[Wien] Crystal structure that XCrySDen cannot visualize

delamora delamora at unam.mx
Fri Mar 4 20:51:20 CET 2016


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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