[Wien] Crystal structure that XCrySDen cannot visualize

[delamora]

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 90.000000 90.000000128.659811
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
Gd1 NPT= 781 R0=0.00001000 RMT= 1.9600 Z: 64.0
ATOM 2: X=0.60000000 Y=0.60000000 Z=0.00000000
O 1 NPT= 781 R0=0.00010000 RMT= 1.6100 Z: 8.0
ATOM 3: X=0.54700000 Y=0.40000000 Z=0.44700000
3: X=0.54700000 Y=0.40000000 Z=0.55300000
H 1 NPT= 781 R0=0.00010000 RMT= 0.6600 Z: 1.0



________________________________
De: wien-bounces at zeus.theochem.tuwien.ac.at <wien-bounces at zeus.theochem.tuwien.ac.at> en nombre de Tomas Kana <kana at 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 90.000000 90.000000121.000000
ATOM -1: X=0.00000000 Y=0.00000000 Z=0.00000000
Gd NPT= 781 R0=0.00001000 RMT= 1.96 Z: 64.0
ATOM -2: X=0.00000000 Y=0.00000000 Z=0.40000000
O NPT= 781 R0=0.00010000 RMT= 1.61 Z: 8.0
ATOM -3: X=0.30000000 Y=0.40600000 Z=0.60000000
H NPT= 781 R0=0.00010000 RMT= 0.66 Z: 1.0
ATOM -4: X=0.40600000 Y=0.30000000 Z=0.60000000
H NPT= 781 R0=0.00010000 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 90.000000 90.000000128.233790
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
Gd1 NPT= 781 R0=0.00001000 RMT= 1.96 Z: 64.0
ATOM 2: X=0.60000000 Y=0.60000000 Z=0.00000000
O 1 NPT= 781 R0=0.00010000 RMT= 1.61 Z: 8.0
ATOM 3: X=0.54700000 Y=0.40000000 Z=0.44700000
3: X=0.54700000 Y=0.40000000 Z=0.55300000
H 1 NPT= 781 R0=0.00010000 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 90.000000 90.000000120.000000

Then, with SGroup I get;
CXZ LATTICE,NONEQUIV.ATOMS: 3 8 Cm
MODE OF CALC=RELA unit=ang
7.558908 12.100156 13.092413 90.000000 90.000000128.659811
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
Gd1 NPT= 781 R0=0.00001000 RMT= 1.9600 Z: 64.0
ATOM 2: X=0.60000000 Y=0.60000000 Z=0.00000000
O 1 NPT= 781 R0=0.00010000 RMT= 1.6100 Z: 8.0
ATOM 3: X=0.54700000 Y=0.40000000 Z=0.44700000
3: X=0.54700000 Y=0.40000000 Z=0.55300000
H 1 NPT= 781 R0=0.00010000 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 90.000000 90.000000128.659811
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
MULT= 1 ISPLIT= 8
Gd1 NPT= 781 R0=0.00001000 RMT= 1.9600 Z: 64.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 2: X=0.60000000 Y=0.60000000 Z=0.00000000
MULT= 1 ISPLIT= 8
O 1 NPT= 781 R0=0.00010000 RMT= 1.6100 Z: 8.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 3: X=0.54700000 Y=0.40000000 Z=0.44700000
MULT= 2 ISPLIT= 8
3: X=0.54700000 Y=0.40000000 Z=0.55300000
H 1 NPT= 781 R0=0.00010000 RMT= 0.6600 Z: 1.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
2 NUMBER OF SYMMETRY OPERATIONS
1 0 0 0.00000000
0 1 0 0.00000000
0 0 1 0.00000000
1
1 0 0 0.00000000
0 1 0 0.00000000
0 0-1 0.00000000
2
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