Re: [Wien] Crystal structure that XCrySDen cannot visualize
11.03.2016 00:29, delamora wrote: I am using the XCrySDen-1.5.25, and maybe it is why I am having this problem. Mine is Version: 1.4.1 Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Crystal structure that XCrySDen cannot visualize
Thank you Lyudmila, I am using the XCrySDen-1.5.25, and maybe it is why I am having this problem. It is a curious problem that does not worry me; If I put an atom in an hexagonal cell; a=b=4A, c=5A Atom 1: 0,0,0 Atom 2: x,x, y the system changes to 8 Cm and I cannot visualize it, but if I change gamma by a small angle then I have no problem, and if I do not change the angle I can go and calculate the electronic properties. If c=6A then I do not have this problem. On the other hand I am studying Gd + H2O -> GdO + H2 Pablo De: wien-boun...@zeus.theochem.tuwien.ac.at <wien-boun...@zeus.theochem.tuwien.ac.at> en nombre de Lyudmila Dobysheva <lyuk...@mail.ru> Enviado: miércoles, 9 de marzo de 2016 04:57 a. m. Para: A Mailing list for WIEN2k users Asunto: Re: [Wien] Crystal structure that XCrySDen cannot visualize 08.03.2016 22:19, delamora wrote: > that there is a problem, but what I see is that it is with XCrySDen and > not with WIEN2k. > Well, this structure cannot be visualized with XCrySDen > Structure that cannot be visualized > more GdO-H2-C.struct Dear Pablo, I have taken your struct file and it passed well through my Xcrysden (see in attachments), so cannot see your problem. By the way, I'd say this is not > Gd and H2O but an oxide of Gd with H2 molecules. Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Crystal structure that XCrySDen cannot visualize
08.03.2016 22:19, delamora wrote: that there is a problem, but what I see is that it is with XCrySDen and not with WIEN2k. Well, this structure cannot be visualized with XCrySDen Structure that cannot be visualized more GdO-H2-C.struct Dear Pablo, I have taken your struct file and it passed well through my Xcrysden (see in attachments), so cannot see your problem. By the way, I'd say this is not > Gd and H2O but an oxide of Gd with H2 molecules. Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- Title CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.558908 12.100156 13.092413 90.00 90.00128.659811 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 8 Gd1NPT= 781 R0=0.1000 RMT=1.9600 Z: 64.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 2: X=0.6000 Y=0.6000 Z=0. MULT= 1 ISPLIT= 8 O 1NPT= 781 R0=0.0001 RMT=1.6100 Z: 8.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 MULT= 2 ISPLIT= 8 3: X=0.5470 Y=0.4000 Z=0.5530 H 1NPT= 781 R0=0.0001 RMT=0.6600 Z: 1.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 2 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 1 0 0 0. 0 1 0 0. 0 0-1 0. 2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Crystal structure that XCrySDen cannot visualize
Dear Tomás (with an accent as in spanish), I am not interested in visualizing the structure, I just want to express that there is a problem, but what I see is that it is with XCrySDen and not with WIEN2k. If you change the gamma angle just a little then the structure can be visualized, for example if you change 128.659811 => 128.759811 then the structure can be visualized. I tried supercell and I did not see a change. Pablo CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.558908 12.100156 13.092413 90.00 90.00128.659811 ATOM 1: X=0. Y=0. Z=0. Gd1 NPT= 781 R0=0.1000 RMT= 1.9600 Z: 64.0 ATOM 2: X=0.6000 Y=0.6000 Z=0. O 1 NPT= 781 R0=0.0001 RMT= 1.6100 Z: 8.0 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 3: X=0.5470 Y=0.4000 Z=0.5530 H 1 NPT= 781 R0=0.0001 RMT= 0.6600 Z: 1.0 De: wien-boun...@zeus.theochem.tuwien.ac.at <wien-boun...@zeus.theochem.tuwien.ac.at> en nombre de Tomas Kana <k...@seznam.cz> Enviado: martes, 8 de marzo de 2016 04:38 a. m. Para: A Mailing list for WIEN2k users Asunto: Re: [Wien] Crystal structure that XCrySDen cannot visualize Dear Pablo, If you want to visualize this structure in XCrysDen, you may try to use x supercell make 1x1x1 supercell with zero shift and zero vacuum and use P when asked for lattice type. cp case_super.struct case.struct and try it again in XCrysden HTH Tomas Dear WIEN2k community, There is a strange thing with a crystal structure, I am playing with Gd and H2O, so I put the following structure (I erased some lines); P LATTICE,NONEQUIV.ATOMS: 4 1_P1 MODE OF CALC=RELA unit=ang 7.558908 7.558908 9.448634 90.00 90.00121.00 ATOM -1: X=0. Y=0. Z=0. Gd NPT= 781 R0=0.1000 RMT= 1.96 Z: 64.0 ATOM -2: X=0. Y=0. Z=0.4000 O NPT= 781 R0=0.0001 RMT= 1.61 Z: 8.0 ATOM -3: X=0.3000 Y=0.4060 Z=0.6000 H NPT= 781 R0=0.0001 RMT= 0.66 Z: 1.0 ATOM -4: X=0.4060 Y=0.3000 Z=0.6000 H NPT= 781 R0=0.0001 RMT= 0.66 Z: 1.0 SGroup changes