20060615054610.27837.99637.Mailman@democritos.sissa.it> Message-ID: <20060701004850.46779.qmail@web54505.mail.yahoo.com> Please see this website: http://www.cryst.ehu.es/cryst/get_kvec.html (The k-vector types and Brillouin zones of the space groups) I think it will be useful to you. --- xcrysden-request@democritos.it wrote: > Send XCrySDen mailing list submissions to > xcrysden@democritos.it > > To subscribe or unsubscribe via the World Wide Web, > visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body > 'help' to > xcrysden-request@democritos.it > > You can reach the person managing the list at > xcrysden-admin@democritos.it > > When replying, please edit your Subject line so it > is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. On k-space path selection (Marcos Verissimo > Alves) > 2. Re: On k-space path selection (Tone Kokalj) > > --__--__-- > > Message: 1 > Date: Wed, 14 Jun 2006 15:06:17 +0200 (CEST) > From: "Marcos Verissimo Alves" > To: xcrysden@democritos.it > Subject: [xcrysden] On k-space path selection > Reply-To: xcrysden@democritos.it > > Hi all, > > I am a newbie to XCrysDen, and I have a few basic > questions about the > k-point path selection feature on XCrysDen. I have > an XSF file I generated > from the output of an ab initio program unsupported > by XCrysDen. To my > delight I found that the program gives me the > Brillouin Zone (BZ) > automatically with high-symmetry points indicated. > The questions are: > > 1) Is this general, or does it come from a set of > pre-defined BZs? I mean, > if I enter any crystal structure and ask for the BZ, > how are the > high-symmetry points found? > > 2) This one is not really related to XCrysDen, but I > feel I might get some > help here. Given three reciprocal space vectors, is > there a way to use the > Bilbao Crystallographic Server to tell me to which > space group my lattice > belongs to? This way, I could get the labels for the > high-symmetry points > of the BZ. > > Thanks, > > Marcos > > -- > Dr. Marcos Verissimo Alves > Post-Doctoral Fellow > Condensed Matter and Statistical Physics Sector > International Centre for Theoretical Physics > Trieste, Italy > > -------- > > I have become so addicted to vi that I try to exit > OpenOffice by typing :wq! > > > --__--__-- > > Message: 2 > Date: Wed, 14 Jun 2006 18:17:32 +0200 (CEST) > Subject: Re: [xcrysden] On k-space path selection > From: "Tone Kokalj" > To: xcrysden@democritos.it > Reply-To: xcrysden@democritos.it > > > I am a newbie to XCrysDen, and I have a few basic > questions about the > > k-point path selection feature on XCrysDen. I have > an XSF file I enerated > > from the output of an ab initio program > unsupported by XCrysDen. To my > > delight I found that the program gives me the > Brillouin Zone (BZ) > > automatically with high-symmetry points indicated. > The questions are: > > > > 1) Is this general, or does it come from a set of > pre-defined BZs? I mean, > > if I enter any crystal structure and ask for the > BZ, how are the > > high-symmetry points found? > > The labeling of the k-points is supported by a few > Bravais lattice > types, and is based on a lookup table of Peter > Blaha: see last part > of the file $XCRYSDEN_TOPDIR/Tcl/kLabels.tcl > > In order for this labelling to work, there should be > info about the > Bravais lattice type in the XSF file. This is > achieved by replacing the > "CRYSTAL" keyword by: > > DIM-GROUP > 3 igroup > > where "3" specifies 3 dimensional periodicity, and > igroup the > lattice type, in particular: > > 1 ... primitive > 2 ... A centered > 3 ... B centered > 4 ... C centered > 5 ... face-centered (i.e. fcc) > 6 ... body-cetered (i.e. bcc) > 7 ... rhombohedral > 8 ... hexagonal > 9 ... trigonal > > > > > 2) This one is not really related to XCrysDen, but > I feel I might get some > > help here. Given three reciprocal space vectors, > is there a way to use the > > Bilbao Crystallographic Server to tell me to which > space group my lattice > > belongs to? This way, I could get the labels for > the high-symmetry points > > of the BZ. > > I don't know. > > Regard, Tone > > > > --__--__-- > > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest > ************************************************* Zhu-feng Hou P.O.Box1169# Physics Department of Xiamen University Xiamen,361005 P.R.China Tel:+86-592-2194744 ************************************************** __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From xcrysden@democritos.it Wed Jul 5 11:54:10 2006 From: xcrysden@democritos.it (Gabriele Sclauzero) Date: Wed, 05 Jul 2006 12:54:10 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? Message-ID: <44AB9A52.7000300@sissa.it> I tried to run the 1.4.1 version with xcrysden --pw_in but the option --pw_in is not recognized. Running xcrysden --pwi accepts this option but the input file for pwi2xsf then generated has a mistake, I suppose: &system ibrav = 6 celldm(1) = 18 celldm(3) = 4.17629475 nat= 19 CALCULATION= "SCF" ATOMIC_POSITIONS ANGSTROM C 1.81396 0.0 0.0 O 2.94454710 0.0 0.0 PT 0.0 0.0 -18.72 PT 0.0 0.0 -16.38 PT 0.0 0.0 -14.04 PT 0.0 0.0 -11.70 PT 0.0 0.0 -9.36 PT 0.0 0.0 -7.02 PT 0.0 0.0 -4.68 PT 0.0 0.0 -2.34 PT 0.0 0.0 0 PT 0.0 0.0 2.34 PT 0.0 0.0 4.68 PT 0.0 0.0 7.02 PT 0.0 0.0 9.36 PT 0.0 0.0 11.70 PT 0.0 0.0 14.04 PT 0.0 0.0 16.38 PT 0.0 0.0 18.72 because the namelist is not ended before the ATOMIC_POSITIONS card starts. Adding a / after the namelist seems to work. Can someone confirm this? Gabriele From xcrysden@democritos.it Mon Jul 10 21:50:21 2006 From: xcrysden@democritos.it (Pedro M. F. J. Costa) Date: 10 Jul 2006 21:50:21 +0100 Subject: [xcrysden] xcrysden installation error on line 156 Message-ID: Dear users list, I am on the process of installing XCrysDen.=20 I have successfully installed CYGWIN on my Windows system. Additionally, my= =20 XCrysDen top directory installation has been successful as the following=20 has been added to my .bashrc:=20 #------------------------------------------------------------------------ #= =20 this is for XCRYSDEN 1.4.1; added by XCRYSDEN installation on # Mon Jul 10= =20 19:09:40 GMTDT 2006=20 #------------------------------------------------------------------------= =20 XCRYSDEN_TOPDIR=3D/home/Pedro XCRYSDEN_SCRATCH=3D/home/Pedro/xcrys_tmp expo= rt=20 XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH=20 PATH=3D"$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/ut= il" However, when I try to run XCrysDen from the TOPDIR, I get the following=20 error message: ./xcrysden: line 156: exec: wish: not found Verifying the xcrysden program lines, I have: if test $valgrind -eq 0 ; then if test $debug -eq 0 ; then =09if test -f ${XCRYSDEN_TOPDIR}/bin/xcrys.dll ; then =09# CYGWIN: xcrys.dll will be loaded from xcInit.tcl !!! =09 exec wish ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- \ =09=09$XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null & =09 wait $! =09else =09 ${XCRYSDEN_TOPDIR}/bin/xcrys \ =09=09${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- \ =09=09$XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null & =09 wait $! =09fi [continues] So the program calls for an executable that involves the file xcInit.tcl.