From bnrj.rudra at yahoo.com Wed Jul 1 16:20:08 2009 From: bnrj.rudra at yahoo.com (Rudra Banerjee) Date: Wed, 1 Jul 2009 07:20:08 -0700 (PDT) Subject: [xcrysden] k points labelling problem Message-ID: <184079.52916.qm@web94107.mail.in2.yahoo.com> Hello friends, i need to check the k-point paths of the xsf file: CRYSTAL PRIMVEC -1.567501 1.567501 1.567501 1.567501 -1.567501 1.567501 1.567501 1.567501 -1.567501 CONVVEC -1..567501 1.567501 1.567501 1.567501 -1.567501 1.567501 1.567501 1.567501 -1.567501 PRIMCOORD 1 1 29 0.000000 0..000000 0.000000 here, xcrysden is giving a warning : - the guessed BRAVAIS LATTICE TYPE : not-supported ((the XSF's group number is 1)) and the k point path selection is not labelling any special point . I do not have CRYSTAL package. Will you please tell me how to overcome this? -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php From zbayyari at rocketmail.com Thu Jul 2 16:47:17 2009 From: zbayyari at rocketmail.com (Zuheir Elbayyari) Date: Thu, 2 Jul 2009 07:47:17 -0700 (PDT) Subject: [xcrysden] point gruop Message-ID: <904259.10653.qm@web112514.mail.gq1.yahoo.com> Hi, Sorry to inform you that I am new to xcrysden and I am not familiar with what you need with the wein2K program and xcrysden. I think there is help on that at the xcrysden webpage. My purpose of using this package to make an interface between it and a molecular dynamics program which we have wrote to plot the atoms at each step as <*.zxy> files. ? Kind regards. Zuheir El-bayyari???????????????? ??????????????????????????????????????????????????? --- On Sun, 6/28/09, Amene Nouri wrote: From: Amene Nouri Subject: [xcrysden] point gruop To: xcrysden at democritos.it Date: Sunday, June 28, 2009, 12:38 AM hello I have a wien2k struct file how can I find it's point group and space group? thanks -----Inline Attachment Follows----- _______________________________________________ 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/20090702/d1a4812a/attachment.htm From jiafasun at yahoo.com.cn Sun Jul 5 07:03:23 2009 From: jiafasun at yahoo.com.cn (=?utf-8?B?5a2Z5a625rOV?=) Date: Sun, 5 Jul 2009 13:03:23 +0800 (CST) Subject: [xcrysden] =?utf-8?b?5Zue5aSN77yaICBpbnN0YWxsYXRpb24gaGVscA==?= Message-ID: <886979.30302.qm@web15704.mail.cnb.yahoo.com> Hello , I think you don't have a remote desk responsed after you excute the command --- 09?6?22????, sreekar guddeti ??? ???: sreekar guddeti ??: [xcrysden] installation help ???: xcrysden at democritos.it ??: 2009?6?22?,??,??5:07 hello, i downloaded the xcrysden source package with external libraries (TCL +TK + Mesa) included and for installation i created a make.sys file as instructed(but i m not sure if i did this the right way) and then for make install the configuration utility? pops in console finally after sourcing the profile i type xcrysden in console i get /home/fubar/Desktop/programming/XCrySDen-1.4.1s/xcrysden: 200: /home/fubar/Desktop/programming/XCrySDen-1.4.1s/bin/xcrys: not found i looked up the bin directory and nothing was there in it... could anyone help out plz. thanks in advance -- Sreekar Guddeti IIT Bombay -----???????