it to; CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.444369 12.028936 13.157877 90.00 90.00128.233790 ATOM 1: X=0. Y=0. Z=0. Gd1 NPT= 781 R0=0.1000 RMT= 1.96 Z: 64.0 ATOM 2: X=0.6000 Y=0.6000 Z=0. O 1 NPT= 781 R0=0.0001 RMT= 1.61 Z: 8.0 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 3: X=0.5470 Y=0.4000 Z=0.5530 H 1 NPT= 781 R0=0.0001 RMT= 0.66 Z: 1.0 and there is no problem visualizing with XCrySDen But when I put gamma as 120 instead of 121 7.558908 7.558908 9.448634 90.00 90.00120.00 Then, with SGroup I get; CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.558908 12.100156 13.092413 90.00 90.00128.659811 ATOM 1: X=0. Y=0. Z=0. Gd1 NPT= 781 R0=0.1000 RMT= 1.9600 Z: 64.0 ATOM 2: X=0.6000 Y=0.6000 Z=0. O 1 NPT= 781 R0=0.0001 RMT= 1.6100 Z: 8.0 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 3: X=0.5470 Y=0.4000 Z=0.5530 H 1 NPT= 781 R0=0.0001 RMT= 0.6600 Z: 1.0 Which has little differences such that there is a larger space after "RMT=" and the RMT is 1.9600 instead of 1.96, although these differences do not seem to be important. Well, this structure cannot be visualized with XCrySDen Pablo = Structure that cannot be visualized more GdO-H2-C.struct --- Title CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.558908 12.100156 13.092413 90.00 90.00128.659811 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 8 Gd1 NPT= 781 R0=0.1000 RMT= 1.9600 Z: 64.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 2: X=0.6000 Y=0.6000 Z=0. MULT= 1 ISPLIT= 8 O 1 NPT= 781 R0=0.0001 RMT= 1.6100 Z: 8.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 MULT= 2 ISPLIT= 8 3: X=0.5470 Y=0.4000 Z=0.5530 H 1 NPT= 781 R0=0.0001 RMT= 0.6600 Z: 1.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 2 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 1 0 0 0. 0 1 0 0. 0 0-1 0. 2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-L
Re: [Wien] Crystal structure that XCrySDen cannot visualize
Dear Pablo, If you want to visualize this structure in XCrysDen, you may try to use x supercell make 1x1x1 supercell with zero shift and zero vacuum and use P when asked for lattice type. cp case_super.struct case.struct and try it again in XCrysden HTH Tomas "Dear WIEN2k community, There is a strange thing with a crystal structure, I am playing with Gd and H2O, so I put the following structure (I erased some lines); P LATTICE,NONEQUIV.ATOMS: 4 1_P1 MODE OF CALC=RELA unit=ang 7.558908 7.558908 9.448634 90.00 90.00121.00 ATOM -1: X=0. Y=0. Z=0. Gd NPT= 781 R0=0.1000 RMT= 1.96 Z: 64.0 ATOM -2: X=0. Y=0. Z=0.4000 O NPT= 781 R0=0.0001 RMT= 1.61 Z: 8.0 ATOM -3: X=0.3000 Y=0.4060 Z=0.6000 H NPT= 781 R0=0.0001 RMT= 0.66 Z: 1.0 ATOM -4: X=0.4060 Y=0.3000 Z=0.6000 H NPT= 781 R0=0.0001 RMT= 0.66 Z: 1.0 SGroup changes it to; CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.444369 12.028936 13.157877 90.00 90.00128.233790 ATOM 1: X=0. Y=0. Z=0. Gd1 NPT= 781 R0=0.1000 RMT= 1.96 Z: 64.0 ATOM 2: X=0.6000 Y=0.6000 Z=0. O 1 NPT= 781 R0=0.0001 RMT= 1.61 Z: 8.0 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 3: X=0.5470 Y=0.4000 Z=0.5530 H 1 NPT= 781 R0=0.0001 RMT= 0.66 Z: 1.0 and there is no problem visualizing with XCrySDen But when I put gamma as 120 instead of 121 7.558908 7.558908 9.448634 90.00 90.00120.00 Then, with SGroup I get; CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.558908 12.100156 13.092413 90.00 90.00128.659811 ATOM 1: X=0. Y=0. Z=0. Gd1 NPT= 781 R0=0.1000 RMT= 1.9600 Z: 64.0 ATOM 2: X=0.6000 Y=0.6000 Z=0. O 1 NPT= 781 R0=0.0001 RMT= 1.6100 Z: 8.0 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 3: X=0.5470 Y=0.4000 Z=0.5530 H 1 NPT= 781 R0=0.0001 RMT= 0.6600 Z: 1.0 Which has little differences such that there is a larger space after "RMT=" and the RMT is 1.9600 instead of 1.96, although these differences do not seem to be important. Well, this structure cannot be visualized with XCrySDen Pablo = Structure that cannot be visualized more GdO-H2-C.struct --- Title CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm MODE OF CALC=RELA unit=ang 7.558908 12.100156 13.092413 90.00 90.00128.659811 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 8 Gd1 NPT= 781 R0=0.1000 RMT= 1.9600 Z: 64.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 2: X=0.6000 Y=0.6000 Z=0. MULT= 1 ISPLIT= 8 O 1 NPT= 781 R0=0.0001 RMT= 1.6100 Z: 8.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 3: X=0.5470 Y=0.4000 Z=0.4470 MULT= 2 ISPLIT= 8 3: X=0.5470 Y=0.4000 Z=0.5530 H 1 NPT= 781 R0=0.0001 RMT= 0.6600 Z: 1.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 2 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0 1 0 0. 0 0 1 0. 1 1 0 0 0. 0 1 0 0. 0 0-1 0. 2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem. tuwien.ac.at/index.html"___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
