We will create the surface structure using the slab (2D) model according to the information found in the following lecture on page 29.
http://susi.theochem.tuwien.ac.at/events/ws2006/WIEN2k-getting_started.pdf
We take the example of chromium as mentioned in the lecture.
The crystal structure in bulk structure is as follows:
Cr-Slab
B LATTICE,NONEQUIV.ATOMS: 1 229_Im-3m
MODE OF CALC=RELA unit=ang
5.461311 5.461311 5.461311 90.000000 90.000000 90.000000
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
MULT= 1 ISPLIT= 2
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
48 NUMBER OF SYMMETRY OPERATIONS
To create the slab structure from the previous structure we take the example of the 001 plane.
We make supercell 1x1x3 P with vaccum of 15 bohr in z direction
Filename of original struct file:
Number of cells in x direction:
Number of cells in y direction:
Number of cells in z direction: 3
Optional shift of all atoms (fractional coordinates)
in x direction:
in y direction:
in z direction:
Enter your target lattice type: P
(Some choices are restricted by symmetry)
For surfaces or isolated molecules: (for P lattice only)
Vacuum in x-direction [bohr]:
Repeat atoms at x=0:
Vacuum in y-direction [bohr]:
Repeat atoms at y=0: Vacuum in z-direction [bohr]: 15
Repeat atoms at z=0:Y
you will get the following structure
Cr-Slab
P LATTICE,NONEQUIV. ATOMS 7
MODE OF CALC=RELA unit=ang
5.461311 5.461311 31.383933 90.000000 90.000000 90.000000
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 2: X=0.00000000 Y=0.00000000 Z=0.17401614
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 3: X=0.00000000 Y=0.00000000 Z=0.34803229
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 4: X=0.00000000 Y=0.00000000 Z=0.52204843
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 5: X=0.50000000 Y=0.50000000 Z=0.08700807
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 6: X=0.50000000 Y=0.50000000 Z=0.26102422
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 7: X=0.50000000 Y=0.50000000 Z=0.43504036
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
0 NUMBER OF SYMMETRY OPERATIONS
If we run sgroup we will get the following structure
Cr-Slab
P LATTICE,NONEQUIV.ATOMS: 4 123 P4/mmm
MODE OF CALC=RELA unit=ang
5.461311 5.461311 31.383933 90.000000 90.000000 90.000000
ATOM 1: X=0.50000000 Y=0.50000000 Z=0.23897578
MULT= 2 ISPLIT= 8
1: X=0.50000000 Y=0.50000000 Z=0.76102422
Cr1 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 2: X=0.50000000 Y=0.50000000 Z=0.58700807
MULT= 2 ISPLIT= 8
2: X=0.50000000 Y=0.50000000 Z=0.41299193
Cr2 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 3: X=0.00000000 Y=0.00000000 Z=0.32598385
MULT= 2 ISPLIT= 8
3: X=0.00000000 Y=0.00000000 Z=0.67401615
Cr3 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 4: X=0.00000000 Y=0.00000000 Z=0.50000000
MULT= 1 ISPLIT= 8
Cr4 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
16 NUMBER OF SYMMETRY OPERATIONS
You can see more information for another compound on this video
Good Luck
http://susi.theochem.tuwien.ac.at/events/ws2006/WIEN2k-getting_started.pdf
We take the example of chromium as mentioned in the lecture.
The crystal structure in bulk structure is as follows:
Cr-Slab
B LATTICE,NONEQUIV.ATOMS: 1 229_Im-3m
MODE OF CALC=RELA unit=ang
5.461311 5.461311 5.461311 90.000000 90.000000 90.000000
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
MULT= 1 ISPLIT= 2
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
48 NUMBER OF SYMMETRY OPERATIONS
To create the slab structure from the previous structure we take the example of the 001 plane.
We make supercell 1x1x3 P with vaccum of 15 bohr in z direction
Filename of original struct file:
Number of cells in x direction:
Number of cells in y direction:
Number of cells in z direction: 3
Optional shift of all atoms (fractional coordinates)
in x direction:
in y direction:
in z direction:
Enter your target lattice type: P
(Some choices are restricted by symmetry)
For surfaces or isolated molecules: (for P lattice only)
Vacuum in x-direction [bohr]:
Repeat atoms at x=0:
Vacuum in y-direction [bohr]:
Repeat atoms at y=0: Vacuum in z-direction [bohr]: 15
Repeat atoms at z=0:Y
you will get the following structure
Cr-Slab
P LATTICE,NONEQUIV. ATOMS 7
MODE OF CALC=RELA unit=ang
5.461311 5.461311 31.383933 90.000000 90.000000 90.000000
ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 2: X=0.00000000 Y=0.00000000 Z=0.17401614
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 3: X=0.00000000 Y=0.00000000 Z=0.34803229
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 4: X=0.00000000 Y=0.00000000 Z=0.52204843
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 5: X=0.50000000 Y=0.50000000 Z=0.08700807
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 6: X=0.50000000 Y=0.50000000 Z=0.26102422
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 7: X=0.50000000 Y=0.50000000 Z=0.43504036
MULT= 1 ISPLIT= 8
Cr NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
0 NUMBER OF SYMMETRY OPERATIONS
If we run sgroup we will get the following structure
Cr-Slab
P LATTICE,NONEQUIV.ATOMS: 4 123 P4/mmm
MODE OF CALC=RELA unit=ang
5.461311 5.461311 31.383933 90.000000 90.000000 90.000000
ATOM 1: X=0.50000000 Y=0.50000000 Z=0.23897578
MULT= 2 ISPLIT= 8
1: X=0.50000000 Y=0.50000000 Z=0.76102422
Cr1 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 2: X=0.50000000 Y=0.50000000 Z=0.58700807
MULT= 2 ISPLIT= 8
2: X=0.50000000 Y=0.50000000 Z=0.41299193
Cr2 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 3: X=0.00000000 Y=0.00000000 Z=0.32598385
MULT= 2 ISPLIT= 8
3: X=0.00000000 Y=0.00000000 Z=0.67401615
Cr3 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM 4: X=0.00000000 Y=0.00000000 Z=0.50000000
MULT= 1 ISPLIT= 8
Cr4 NPT= 781 R0=0.00005000 RMT= 2.3500 Z: 24.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
16 NUMBER OF SYMMETRY OPERATIONS
You can see more information for another compound on this video
Good Luck
2 Comments
This is truly a great read for me. I have bookmarked it and I am looking forward to reading new articles. Keep up the good work!. patronato genova
ReplyDeleteGood luck
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