= =20 Now, from other posts I noticed that my error message could be a case of=20 missing of Tcl package. I have verified my TOPDIR directory and I found=20 that I have the Tcl directory installed and that furthermore there is a=20 file inside with the name xcInit.tcl. Strangely enough the file xcrys.dll= =20 is also in its right place (TOPDIR/bin/) but that does not seem to make any= =20 difference to the proper execution of the program. So, as far as I understand, I have the CYGWIN and XCrysDen installed in=20 their proper directories but there is still something missing. Is it a=20 matter of extra packages needed? If it is how can I get a list of those=20 required? Could anyone please help me with this error?=20 My best regards, Pedro --=20 ************************************************************************** Pedro Miguel F. J. Costa Department of Materials Science and Metallurgy New Museums Site, Pembroke Street Cambridge, CB2 3QZ, United Kingdom Tel.(office): +44 (0)1223 334474 Fax: +44 (0)1223 334437 ************************************************************************** From xcrysden@democritos.it Thu Jul 13 17:56:57 2006 From: xcrysden@democritos.it (xcrysden@democritos.it) Date: Thu, 13 Jul 2006 11:56:57 -0500 Subject: [xcrysden] rhombohedral bi and xcrysden Message-ID: <20060713115657.ru88m78t3dww0osw@mail.ph.utexas.edu> Hi, I used the bi.struct file, provided with wien2k source in example_struct_files directory, in xcrysden(loaded on linux machine) to generate k-list file for band structure calculation. It gives the error: The guessed Bravais lattice type: not-supported ((the XSF's group number is = 7) The struct file used was: _________________ Bismut R LATTICE,NONEQUIV. ATOMS 1 MODE OF CALC=3DRELA 8.590000 8.590000 22.415000 90.000000 90.000000 90.000000 ATOM -1: X=3D0.23400000 Y=3D0.23400000 Z=3D0.23400000 MULT=3D 2 ISPLIT=3D 4 ATOM -1: X=3D0.76600000 Y=3D0.76600000 Z=3D0.76600000 Bi NPT=3D 781 R0=3D0.00001000 RMT=3D 2.8000 Z: 83.0 1.000000000.000000000.00000000 0.000000001.000000000.00000000 0.000000000.000000001.00000000 12 SYMMETRY OPERATIONS: 1 0 0 0.0000000 0 1 0 0.0000000 0 0 1 0.0000000 1 -1 0 0 0.0000000 0-1 0 0.0000000 0 0-1 0.0000000 2 0 0 1 0.0000000 1 0 0 0.0000000 0 1 0 0.0000000 3 0 0-1 0.0000000 0-1 0 0.0000000 -1 0 0 0.0000000 4 -1 0 0 0.0000000 0 0-1 0.0000000 0-1 0 0.0000000 5 0 1 0 0.0000000 0 0 1 0.0000000 1 0 0 0.0000000 6 0-1 0 0.0000000 0 0-1 0.0000000 -1 0 0 0.0000000 7 1 0 0 0.0000000 0 0 1 0.0000000 0 1 0 0.0000000 8 0 0 1 0.0000000 0 1 0 0.0000000 1 0 0 0.0000000 9 0 0-1 0.0000000 -1 0 0 0.0000000 0-1 0 0.0000000 10 0 1 0 0.0000000 1 0 0 0.0000000 0 0 1 0.0000000 11 0-1 0 0.0000000 -1 0 0 0.0000000 0 0-1 0.0000000 12 I checked the struct files of fcc structure, bcc stucture, hexagonal structure, xcrysden correctly identifies the symmetry and gives the corresponding BZ for selection of k-points. Is there any thing wrong with the struct file or the xcrysden for =20 rhombohderal lattices with hexagoal lattice constants and rhombohderal =20 positons? I noticed that the lattice constants are hexagonal (as the user manual says) but the angles are not!! it should be 90 90 120 instead of 90 90 90 in the bi.struct. Sahu From xcrysden@democritos.it Fri Jul 14 10:07:29 2006 From: xcrysden@democritos.it (Xunlei Ding) Date: Fri, 14 Jul 2006 11:07:29 +0200 Subject: [xcrysden] Problem when plot 2D grid with color black_brown_white Message-ID: <44B75ED1.8030802@sissa.it> Dear All, I have a problem. When I plot a 2D grid in a xsf file using xcrysden, with black_brown_white color basis, it gives an error as below. When ploting 3D data , or using other color basis, there is no problem. What's wrong I may make? Thank you! wanted integer, but got "COLORBASE_MONO" while executing xc_iso isoplane 0 COLORBASE_MONO 0 while executing "xc_iso isoplane 0 $basis $func $what " invoked from within "if $upd { if { $isoControl(colorplane) && !$isoControl(isoline) } { set what "colorplane" } elseif { !$isoControl(colorplane) && $isoControl(is..." (procedure "UpdatePropertyPlane" line 52) invoked from within "UpdatePropertyPlane" invoked from within ".iso2D.f3.sub invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .iso2D.f3.sub" (command bound to event) Yours sincerely, Ding From xcrysden@democritos.it Fri Jul 14 14:43:09 2006 From: xcrysden@democritos.it (Peter Blaha) Date: Fri, 14 Jul 2006 15:43:09 +0200 (CEST) Subject: [xcrysden] Re: rhombohedral bi and xcrysden In-Reply-To: <20060713115657.ru88m78t3dww0osw@mail.ph.utexas.edu> References: <20060713115657.ru88m78t3dww0osw@mail.ph.utexas.edu> Message-ID: If you read the message carefully, it says, that the k-point labelling (i.e. the naming with Gamma,X,Z,...) is implemented only for a few spacegroups, and the R-lattice is not included. Thus no big deal. The k-mesh is ok, but eventually you have to give names to the k-points yourself. > I used the bi.struct file, provided with wien2k source in > example_struct_files directory, in xcrysden(loaded on linux machine) to > generate > k-list file for band structure calculation. It gives the error: > > The guessed Bravais lattice type: not-supported ((the XSF's group number is 7) > > The struct file used was: > _________________ > Bismut > R LATTICE,NONEQUIV. ATOMS 1 > MODE OF CALC=RELA > 8.590000 8.590000 22.415000 90.000000 90.000000 90.000000 > ATOM -1: X=0.23400000 Y=0.23400000 Z=0.23400000 > MULT= 2 ISPLIT= 4 > ATOM -1: X=0.76600000 Y=0.76600000 Z=0.76600000 > Bi NPT= 781 R0=0.00001000 RMT= 2.8000 Z: 83.0 > 1.000000000.000000000.00000000 > 0.000000001.000000000.00000000 > 0.000000000.000000001.00000000 > 12 SYMMETRY OPERATIONS: > 1 0 0 0.0000000 > 0 1 0 0.0000000 > 0 0 1 0.0000000 > 1 > -1 0 0 0.0000000 > 0-1 0 0.0000000 > 0 0-1 0.0000000 > 2 > 0 0 1 0.0000000 > 1 0 0 0.0000000 > 0 1 0 0.0000000 > 3 > 0 0-1 0.0000000 > 0-1 0 0.0000000 > -1 0 0 0.0000000 > 4 > -1 0 0 0.0000000 > 0 0-1 0.0000000 > 0-1 0 0.0000000 > 5 > 0 1 0 0.0000000 > 0 0 1 0.0000000 > 1 0 0 0.0000000 > 6 > 0-1 0 0.0000000 > 0 0-1 0.0000000 > -1 0 0 0.0000000 > 7 > 1 0 0 0.0000000 > 0 0 1 0.0000000 > 0 1 0 0.0000000 > 8 > 0 0 1 0.0000000 > 0 1 0 0.0000000 > 1 0 0 0.0000000 > 9 > 0 0-1 0.0000000 > -1 0 0 0.0000000 > 0-1 0 0.0000000 > 10 > 0 1 0 0.0000000 > 1 0 0 0.0000000 > 0 