----- _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090705/fe0fb519/attachment.htm From vaskarpour at yahoo.com Fri Jul 17 03:01:38 2009 From: vaskarpour at yahoo.com (Vahid Askarpour) Date: Thu, 16 Jul 2009 18:01:38 -0700 (PDT) Subject: [xcrysden] LIBRARY-RELATED ERROR Message-ID: <794492.78471.qm@web51510.mail.re2.yahoo.com> Dear xcrysden experts, I downloaded the shared 1.5.17 version for Mac (mine is 10.4.11) and when running xcrysden from the X11 window, I get the following. The error is apparently due to incompatible libraries. I searched the web to download the libXmu version 12.0.0 but can't find it. Any suggestions will be appreciated. Regards, Vahid Defiant:~/XCrySDen-1.5.17-bin Vahid$ xcrysden +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2004 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 1.5.17 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/. TCL_LIBRARY=/Users/Vahid/XCrySDen-1.5.17-bin/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/Users/Vahid/XCrySDen-1.5.17-bin XCRYSDEN_SCRATCH=/Users/Vahid/xcrys_tmp dyld: Library not loaded: /usr/X11/lib/libXmu.6.dylib Referenced from: /Users/Vahid/XCrySDen-1.5.17-bin/bin/xcrys Reason: Incompatible library version: xcrys requires version 9.0.0 or later, b ut libXmu.6.dylib provides version 6.2.0 /Users/Vahid/XCrySDen-1.5.17-bin/xcrysden: line 248: 371 Trace/BPT trap ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYS DEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null From decboy9 at gmail.com Fri Jul 17 09:37:32 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 17 Jul 2009 13:07:32 +0530 Subject: [xcrysden] Bismuth Titanate Structure Message-ID: Hi all, I am new to PWscf and XCrysden. My Input file for Bismuth Titanate is below. The output structure in XCRYSden window is seemed to be right but it is giving mssg ......... typed below. Please help or give suggestion. Number of Atoms: 133 Number of Frames: 12 WARNING: Atom 1 and atom 12 are very close !!! Atom 12 deleted !!! WARNING: Atom 2 and atom 122 are very close !!! Atom 122 deleted !!! WARNING: Atom 3 and atom 14 are very close !!! Atom 14 deleted !!! WARNING: Atom 4 and atom 123 are very close !!! Atom 123 deleted !!! WARNING: Atom 5 and atom 16 are very close !!! Atom 16 deleted !!! WARNING: Atom 6 and atom 124 are very close !!! Atom 124 deleted !!!...... ......................................................... ...... and because of this PWScf SCF run stops and gives the mssg wrong atomic co-ordinates. &control calculation='scf', restart_mode='from_scratch', prefix='bit' pseudo_dir = '/home/physics/pseudo/', outdir='/home/physics/work/bit/temp' / &system ibrav = 7, a=3.86334, b= 3.86334, c=33.2942 , nat =38, ntyp= 3, ecutwfc = 60.0,ecutrho=200, occupations='smearing', smearing = "methfessel-paxton", degauss=0.01, / &electrons mixing_beta = 0.50 conv_thr = 1.0e-6 / &ions / ATOMIC_SPECIES Bi 208.980 Bi.pbe-d-mt.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS {bohr} Bi 3.65032726386637 3.65032726386637 4.24815040995715 Bi 3.65032726386637 3.65032726386637 13.30504053709336 Ti 3.65032726386637 3.65032726386637 23.32581852937194 O 3.65032726386637 3.65032726386637 27.75265329698888 O 3.65032726386637 3.65032726386637 19.74332980289407 Bi 0.00000000000000 0.00000000000000 35.70661018533794 Bi 0.00000000000000 0.00000000000000 44.76350031247415 Ti 0.00000000000000 0.00000000000000 54.78427830475272 O 0.00000000000000 0.00000000000000 -3.70580647839191 O 0.00000000000000 0.00000000000000 51.20178957827486 Bi 3.65032726386637 3.65032726386637 58.66876914080443 Bi 3.65032726386637 3.65032726386637 49.61187901366822 Ti 3.65032726386637 3.65032726386637 39.59110102138964 O 3.65032726386637 3.65032726386637 35.16426625377269 O 3.65032726386637 3.65032726386637 43.17358974786750 