0 1 0.0000000 > 11 > 0-1 0 0.0000000 > -1 0 0 0.0000000 > 0 0-1 0.0000000 > 12 > I checked the struct files of fcc structure, bcc stucture, > hexagonal > structure, xcrysden correctly identifies the symmetry and gives the > corresponding BZ for selection of k-points. > > Is there any thing wrong with the struct file or the xcrysden for rhombohderal > lattices with hexagoal lattice constants and rhombohderal positons? I > noticed > that the lattice > constants are hexagonal (as the user manual says) but the angles are > not!! > it should be 90 90 120 instead of 90 90 90 in the bi.struct. > > Sahu > P.Blaha -------------------------------------------------------------------------- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha@theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/ -------------------------------------------------------------------------- From xcrysden@democritos.it Sat Jul 15 22:38:48 2006 From: xcrysden@democritos.it (Wesley J Fabella) Date: Sat, 15 Jul 2006 17:38:48 -0400 Subject: [xcrysden] CHGCAR.xsf Message-ID: <200607151738.48655.wfabella@shell.cas.usf.edu> Hello Users, I have a technical question as to how CHGCAR.xsf is read by xcrysden? Specifically, I want to plot a specified plane within my unit cell ... not only xy, xz, and yz. How would I go about plotting say 111 direction of my crystal given CHGCAR.xsf file? Is this possible, has anyone written a script to do this? I know that WIEN2k code has this functionality within charge density plotting tool. I imagine CHGCAR.xsf has the info to plot charge density of a specified crystal plane? Thankx W -- "The way is not difficult; only there must be no wanting or not wanting." -Chao-Chou <++++++++++++++++++++++++++++++> Wesley J. Fabella Department of Physics University of South Florida 4202 East Fowler Avenue Tampa, Florida 33620 http://shell.cas.usf.edu/~wfabella <------------------------------> From xcrysden@democritos.it Wed Jul 26 21:25:54 2006 From: xcrysden@democritos.it (Oscar U. Ojeda) Date: Wed, 26 Jul 2006 15:25:54 -0500 Subject: [xcrysden] Help! Message-ID: <1153945554.924b485cOscar.Ojeda@chemail.tamu.edu> Hi Im trying to set up XCRYSDEN to be able to create movies. Im using CYGWIN, and the lines: The lines set xcMisc(mpeg_encode) /cygwin/usr/softwares/mpeg_encode/mpeg_encode are properly set up in the customs_definitions file Even when I load the animated.asxf example, I cannot press the ANIMATED GIF= /MPEG>> button. What can I do? Oscar Ojeda Dr. Cagin's group Texas A&M University (979)845-1432 532 JACK E BROWN BUILDING COLLEGE STATION, TX 77843-3122 MS-3122 From xcrysden@democritos.it Thu Jul 27 14:43:40 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:43:40 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? In-Reply-To: <44AB9A52.7000300@sissa.it> References: <44AB9A52.7000300@sissa.it> Message-ID: <1154007820.5911.16.camel@localhost.localdomain> On Wed, 2006-07-05 at 12:54 +0200, Gabriele Sclauzero wrote: > I tried to run the 1.4.1 version with > > xcrysden --pw_in > > but the option --pw_in is not recognized. Indeed, because the correct spelling is --pw_inp. There was a typo in the "xcrysden --help" message. Thanks for spotting this. > Running > > xcrysden --pwi > > accepts this option but the input file for pwi2xsf then generated has a > mistake, I suppose: > > &system > ibrav = 6 > celldm(1) = 18 > celldm(3) = 4.17629475 > nat= 19 > CALCULATION= "SCF" > > ATOMIC_POSITIONS ANGSTROM > C 1.81396 0.0 0.0 > ..... > because the namelist is not ended before the > ATOMIC_POSITIONS card starts. I cannot reproduce your error. Can you send me your PW.X input file. Regards, Tone From xcrysden@democritos.it Thu Jul 27 14:49:37 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:49:37 +0200 Subject: [xcrysden] xcrysden installation error on line 156 In-Reply-To: References: Message-ID: <1154008177.5911.23.camel@localhost.localdomain> On Mon, 2006-07-10 at 21:50 +0100, Pedro M. F. J. Costa wrote: > > However, when I try to run XCrysDen from the TOPDIR, I get the following > error message: > > ./xcrysden: line 156: exec: wish: not found This is because your cygwin does not have Tcl/Tk installed. It is required by xcrysden. Here is a list of packagaes that are needed by xcrysden (most likely I miss to name a few): bash, bc, gawk, grep, gzip, less, more, opengl, tcltk, coreutils Best regards, Tone From xcrysden@democritos.it Thu Jul 27 14:53:16 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:53:16 +0200 Subject: [xcrysden] Problem when plot 2D grid with color black_brown_white In-Reply-To: <44B75ED1.8030802@sissa.it> References: <44B75ED1.8030802@sissa.it> Message-ID: <1154008397.5911.27.camel@localhost.localdomain> On Fri, 2006-07-14 at 11:07 +0200, Xunlei Ding wrote: > Dear All, > > I have a problem. When I plot a 2D grid in a xsf file using xcrysden, > with black_brown_white color basis, it gives an error as below. > When ploting 3D data , or using other color basis, there is no problem. > What's wrong I may make? Thank you! > > wanted integer, but got "COLORBASE_MONO" while executing xc_iso isoplane > 0 COLORBASE_MONO 0 You spotted a bug, which is as you indicated, specific to 2D data-grid. (I rarely use the 2D data-grid.) Thanks, Tone From xcrysden@democritos.it Thu Jul 27 14:56:07 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:56:07 +0200 Subject: [xcrysden] CHGCAR.xsf In-Reply-To: <200607151738.48655.wfabella@shell.cas.usf.edu> References: <200607151738.48655.wfabella@shell.cas.usf.edu> Message-ID: <1154008567.5911.30.camel@localhost.localdomain> On Sat, 2006-07-15 at 17:38 -0400, Wesley J Fabella wrote: > Hello Users, > > I have a technical question as to how CHGCAR.xsf is read by xcrysden? > Specifically, I want to plot a specified plane within my unit cell ... not > only xy, xz, and yz. And this is all you can do with the 3D grid. If you want a specific 2D plane, calculate the charge on that specific plane, and then you can visualize it. (I know it's cumbersome to do a separate calculation for each arbitrary plane. ) Regards, Tone From xcrysden@democritos.it Thu Jul 27 15:00:44 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 16:00:44 +0200 Subject: [xcrysden] Help! In-Reply-To: <1153945554.924b485cOscar.Ojeda@chemail.tamu.edu> References: <1153945554.924b485cOscar.Ojeda@chemail.tamu.edu> Message-ID: <1154008844.5911.34.camel@localhost.localdomain> On Wed, 2006-07-26 at 15:25 -0500, Oscar U. Ojeda wrote: > Hi > Im trying to set up XCRYSDEN to be able to create movies. > Im using CYGWIN, and the lines: > The lines > > set xcMisc(mpeg_encode) /cygwin/usr/softwares/mpeg_encode/mpeg_encode > are properly set up in the customs_definitions file > Even when I load the animated.asxf example, I cannot press the ANIMATED GIF/MPEG>> button. This is due to some inconsistency in xcrysden routine: it checks just for the whirlgif program, and if it is defined, then the button is enabled. The work-around is to define in $HOME/.xcrysden/custom-definitions file a fake whirlgif, e.g.: set xcMisc(whirlgif) just_to_define_it Now this will enable the button, and you will be able to make a MPEG movies. Regards, Tone From xcrysden@democritos.it Fri Jul 28 09:26:11 2006 From: xcrysden@democritos.it (Gabriele Sclauzero) Date: Fri, 28 Jul 2006 10:26:11 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? In-Reply-To: <1154007820.5911.16.camel@localhost.localdomain> References: <44AB9A52.7000300@sissa.it> <1154007820.5911.16.camel@localhost.localdomain> Message-ID: <44C9CA23.7090106@sissa.it> Tone Kokalj wrote: >>Running >> >>xcrysden --pwi >> >>accepts this option but the input file for pwi2xsf then generated has a >>mistake, I suppose: >> >> &system >> ibrav = 6 >> celldm(1) = 18 >> celldm(3) = 4.17629475 >> nat= 19 >> CALCULATION= "SCF" >> >>ATOMIC_POSITIONS ANGSTROM >>C 1.81396 0.0 0.0 >>..... > > >>because the namelist is not ended before the >>ATOMIC_POSITIONS card starts. > > > I cannot reproduce your error. Can you send me your PW.X input file. yes sure, here it is: ----- &control calculation= "scf", restart_mode= "from_scratch", tprnfor= .TRUE., pseudo_dir= "/u/cm/sclauzer/Pseudo_/", outdir= "/local_scratch/sclauzer/tmp/", prefix= "COatPtwire17Pt_1rel" / &system ibrav = 6, celldm(1) = 18, celldm(3) = 4.17629475, nat= 19, ntyp= 3, ecutwfc= 32, ecutrho= 300, noncolin= .TRUE., lspinorb= .TRUE., occupations= "smearing", smearing= "m-p", degauss= 0.01 / &electrons conv_thr= 1.0e-8, mixing_beta= 0.4 / ATOMIC_SPECIES Pt 195.078 Pt.rel-pz-n-rrkjus.UPF C 12.0107 Crel.13.16.RRKJ3.UPF O 15.9994 Orel.14.16.RRKJ3.UPF ATOMIC_POSITIONS ANGSTROM C 1.816 0.0 18.72 O 2.95955194 0.0 18.72 Pt 0.0 0.0 0 Pt 0.0 0.0 2.34 Pt 0.0 0.0 4.68 Pt 0.0 0.0 7.02 Pt 0.0 0.0 9.36 Pt 0.0 0.0 11.70 Pt 0.0 0.0 14.04 Pt 0.0 0.0 16.38 Pt 0.0 0.0 18.72 Pt 0.0 0.0 21.06 Pt 0.0 0.0 23.40 Pt 0.0 0.0 25.74 Pt 0.0 0.0 28.08 Pt 0.0 0.0 30.42 Pt 0.0 0.0 32.76 Pt 0.0 0.0 35.10 Pt 0.0 0.0 37.44 K_POINTS AUTOMATIC 1 1 13 0 0 1 ---- The bash output I get is: TEXT-WIDGET: .a1.f1.t Executing: sh /scratch/Sclauzero/XCrySDen-1.4.1s/scripts/pwi2xsf.sh /scratch/Sclauzero/Calc_montoz/COatPtwire-top_mon/Scf/FR-LDA/COatPtwire_1.scf.d TEXT-WIDGET: .a0.f1.t Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 while the error message box says forrtl: severe (18): too many values for NAMELIST variable, unit 5, file stdin, ... Gabriele > > > Regards, Tone > > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > From xcrysden@democritos.it Fri Jul 28 14:41:37 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Fri, 28 Jul 2006 15:41:37 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? In-Reply-To: <44C9CA23.7090106@sissa.it> References: <44AB9A52.7000300@sissa.it> <1154007820.5911.16.camel@localhost.localdomain> <44C9CA23.7090106@sissa.it> Message-ID: <1154094097.15282.2.camel@localhost.localdomain> --=-uDq9S/6fRwgmb3hLKHlu Content-Type: text/plain Content-Transfer-Encoding: 7bit On Fri, 2006-07-28 at 10:26 +0200, Gabriele Sclauzero wrote: > > > > I cannot reproduce your error. Can you send me your PW.X input file. > > yes sure, here it is: Thanks! I've reproduced your problem, and fixed pwi2xsf.sh (attached; put it into $XCRYSDEN_TOPDIR/scripts/). Regards, Tone --=-uDq9S/6fRwgmb3hLKHlu Content-Disposition: attachment; filename=pwi2xsf.sh Content-Type: application/x-shellscript; name=pwi2xsf.sh Content-Transfer-Encoding: 7bit #!/bin/sh ############################################################################# # Author: # # ------ # # Anton Kokalj Email: Tone.Kokalj@ijs.si # # Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 # # Jozef Stefan Institute Fax: x 386 1 477 3811 # # Jamova 39, SI-1000 Ljubljana # # SLOVENIA # # # # Source: $XCRYSDEN_TOPDIR/scripts/pwi2xsf.sh # ------ # # Copyright (c) 1996-2003 by Anton Kokalj # ############################################################################# # set locales to C LANG=C LC_ALL=C export LANG LC_ALL # # pwi2xsf.sh: PW-input to XSF converison # # Usage: pwi2xsf [-r] pw-input-file # # Written by Tone Kokalj on Tue May 8 20:43:44 2001 # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if [ "$#" -lt 1 ]; then echo " Usage: pwi2xsf.sh [-r] pw-input Option for PWscf version < 1.2: -r ... one must spefify i.e. ityp->nat conversion, and the corresponding data are writen to file nuclei.charges. The -r flag deletes this file. " exit 1 fi r=0 if [ "$1" = "-r" ]; then r=1 shift fi ####################################### if test -f $XCRYSDEN_TOPDIR/scripts/pwLib_old.sh ; then . $XCRYSDEN_TOPDIR/scripts/pwLib_old.sh else . pwLib_old.sh fi ####################################### # # check if we have OLD or NEW PW.X input format # new_format1=`grep 'ATOMIC_POSITIONS' $1` new_format2=`grep -i '&system' $1` if [ "$new_format1" != "" -a "$new_format2" != "" ]; then # we have NEW PW.X input format # cat $1 | awk 'BEGIN {RS=",";} {print $0}' | awk ' BEGIN { calculation=""; num_of_images=""; nml_end=0; nml_end_string=""; } toupper($0) ~ /&SYSTEM/ { print; } /=/ { if ( toupper($1) ~ /^IBRAV($|=)|^CELLDM\([1-6]\)($|=)|^NAT($|=)|^A($|=)|^B($|=)|^C($|=)|^COSAB($|=)|^COSAC($|=)|^COSBC($|=)/ ) { print; } if ( toupper($1) ~ /^CALCULATION($|=)/ ) { calculation=toupper($0); } if ( toupper($1) ~ /^NUM_OF_IMAGES($|=)/ ) { num_of_images=toupper($0); } } /ATOMIC_POSITIONS|CELL_PARAMETERS/ { if ( !nml_end) { # first finish the namelist nml_end=1; if (calculation != "") print calculation; if (num_of_images != "") print num_of_images; print nml_end_string; } # now print the current record print_line=1; print toupper($0); next; } toupper($0) ~ /&END|^\/|^ +\// { nml_end_string=$0; } /a*/ { if ( print_line == 1 ) { print toupper($0); } }'> pw.$$ PWI2XSF=pwi2xsf else # we have OLD PW.X input format pwNucleiCharges $1 /dev/null cat $1 | awk 'BEGIN {RS=",";} {print}' | awk ' BEGIN { end=0; } toupper($0) ~ /&INPUT|CELLDM|NAT|LTAUCRY/ { print; } toupper($0) ~ /IBRAV/ { print; split($0,a,"="); split(a[1],b,","); ibrav = b[1]; } toupper($0) ~ /&END|^\/|^ \// { end=1; } /a*/ { if ( end == 1 ) print; }' > pw.$$ PWI2XSF=pwi2xsf_old fi # # execute $PWI2XSF fortran program and print the XSF file # if test -f $XCRYSDEN_TOPDIR/bin/$PWI2XSF ; then $XCRYSDEN_TOPDIR/bin/$PWI2XSF < pw.$$ | tee pwi2xsf.xsf_out else $PWI2XSF < pw.$$ | tee pwi2xsf.xsf_out fi rm -f pw.$$ if [ "$r" -eq 1 ]; then if [ -f nuclei.charges ]; then rm nuclei.charges; fi fi exit 0 --=-uDq9S/6fRwgmb3hLKHlu-- From xcrysden@democritos.it Sat Jul 1 01:48:50 2006 From: xcrysden@democritos.it (Zhufeng Hou) Date: Fri, 30 Jun 2006 17:48:50 -0700 (PDT) Subject: [xcrysden] Re: XCrySDen digest, Vol 1 #100 - 2 msgs In-Reply-To: <20060615054610.27837.99637.Mailman@democritos.sissa.it> Message-ID: <20060701004850.46779.qmail@web54505.mail.yahoo.com> Please see this website: http://www.cryst.ehu.es/cryst/get_kvec.html (The k-vector types and Brillouin zones of the space groups) I think it will be useful to you. --- xcrysden-request@democritos.it wrote: > Send XCrySDen mailing list submissions to > xcrysden@democritos.it > > To subscribe or unsubscribe via the World Wide Web, > visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body > 'help' to > xcrysden-request@democritos.it > > You can reach the person managing the list at > xcrysden-admin@democritos.it > > When replying, please edit your Subject line so it > is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. On k-space path selection (Marcos Verissimo > Alves) > 2. Re: On k-space path selection (Tone Kokalj) > > --__--__-- > > Message: 1 > Date: Wed, 14 Jun 2006 15:06:17 +0200 (CEST) > From: "Marcos Verissimo Alves" > To: xcrysden@democritos.it > Subject: [xcrysden] On k-space path selection > Reply-To: xcrysden@democritos.it > > Hi all, > > I am a newbie to XCrysDen, and I have a few basic > questions about the > k-point path selection feature on XCrysDen. I have > an XSF file I generated > from the output of an ab initio program unsupported > by XCrysDen. To my > delight I found that the program gives me the > Brillouin Zone (BZ) > automatically with high-symmetry points indicated. > The questions are: > > 1) Is this general, or does it come from a set of > pre-defined BZs? I mean, > if I enter any crystal structure and ask for the BZ, > how are the > high-symmetry points found? > > 2) This one is not really related to XCrysDen, but I > feel I might get some > help here. Given three reciprocal space vectors, is > there a way to use the > Bilbao Crystallographic Server to tell me to which > space group my lattice > belongs to? This way, I could get the labels for the > high-symmetry points > of the BZ. > > Thanks, > > Marcos > > -- > Dr. Marcos Verissimo Alves > Post-Doctoral Fellow > Condensed Matter and Statistical Physics Sector > International Centre for Theoretical Physics > Trieste, Italy > > -------- > > I have become so addicted to vi that I try to exit > OpenOffice by typing :wq! > > > --__--__-- > > Message: 2 > Date: Wed, 14 Jun 2006 18:17:32 +0200 (CEST) > Subject: Re: [xcrysden] On k-space path selection > From: "Tone Kokalj" > To: xcrysden@democritos.it > Reply-To: xcrysden@democritos.it > > > I am a newbie to XCrysDen, and I have a few basic > questions about the > > k-point path selection feature on XCrysDen. I have > an XSF file I enerated > > from the output of an ab initio program > unsupported by XCrysDen. To my > > delight I found that the program gives me the > Brillouin Zone (BZ) > > automatically with high-symmetry points indicated. > The questions are: > > > > 1) Is this general, or does it come from a set of > pre-defined BZs? I mean, > > if I enter any crystal structure and ask for the > BZ, how are the > > high-symmetry points found? > > The labeling of the k-points is supported by a few > Bravais lattice > types, and is based on a lookup table of Peter > Blaha: see last part > of the file $XCRYSDEN_TOPDIR/Tcl/kLabels.tcl > > In order for this labelling to work, there should be > info about the > Bravais lattice type in the XSF file. This is > achieved by replacing the > "CRYSTAL" keyword by: > > DIM-GROUP > 3 igroup > > where "3" specifies 3 dimensional periodicity, and > igroup the > lattice type, in particular: > > 1 ... primitive > 2 ... A centered > 3 ... B centered > 4 ... C centered > 5 ... face-centered (i.e. fcc) > 6 ... body-cetered (i.e. bcc) > 7 ... rhombohedral > 8 ... hexagonal > 9 ... trigonal > > > > > 2) This one is not really related to XCrysDen, but > I feel I might get some > > help here. Given three reciprocal space vectors, > is there a way to use the > > Bilbao Crystallographic Server to tell me to which > space group my lattice > > belongs to? This way, I could get the labels for > the high-symmetry points > > of the BZ. > > I don't know. > > Regard, Tone > > > > --__--__-- > > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest > ************************************************* Zhu-feng Hou P.O.Box1169# Physics Department of Xiamen University Xiamen,361005 P.R.China Tel:+86-592-2194744 ************************************************** __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From xcrysden@democritos.it Wed Jul 5 11:54:10 2006 From: xcrysden@democritos.it (Gabriele Sclauzero) Date: Wed, 05 Jul 2006 12:54:10 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? Message-ID: <44AB9A52.7000300@sissa.it> I tried to run the 1.4.1 version with xcrysden --pw_in but the option --pw_in is not recognized. Running xcrysden --pwi accepts this option but the input file for pwi2xsf then generated has a mistake, I suppose: &system ibrav = 6 celldm(1) = 18 celldm(3) = 4.17629475 nat= 19 CALCULATION= "SCF" ATOMIC_POSITIONS ANGSTROM C 1.81396 0.0 0.0 O 2.94454710 0.0 0.0 PT 0.0 0.0 -18.72 PT 0.0 0.0 -16.38 PT 0.0 0.0 -14.04 PT 0.0 0.0 -11.70 PT 0.0 0.0 -9.36 PT 0.0 0.0 -7.02 PT 0.0 0.0 -4.68 PT 0.0 0.0 -2.34 PT 0.0 0.0 0 PT 0.0 0.0 2.34 PT 0.0 0.0 4.68 PT 0.0 0.0 7.02 PT 0.0 0.0 9.36 PT 0.0 0.0 11.70 PT 0.0 0.0 14.04 PT 0.0 0.0 16.38 PT 0.0 0.0 18.72 because the namelist is not ended before the ATOMIC_POSITIONS card starts. Adding a / after the namelist seems to work. Can someone confirm this? Gabriele From xcrysden@democritos.it Mon Jul 10 21:50:21 2006 From: xcrysden@democritos.it (Pedro M. F. J. Costa) Date: 10 Jul 2006 21:50:21 +0100 Subject: [xcrysden] xcrysden installation error on line 156 Message-ID: Dear users list, I am on the process of installing XCrysDen.=20 I have successfully installed CYGWIN on my Windows system. Additionally, my= =20 XCrysDen top directory installation has been successful as the following=20 has been added to my .bashrc:=20 #------------------------------------------------------------------------ #= =20 this is for XCRYSDEN 1.4.1; added by XCRYSDEN installation on # Mon Jul 10= =20 19:09:40 GMTDT 2006=20 #------------------------------------------------------------------------= =20 XCRYSDEN_TOPDIR=3D/home/Pedro XCRYSDEN_SCRATCH=3D/home/Pedro/xcrys_tmp expo= rt=20 XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH=20 PATH=3D"$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/ut= il" However, when I try to run XCrysDen from the TOPDIR, I get the following=20 error message: ./xcrysden: line 156: exec: wish: not found Verifying the xcrysden program lines, I have: if test $valgrind -eq 0 ; then if test $debug -eq 0 ; then =09if test -f ${XCRYSDEN_TOPDIR}/bin/xcrys.dll ; then =09# CYGWIN: xcrys.dll will be loaded from xcInit.tcl !!! =09 exec wish ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- \ =09=09$XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null & =09 wait $! =09else =09 ${XCRYSDEN_TOPDIR}/bin/xcrys \ =09=09${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- \ =09=09$XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null & =09 wait $! =09fi [continues] So the program calls for an executable that involves the file xcInit.tcl.