Bi 0.00000000000000 0.00000000000000 27.21030936542364 Bi 0.00000000000000 0.00000000000000 18.15341923828743 Ti 0.00000000000000 0.00000000000000 8.13264124600885 O 0.00000000000000 0.00000000000000 3.70580647839191 O 0.00000000000000 0.00000000000000 11.71512997248671 Ti 3.65032726386637 3.65032726386637 31.45845977538078 Ti 0.00000000000000 0.00000000000000 0.00000000000000 O 3.65032726386637 0.00000000000000 0.00000000000000 O 0.00000000000000 3.65032726386637 31.45845977538078 O 0.00000000000000 3.65032726386637 0.00000000000000 O 3.65032726386637 0.00000000000000 31.45845977538078 O 3.65032726386637 0.00000000000000 15.72922988769039 O 0.00000000000000 3.65032726386637 15.72922988769039 O 3.65032726386637 0.00000000000000 47.18768966307118 O 0.00000000000000 3.65032726386637 47.18768966307118 O 3.65032726386637 0.00000000000000 7.40406298501923 O 0.00000000000000 3.65032726386637 38.86252276040002 O 0.00000000000000 3.65032726386637 7.40406298501923 O 3.65032726386637 0.00000000000000 38.86252276040002 O 3.65032726386637 0.00000000000000 55.51285656574235 O 0.00000000000000 3.65032726386637 24.05439679036155 O 0.00000000000000 3.65032726386637 55.51285656574235 O 3.65032726386637 0.00000000000000 24.05439679036155 K_POINTS {automatic} 4 4 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090717/bea84b8c/attachment.htm From decboy9 at gmail.com Fri Jul 17 10:58:18 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 17 Jul 2009 14:28:18 +0530 Subject: [xcrysden] B2cb Space Group Message-ID: Hi all, Can any body tell ibrav for B2cb and B1a1 space group. Thanks Dev Sharma, JRF University of Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090717/bec0c5ad/attachment.htm From degironc at sissa.it Fri Jul 17 11:09:23 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 17 Jul 2009 11:09:23 +0200 Subject: [xcrysden] B2cb Space Group In-Reply-To: References: Message-ID: <4A603FC3.3070005@sissa.it> google says orthorhombic for B2cb and monoclinic for B1a1 stefano dev sharma wrote: > > > Hi all, > Can any body tell ibrav for B2cb and B1a1 space group. > Thanks > > > Dev Sharma, > JRF > University of Delhi > ------------------------------------------------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > From decboy9 at gmail.com Fri Jul 17 12:36:55 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 17 Jul 2009 16:06:55 +0530 Subject: [xcrysden] Bismuth Titanate Structure In-Reply-To: References: Message-ID: Hi all, I am new to PWscf and XCrysden. My Input file for Bismuth Titanate is below. The output structure in XCRYSden window is seemed to be right but it is giving mssg ......... typed below. Please help or give suggestion. Number of Atoms: 133 Number of Frames: 12 WARNING: Atom 1 and atom 12 are very close !!! Atom 12 deleted !!! WARNING: Atom 2 and atom 122 are very close !!! Atom 122 deleted !!! WARNING: Atom 3 and atom 14 are very close !!! Atom 14 deleted !!! WARNING: Atom 4 and atom 123 are very close !!! Atom 123 deleted !!! WARNING: Atom 5 and atom 16 are very close !!! Atom 16 deleted !!! WARNING: Atom 6 and atom 124 are very close !!! Atom 124 deleted !!!...... ......................................................... ...... and because of this PWScf SCF run stops and gives the mssg wrong atomic co-ordinates. &control calculation='scf', restart_mode='from_scratch', prefix='bit' pseudo_dir = '/home/physics/pseudo/', outdir='/home/physics/work/bit/temp' / &system ibrav = 7, a=3.86334, b= 3.86334, c=33.2942 , nat =38, ntyp= 3, ecutwfc = 60.0,ecutrho=200, occupations='smearing', smearing = "methfessel-paxton", degauss=0.01, / &electrons mixing_beta = 0.50 conv_thr = 1.0e-6 / &ions / ATOMIC_SPECIES Bi 208.980 Bi.pbe-d-mt.