= =20 Now, from other posts I noticed that my error message could be a case of=20 missing of Tcl package. I have verified my TOPDIR directory and I found=20 that I have the Tcl directory installed and that furthermore there is a=20 file inside with the name xcInit.tcl. Strangely enough the file xcrys.dll= =20 is also in its right place (TOPDIR/bin/) but that does not seem to make any= =20 difference to the proper execution of the program. So, as far as I understand, I have the CYGWIN and XCrysDen installed in=20 their proper directories but there is still something missing. Is it a=20 matter of extra packages needed? If it is how can I get a list of those=20 required? Could anyone please help me with this error?=20 My best regards, Pedro --=20 ************************************************************************** Pedro Miguel F. J. Costa Department of Materials Science and Metallurgy New Museums Site, Pembroke Street Cambridge, CB2 3QZ, United Kingdom Tel.(office): +44 (0)1223 334474 Fax: +44 (0)1223 334437 ************************************************************************** From xcrysden@democritos.it Thu Jul 13 17:56:57 2006 From: xcrysden@democritos.it (xcrysden@democritos.it) Date: Thu, 13 Jul 2006 11:56:57 -0500 Subject: [xcrysden] rhombohedral bi and xcrysden Message-ID: <20060713115657.ru88m78t3dww0osw@mail.ph.utexas.edu> Hi, I used the bi.struct file, provided with wien2k source in example_struct_files directory, in xcrysden(loaded on linux machine) to generate k-list file for band structure calculation. It gives the error: The guessed Bravais lattice type: not-supported ((the XSF's group number is = 7) The struct file used was: _________________ Bismut R LATTICE,NONEQUIV. ATOMS 1 MODE OF CALC=3DRELA 8.590000 8.590000 22.415000 90.000000 90.000000 90.000000 ATOM -1: X=3D0.23400000 Y=3D0.23400000 Z=3D0.23400000 MULT=3D 2 ISPLIT=3D 4 ATOM -1: X=3D0.76600000 Y=3D0.76600000 Z=3D0.76600000 Bi NPT=3D 781 R0=3D0.00001000 RMT=3D 2.8000 Z: 83.0 1.000000000.000000000.00000000 0.000000001.000000000.00000000 0.000000000.000000001.00000000 12 SYMMETRY OPERATIONS: 1 0 0 0.0000000 0 1 0 0.0000000 0 0 1 0.0000000 1 -1 0 0 0.0000000 0-1 0 0.0000000 0 0-1 0.0000000 2 0 0 1 0.0000000 1 0 0 0.0000000 0 1 0 0.0000000 3 0 0-1 0.0000000 0-1 0 0.0000000 -1 0 0 0.0000000 4 -1 0 0 0.0000000 0 0-1 0.0000000 0-1 0 0.0000000 5 0 1 0 0.0000000 0 0 1 0.0000000 1 0 0 0.0000000 6 0-1 0 0.0000000 0 0-1 0.0000000 -1 0 0 0.0000000 7 1 0 0 0.0000000 0 0 1 0.0000000 0 1 0 0.0000000 8 0 0 1 0.0000000 0 1 0 0.0000000 1 0 0 0.0000000 9 0 0-1 0.0000000 -1 0 0 0.0000000 0-1 0 0.0000000 10 0 1 0 0.0000000 1 0 0 0.0000000 0 0 1 0.0000000 11 0-1 0 0.0000000 -1 0 0 0.0000000 0 0-1 0.0000000 12 I checked the struct files of fcc structure, bcc stucture, hexagonal structure, xcrysden correctly identifies the symmetry and gives the corresponding BZ for selection of k-points. Is there any thing wrong with the struct file or the xcrysden for =20 rhombohderal lattices with hexagoal lattice constants and rhombohderal =20 positons? I noticed that the lattice constants are hexagonal (as the user manual says) but the angles are not!! it should be 90 90 120 instead of 90 90 90 in the bi.struct. Sahu From xcrysden@democritos.it Fri Jul 14 10:07:29 2006 From: xcrysden@democritos.it (Xunlei Ding) Date: Fri, 14 Jul 2006 11:07:29 +0200 Subject: [xcrysden] Problem when plot 2D grid with color black_brown_white Message-ID: <44B75ED1.8030802@sissa.it> Dear All, I have a problem. When I plot a 2D grid in a xsf file using xcrysden, with black_brown_white color basis, it gives an error as below. When ploting 3D data , or using other color basis, there is no problem. What's wrong I may make? Thank you! wanted integer, but got "COLORBASE_MONO" while executing xc_iso isoplane 0 COLORBASE_MONO 0 while executing "xc_iso isoplane 0 $basis $func $what " invoked from within "if $upd { if { $isoControl(colorplane) && !$isoControl(isoline) } { set what "colorplane" } elseif { !$isoControl(colorplane) && $isoControl(is..." (procedure "UpdatePropertyPlane" line 52) invoked from within "UpdatePropertyPlane" invoked from within ".iso2D.f3.sub invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .iso2D.f3.sub" (command bound to event) Yours sincerely, Ding From xcrysden@democritos.it Fri Jul 14 14:43:09 2006 From: xcrysden@democritos.it (Peter Blaha) Date: Fri, 14 Jul 2006 15:43:09 +0200 (CEST) Subject: [xcrysden] Re: rhombohedral bi and xcrysden In-Reply-To: <20060713115657.ru88m78t3dww0osw@mail.ph.utexas.edu> References: <20060713115657.ru88m78t3dww0osw@mail.ph.utexas.edu> Message-ID: If you read the message carefully, it says, that the k-point labelling (i.e. the naming with Gamma,X,Z,...) is implemented only for a few spacegroups, and the R-lattice is not included. Thus no big deal. The k-mesh is ok, but eventually you have to give names to the k-points yourself. > I used the bi.struct file, provided with wien2k source in > example_struct_files directory, in xcrysden(loaded on linux machine) to > generate > k-list file for band structure calculation. It gives the error: > > The guessed Bravais lattice type: not-supported ((the XSF's group number is 7) > > The struct file used was: > _________________ > Bismut > R LATTICE,NONEQUIV. ATOMS 1 > MODE OF CALC=RELA > 8.590000 8.590000 22.415000 90.000000 90.000000 90.000000 > ATOM -1: X=0.23400000 Y=0.23400000 Z=0.23400000 > MULT= 2 ISPLIT= 4 > ATOM -1: X=0.76600000 Y=0.76600000 Z=0.76600000 > Bi NPT= 781 R0=0.00001000 RMT= 2.8000 Z: 83.0 > 1.000000000.000000000.00000000 > 0.000000001.000000000.00000000 > 0.000000000.000000001.00000000 > 12 SYMMETRY OPERATIONS: > 1 0 0 0.0000000 > 0 1 0 0.0000000 > 0 0 1 0.0000000 > 1 > -1 0 0 0.0000000 > 0-1 0 0.0000000 > 0 0-1 0.0000000 > 2 > 0 0 1 0.0000000 > 1 0 0 0.0000000 > 0 1 0 0.0000000 > 3 > 0 0-1 0.0000000 > 0-1 0 0.0000000 > -1 0 0 0.0000000 > 4 > -1 0 0 0.0000000 > 0 0-1 0.0000000 > 0-1 0 0.0000000 > 5 > 0 1 0 0.0000000 > 0 0 1 0.0000000 > 1 0 0 0.0000000 > 6 > 0-1 0 0.0000000 > 0 0-1 0.0000000 > -1 0 0 0.0000000 > 7 > 1 0 0 0.0000000 > 0 0 1 0.0000000 > 0 1 0 0.0000000 > 8 > 0 0 1 0.0000000 > 0 1 0 0.0000000 > 1 0 0 0.0000000 > 9 > 0 0-1 0.0000000 > -1 0 0 0.0000000 > 0-1 0 0.0000000 > 10 > 0 1 0 0.0000000 > 1 0 0 0.0000000 > 0 0 1 0.0000000 > 11 > 0-1 0 0.0000000 > -1 0 0 0.0000000 > 0 0-1 0.0000000 > 12 > I checked the struct files of fcc structure, bcc stucture, > hexagonal > structure, xcrysden correctly identifies the symmetry and gives the > corresponding BZ for selection of k-points. > > Is there any thing wrong with the struct file or the xcrysden for rhombohderal > lattices with hexagoal lattice constants and rhombohderal positons? I > noticed > that the lattice > constants are hexagonal (as the user manual says) but the angles are > not!! > it should be 90 90 120 instead of 90 90 90 in the bi.struct. > > Sahu > P.Blaha -------------------------------------------------------------------------- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha@theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/ -------------------------------------------------------------------------- From xcrysden@democritos.it Sat Jul 15 22:38:48 2006 From: xcrysden@democritos.it (Wesley J Fabella) Date: Sat, 15 Jul 2006 17:38:48 -0400 Subject: [xcrysden] CHGCAR.xsf Message-ID: <200607151738.48655.wfabella@shell.cas.usf.edu> Hello Users, I have a technical question as to how CHGCAR.xsf is read by xcrysden? Specifically, I want to plot a specified plane within my unit cell ... not only xy, xz, and yz. How would I go about plotting say 111 direction of my crystal given CHGCAR.xsf file? Is this possible, has anyone written a script to do this? I know that WIEN2k code has this functionality within charge density plotting tool. I imagine CHGCAR.xsf has the info to plot charge density of a specified crystal plane? Thankx W -- "The way is not difficult; only there must be no wanting or not wanting." -Chao-Chou <++++++++++++++++++++++++++++++> Wesley J. Fabella Department of Physics University of South Florida 4202 East Fowler Avenue Tampa, Florida 33620 http://shell.cas.usf.edu/~wfabella <------------------------------> From xcrysden@democritos.it Wed Jul 26 21:25:54 2006 From: xcrysden@democritos.it (Oscar U. Ojeda) Date: Wed, 26 Jul 2006 15:25:54 -0500 Subject: [xcrysden] Help! Message-ID: <1153945554.924b485cOscar.Ojeda@chemail.tamu.edu> Hi Im trying to set up XCRYSDEN to be able to create movies. Im using CYGWIN, and the lines: The lines set xcMisc(mpeg_encode) /cygwin/usr/softwares/mpeg_encode/mpeg_encode are properly set up in the customs_definitions file Even when I load the animated.asxf example, I cannot press the ANIMATED GIF= /MPEG>> button. What can I do? Oscar Ojeda Dr. Cagin's group Texas A&M University (979)845-1432 532 JACK E BROWN BUILDING COLLEGE STATION, TX 77843-3122 MS-3122 From xcrysden@democritos.it Thu Jul 27 14:43:40 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:43:40 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? In-Reply-To: <44AB9A52.7000300@sissa.it> References: <44AB9A52.7000300@sissa.it> Message-ID: <1154007820.5911.16.camel@localhost.localdomain> On Wed, 2006-07-05 at 12:54 +0200, Gabriele Sclauzero wrote: > I tried to run the 1.4.1 version with > > xcrysden --pw_in > > but the option --pw_in is not recognized. Indeed, because the correct spelling is --pw_inp. There was a typo in the "xcrysden --help" message. Thanks for spotting this. > Running > > xcrysden --pwi > > accepts this option but the input file for pwi2xsf then generated has a > mistake, I suppose: > > &system > ibrav = 6 > celldm(1) = 18 > celldm(3) = 4.17629475 > nat= 19 > CALCULATION= "SCF" > > ATOMIC_POSITIONS ANGSTROM > C 1.81396 0.0 0.0 > ..... > because the namelist is not ended before the > ATOMIC_POSITIONS card starts. I cannot reproduce your error. Can you send me your PW.X input file. Regards, Tone From xcrysden@democritos.it Thu Jul 27 14:49:37 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:49:37 +0200 Subject: [xcrysden] xcrysden installation error on line 156 In-Reply-To: References: Message-ID: <1154008177.5911.23.camel@localhost.localdomain> On Mon, 2006-07-10 at 21:50 +0100, Pedro M. F. J. Costa wrote: > > However, when I try to run XCrysDen from the TOPDIR, I get the following > error message: > > ./xcrysden: line 156: exec: wish: not found This is because your cygwin does not have Tcl/Tk installed. It is required by xcrysden. Here is a list of packagaes that are needed by xcrysden (most likely I miss to name a few): bash, bc, gawk, grep, gzip, less, more, opengl, tcltk, coreutils Best regards, Tone From xcrysden@democritos.it Thu Jul 27 14:53:16 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:53:16 +0200 Subject: [xcrysden] Problem when plot 2D grid with color black_brown_white In-Reply-To: <44B75ED1.8030802@sissa.it> References: <44B75ED1.8030802@sissa.it> Message-ID: <1154008397.5911.27.camel@localhost.localdomain> On Fri, 2006-07-14 at 11:07 +0200, Xunlei Ding wrote: > Dear All, > > I have a problem. When I plot a 2D grid in a xsf file using xcrysden, > with black_brown_white color basis, it gives an error as below. > When ploting 3D data , or using other color basis, there is no problem. > What's wrong I may make? Thank you! > > wanted integer, but got "COLORBASE_MONO" while executing xc_iso isoplane > 0 COLORBASE_MONO 0 You spotted a bug, which is as you indicated, specific to 2D data-grid. (I rarely use the 2D data-grid.) Thanks, Tone From xcrysden@democritos.it Thu Jul 27 14:56:07 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 15:56:07 +0200 Subject: [xcrysden] CHGCAR.xsf In-Reply-To: <200607151738.48655.wfabella@shell.cas.usf.edu> References: <200607151738.48655.wfabella@shell.cas.usf.edu> Message-ID: <1154008567.5911.30.camel@localhost.localdomain> On Sat, 2006-07-15 at 17:38 -0400, Wesley J Fabella wrote: > Hello Users, > > I have a technical question as to how CHGCAR.xsf is read by xcrysden? > Specifically, I want to plot a specified plane within my unit cell ... not > only xy, xz, and yz. And this is all you can do with the 3D grid. If you want a specific 2D plane, calculate the charge on that specific plane, and then you can visualize it. (I know it's cumbersome to do a separate calculation for each arbitrary plane. ) Regards, Tone From xcrysden@democritos.it Thu Jul 27 15:00:44 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 27 Jul 2006 16:00:44 +0200 Subject: [xcrysden] Help! In-Reply-To: <1153945554.924b485cOscar.Ojeda@chemail.tamu.edu> References: <1153945554.924b485cOscar.Ojeda@chemail.tamu.edu> Message-ID: <1154008844.5911.34.camel@localhost.localdomain> On Wed, 2006-07-26 at 15:25 -0500, Oscar U. Ojeda wrote: > Hi > Im trying to set up XCRYSDEN to be able to create movies. > Im using CYGWIN, and the lines: > The lines > > set xcMisc(mpeg_encode) /cygwin/usr/softwares/mpeg_encode/mpeg_encode > are properly set up in the customs_definitions file > Even when I load the animated.asxf example, I cannot press the ANIMATED GIF/MPEG>> button. This is due to some inconsistency in xcrysden routine: it checks just for the whirlgif program, and if it is defined, then the button is enabled. The work-around is to define in $HOME/.xcrysden/custom-definitions file a fake whirlgif, e.g.: set xcMisc(whirlgif) just_to_define_it Now this will enable the button, and you will be able to make a MPEG movies. Regards, Tone From xcrysden@democritos.it Fri Jul 28 09:26:11 2006 From: xcrysden@democritos.it (Gabriele Sclauzero) Date: Fri, 28 Jul 2006 10:26:11 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? In-Reply-To: <1154007820.5911.16.camel@localhost.localdomain> References: <44AB9A52.7000300@sissa.it> <1154007820.5911.16.camel@localhost.localdomain> Message-ID: <44C9CA23.7090106@sissa.it> Tone Kokalj wrote: >>Running >> >>xcrysden --pwi >> >>accepts this option but the input file for pwi2xsf then generated has a >>mistake, I suppose: >> >> &system >> ibrav = 6 >> celldm(1) = 18 >> celldm(3) = 4.17629475 >> nat= 19 >> CALCULATION= "SCF" >> >>ATOMIC_POSITIONS ANGSTROM >>C 1.81396 0.0 0.0 >>..... > > >>because the namelist is not ended before the >>ATOMIC_POSITIONS card starts. > > > I cannot reproduce your error. Can you send me your PW.X input file. yes sure, here it is: ----- &control calculation= "scf", restart_mode= "from_scratch", tprnfor= .TRUE., pseudo_dir= "/u/cm/sclauzer/Pseudo_/", outdir= "/local_scratch/sclauzer/tmp/", prefix= "COatPtwire17Pt_1rel" / &system ibrav = 6, celldm(1) = 18, celldm(3) = 4.17629475, nat= 19, ntyp= 3, ecutwfc= 32, ecutrho= 300, noncolin= .TRUE., lspinorb= .TRUE., occupations= "smearing", smearing= "m-p", degauss= 0.01 / &electrons conv_thr= 1.0e-8, mixing_beta= 0.4 / ATOMIC_SPECIES Pt 195.078 Pt.rel-pz-n-rrkjus.UPF C 12.0107 Crel.13.16.RRKJ3.UPF O 15.9994 Orel.14.16.RRKJ3.UPF ATOMIC_POSITIONS ANGSTROM C 1.816 0.0 18.72 O 2.95955194 0.0 18.72 Pt 0.0 0.0 0 Pt 0.0 0.0 2.34 Pt 0.0 0.0 4.68 Pt 0.0 0.0 7.02 Pt 0.0 0.0 9.36 Pt 0.0 0.0 11.70 Pt 0.0 0.0 14.04 Pt 0.0 0.0 16.38 Pt 0.0 0.0 18.72 Pt 0.0 0.0 21.06 Pt 0.0 0.0 23.40 Pt 0.0 0.0 25.74 Pt 0.0 0.0 28.08 Pt 0.0 0.0 30.42 Pt 0.0 0.0 32.76 Pt 0.0 0.0 35.10 Pt 0.0 0.0 37.44 K_POINTS AUTOMATIC 1 1 13 0 0 1 ---- The bash output I get is: TEXT-WIDGET: .a1.f1.t Executing: sh /scratch/Sclauzero/XCrySDen-1.4.1s/scripts/pwi2xsf.sh /scratch/Sclauzero/Calc_montoz/COatPtwire-top_mon/Scf/FR-LDA/COatPtwire_1.scf.d TEXT-WIDGET: .a0.f1.t Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 while the error message box says forrtl: severe (18): too many values for NAMELIST variable, unit 5, file stdin, ... Gabriele > > > Regards, Tone > > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > From xcrysden@democritos.it Fri Jul 28 14:41:37 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Fri, 28 Jul 2006 15:41:37 +0200 Subject: [xcrysden] Small bug in pwi2xsf.sh? In-Reply-To: <44C9CA23.7090106@sissa.it> References: <44AB9A52.7000300@sissa.it> <1154007820.5911.16.camel@localhost.localdomain> <44C9CA23.7090106@sissa.it> Message-ID: <1154094097.15282.2.camel@localhost.localdomain> --=-uDq9S/6fRwgmb3hLKHlu Content-Type: text/plain Content-Transfer-Encoding: 7bit On Fri, 2006-07-28 at 10:26 +0200, Gabriele Sclauzero wrote: > > > > I cannot reproduce your error. Can you send me your PW.X input file. > > yes sure, here it is: Thanks! I've reproduced your problem, and fixed pwi2xsf.sh (attached; put it into $XCRYSDEN_TOPDIR/scripts/). Regards, Tone --=-uDq9S/6fRwgmb3hLKHlu Content-Disposition: attachment; filename=pwi2xsf.sh Content-Type: application/x-shellscript; name=pwi2xsf.sh Content-Transfer-Encoding: 7bit #!/bin/sh ############################################################################# # Author: # # ------ # # Anton Kokalj Email: Tone.Kokalj@ijs.si # # Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 # # Jozef Stefan Institute Fax: x 386 1 477 3811 # # Jamova 39, SI-1000 Ljubljana # # SLOVENIA # # # # Source: $XCRYSDEN_TOPDIR/scripts/pwi2xsf.sh # ------ # # Copyright (c) 1996-2003 by Anton Kokalj # ############################################################################# # set locales to C LANG=C LC_ALL=C export LANG LC_ALL # # pwi2xsf.sh: PW-input to XSF converison # # Usage: pwi2xsf [-r] pw-input-file # # Written by Tone Kokalj on Tue May 8 20:43:44 2001 # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if [ "$#" -lt 1 ]; then echo " Usage: pwi2xsf.sh [-r] pw-input Option for PWscf version < 1.2: -r ... one must spefify i.e. ityp->nat conversion, and the corresponding data are writen to file nuclei.charges. The -r flag deletes this file. " exit 1 fi r=0 if [ "$1" = "-r" ]; then r=1 shift fi ####################################### if test -f $XCRYSDEN_TOPDIR/scripts/pwLib_old.sh ; then . $XCRYSDEN_TOPDIR/scripts/pwLib_old.sh else . pwLib_old.sh fi ####################################### # # check if we have OLD or NEW PW.X input format # new_format1=`grep 'ATOMIC_POSITIONS' $1` new_format2=`grep -i '&system' $1` if [ "$new_format1" != "" -a "$new_format2" != "" ]; then # we have NEW PW.X input format # cat $1 | awk 'BEGIN {RS=",";} {print $0}' | awk ' BEGIN { calculation=""; num_of_images=""; nml_end=0; nml_end_string=""; } toupper($0) ~ /&SYSTEM/ { print; } /=/ { if ( toupper($1) ~ /^IBRAV($|=)|^CELLDM\([1-6]\)($|=)|^NAT($|=)|^A($|=)|^B($|=)|^C($|=)|^COSAB($|=)|^COSAC($|=)|^COSBC($|=)/ ) { print; } if ( toupper($1) ~ /^CALCULATION($|=)/ ) { calculation=toupper($0); } if ( toupper($1) ~ /^NUM_OF_IMAGES($|=)/ ) { num_of_images=toupper($0); } } /ATOMIC_POSITIONS|CELL_PARAMETERS/ { if ( !nml_end) { # first finish the namelist nml_end=1; if (calculation != "") print calculation; if (num_of_images != "") print num_of_images; print nml_end_string; } # now print the current record print_line=1; print toupper($0); next; } toupper($0) ~ /&END|^\/|^ +\// { nml_end_string=$0; } /a*/ { if ( print_line == 1 ) { print toupper($0); } }'> pw.$$ PWI2XSF=pwi2xsf else # we have OLD PW.X input format pwNucleiCharges $1 /dev/null cat $1 | awk 'BEGIN {RS=",";} {print}' | awk ' BEGIN { end=0; } toupper($0) ~ /&INPUT|CELLDM|NAT|LTAUCRY/ { print; } toupper($0) ~ /IBRAV/ { print; split($0,a,"="); split(a[1],b,","); ibrav = b[1]; } toupper($0) ~ /&END|^\/|^ \// { end=1; } /a*/ { if ( end == 1 ) print; }' > pw.$$ PWI2XSF=pwi2xsf_old fi # # execute $PWI2XSF fortran program and print the XSF file # if test -f $XCRYSDEN_TOPDIR/bin/$PWI2XSF ; then $XCRYSDEN_TOPDIR/bin/$PWI2XSF < pw.$$ | tee pwi2xsf.xsf_out else $PWI2XSF < pw.$$ | tee pwi2xsf.xsf_out fi rm -f pw.$$ if [ "$r" -eq 1 ]; then if [ -f nuclei.charges ]; then rm nuclei.charges; fi fi exit 0 --=-uDq9S/6fRwgmb3hLKHlu--