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS {bohr} Bi 3.65032726386637 3.65032726386637 4.24815040995715 Bi 3.65032726386637 3.65032726386637 13.30504053709336 Ti 3.65032726386637 3.65032726386637 23.32581852937194 O 3.65032726386637 3.65032726386637 27.75265329698888 O 3.65032726386637 3.65032726386637 19.74332980289407 Bi 0.00000000000000 0.00000000000000 35.70661018533794 Bi 0.00000000000000 0.00000000000000 44.76350031247415 Ti 0.00000000000000 0.00000000000000 54.78427830475272 O 0.00000000000000 0.00000000000000 -3.70580647839191 O 0.00000000000000 0.00000000000000 51.20178957827486 Bi 3.65032726386637 3.65032726386637 58.66876914080443 Bi 3.65032726386637 3.65032726386637 49.61187901366822 Ti 3.65032726386637 3.65032726386637 39.59110102138964 O 3.65032726386637 3.65032726386637 35.16426625377269 O 3.65032726386637 3.65032726386637 43.17358974786750 Bi 0.00000000000000 0.00000000000000 27.21030936542364 Bi 0.00000000000000 0.00000000000000 18.15341923828743 Ti 0.00000000000000 0.00000000000000 8.13264124600885 O 0.00000000000000 0.00000000000000 3.70580647839191 O 0.00000000000000 0.00000000000000 11.71512997248671 Ti 3.65032726386637 3.65032726386637 31.45845977538078 Ti 0.00000000000000 0.00000000000000 0.00000000000000 O 3.65032726386637 0.00000000000000 0.00000000000000 O 0.00000000000000 3.65032726386637 31.45845977538078 O 0.00000000000000 3.65032726386637 0.00000000000000 O 3.65032726386637 0.00000000000000 31.45845977538078 O 3.65032726386637 0.00000000000000 15.72922988769039 O 0.00000000000000 3.65032726386637 15.72922988769039 O 3.65032726386637 0.00000000000000 47.18768966307118 O 0.00000000000000 3.65032726386637 47.18768966307118 O 3.65032726386637 0.00000000000000 7.40406298501923 O 0.00000000000000 3.65032726386637 38.86252276040002 O 0.00000000000000 3.65032726386637 7.40406298501923 O 3.65032726386637 0.00000000000000 38.86252276040002 O 3.65032726386637 0.00000000000000 55.51285656574235 O 0.00000000000000 3.65032726386637 24.05439679036155 O 0.00000000000000 3.65032726386637 55.51285656574235 O 3.65032726386637 0.00000000000000 24.05439679036155 K_POINTS {automatic} 4 4 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090717/890da69a/attachment.htm From spbeckman at gmail.com Fri Jul 17 14:44:17 2009 From: spbeckman at gmail.com (Scott Beckman) Date: Fri, 17 Jul 2009 07:44:17 -0500 Subject: [xcrysden] Bismuth Titanate Structure In-Reply-To: References: Message-ID: PWSCF is failing because there are atoms that are on top of each other. Xcrysden compensates by deleting the mistake. When I see this error it is because I made a mistake with the units. I think you might be mixing units because a,b,c are by default Angstrom, but you're using atomic positions in Bohr. It isn't necessary to have a uniform unit scheme, but it is easier to avoid mistakes if you do. For reference see: http://www.quantum-espresso.org/input-syntax/ INPUT_PW.html On Jul 17, 2009, at 5:36 AM, dev sharma wrote: > > > > > Hi all, > > I am new to PWscf and XCrysden. My Input file for Bismuth Titanate > is below. The output structure in XCRYSden window is seemed to be > right but it is giving mssg ......... typed below. Please help or > give suggestion. > > Number of Atoms: 133 > Number of Frames: 12 > WARNING: Atom 1 and atom 12 are very close !!! > Atom 12 deleted !!! > WARNING: Atom 2 and atom 122 are very close !!! > Atom 122 deleted !!! > WARNING: Atom 3 and atom 14 are very close !!! > Atom 14 deleted !!! > WARNING: Atom 4 and atom 123 are very close !!! > Atom 123 deleted !!! > WARNING: Atom 5 and atom 16 are very close !!! > Atom 16 deleted !!! > WARNING: Atom 6 and atom 124 are very close !!! > Atom 124 deleted !!!...... > ......................................................... > ...... > > and because of this PWScf SCF run stops and gives the mssg wrong > atomic co-ordinates. > > > &control > calculation='scf', > restart_mode='from_scratch', > prefix='bit' > pseudo_dir = '/home/physics/pseudo/', > outdir='/home/physics/work/bit/temp' > / > &system > ibrav = 7, a=3.86334, b= 3.86334, c=33.2942 > , nat =38, ntyp= 3, > ecutwfc = 60.0,ecutrho=200, > occupations='smearing', smearing = "methfessel-paxton", > degauss=0.01, > > / > &electrons > mixing_beta = 0.50 > conv_thr = 1.0e-6 > / > &ions > / > > ATOMIC_SPECIES > Bi 208.980 Bi.pbe-d-mt.UPF > Ti 47.867 Ti.pbe-sp-van_ak.UPF > O 15.9994 O.pbe-van_ak.UPF > ATOMIC_POSITIONS {bohr} > Bi 3.65032726386637 3.65032726386637 > 4.24815040995715 > Bi 3.65032726386637 3.65032726386637 > 13.30504053709336 > Ti 3.65032726386637 3.65032726386637 > 23.32581852937194 > O 3.65032726386637 3.65032726386637 27.75265329698888 > O 3.65032726386637 3.65032726386637 19.74332980289407 > Bi 0.00000000000000 0.00000000000000 > 35.70661018533794 > Bi 0.00000000000000 0.00000000000000 > 44.76350031247415 > Ti 0.00000000000000 0.00000000000000 > 54.78427830475272 > O 0.00000000000000 0.00000000000000 -3.70580647839191 > O 0.00000000000000 0.00000000000000 51.20178957827486 > Bi 3.65032726386637 3.65032726386637 > 58.66876914080443 > Bi 3.65032726386637 3.65032726386637 > 49.61187901366822 > Ti 3.65032726386637 3.65032726386637 > 39.59110102138964 > O 3.65032726386637 3.65032726386637 > 35.16426625377269 > O 3.65032726386637 3.65032726386637 > 43.17358974786750 > Bi 0.00000000000000 0.00000000000000 > 27.21030936542364 > Bi 0.00000000000000 0.00000000000000 > 18.15341923828743 > Ti 0.00000000000000 0.00000000000000 > 8.13264124600885 > O 0.00000000000000 0.00000000000000 3.70580647839191 > O 0.00000000000000 0.00000000000000 > 11.71512997248671 > Ti 3.65032726386637 3.65032726386637 > 31.45845977538078 > Ti 0.00000000000000 0.00000000000000 > 0.00000000000000 > O 3.65032726386637 0.00000000000000 0.00000000000000 > O 0.00000000000000 3.65032726386637 31.45845977538078 > O 0.00000000000000 3.65032726386637 0.00000000000000 > O 3.65032726386637 0.00000000000000 31.45845977538078 > O 3.65032726386637 0.00000000000000 15.72922988769039 > O 0.00000000000000 3.65032726386637 15.72922988769039 > O 3.65032726386637 0.00000000000000 47.18768966307118 > O 0.00000000000000 3.65032726386637 47.18768966307118 > O 3.65032726386637 0.00000000000000 7.40406298501923 > O 0.00000000000000 3.65032726386637 38.86252276040002 > O 0.00000000000000 3.65032726386637 7.40406298501923 > O 3.65032726386637 0.00000000000000 38.86252276040002 > O 3.65032726386637 0.00000000000000 55.51285656574235 > O 0.00000000000000 3.65032726386637 24.05439679036155 > O 0.00000000000000 3.65032726386637 55.51285656574235 > O 3.65032726386637 0.00000000000000 24.05439679036155 > > K_POINTS {automatic} > 4 4 1 0 0 0 > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden