[Wien] [SPAM?] Re: Regarding supercell
Laurence Marks
L-marks at northwestern.edu
Wed Jul 11 15:32:59 CEST 2018
As the supercell program tells you when you run it, you have to displace an
atom or change it's name to prevent the cell being reduced back.
On Wed, Jul 11, 2018 at 8:21 AM, Riyajul Islam <riyajul80 at gmail.com> wrote:
> Dear Wien2k users,
> I want create a 2x2x2 supercell of an orthorombic structure.
> Aftercreating the supercell I copied case_super.struct to case.struct
> the ran x nn wich gave me another structure and copied it to the
> case.struct file. But when I ran x sgroup it gave me a spacegroup
> 51_Pmma. If I accept the structure created by x sgroup the supercell
> reduces to 1x1x1, but if I don't accept it then I get an error in x
> symmetry
>
> GLSYM: THE CRYSTAL SYSTEM IS CUBIC
> PGLSYM: ORDER OF LATTICE POINT GROUP (NO BASE) = 48
> PGBSYM: ORDER OF LATTICE SPACE GROUP (WITH BASE) = 8
> PGBSYM: NON-SYMMORPHIC SPACE GROUP OR NON-STANDARD ORIGIN OF COORDINATES
> PGBSYM: SPACE GROUP CONTAINS INVERSION
> SPACE GROUP CONTAINS INVERSION
> BUT ATOMS SHOULD BE SHIFTED BY -0.25000000 -0.25000000
> -0.25000000
> BUT ATOMS SHOULD BE SHIFTED BY -0.25000000 -0.25000000
> -0.25000000
> number of atoms: 448
>
> ATOM: -1
> Ca1 operation # 1 1
> Ca1 operation # 5 2 || z
> Ca1 operation # 12 m n 110
> Ca1 operation # 13 m n -110
> pointgroup is mm2 (neg. iatnr!!)
> axes should be: 2 || z, m n y
> z-rotation vector: 0.0000 0.0000 1.0000
> y-rotation vector: 1.0000 1.0000 0.0000 2
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.7071068 0.7071068 0.0000000 1.0000000 0.0000000 0.0000000
> -0.7071068 0.7071068 0.0000000 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6
> 2 6 4 6 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 1 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 8 ISYM: 4 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -2
> Mn2 operation # 1 1
> Mn2 operation # 5 2 || z
> Mn2 operation # 12 m n 110
> Mn2 operation # 13 m n -110
> pointgroup is mm2 (neg. iatnr!!)
> axes should be: 2 || z, m n y
> z-rotation vector: 0.0000 0.0000 1.0000
> y-rotation vector: 1.0000 1.0000 0.0000 2
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.7071068 0.7071068 0.0000000 1.0000000 0.0000000 0.0000000
> -0.7071068 0.7071068 0.0000000 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6
> 2 6 4 6 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 2 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 8 ISYM: 4 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -3
> Fe3 operation # 1 1
> Fe3 operation # 2 -1
> Fe3 operation # 13 m n -110
> Fe3 operation # 19 2 || -110
> pointgroup is 2/m (neg. iatnr!!)
> axes should be: 2 || z, m n z
> z-rotation vector: -1.0000 1.0000 0.0000
> y-rotation vector: 0.7071 -0.7071 0.0000 0
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.0000000-0.7071068-0.7071068 1.0000000 0.0000000 0.0000000
> 0.0000000-0.7071068 0.7071068 0.0000000 1.0000000 0.0000000
> -1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 2 0 2 2 -2 2 4 0 4 2 -4 2 4 4 -4 4 6 0 6 2 -6 2 6 4 -6
> 4 6 6 -6 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 3 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 8 ISYM: 4 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -4
> Fe4 operation # 1 1
> Fe4 operation # 12 m n 110
> pointgroup is m (neg. iatnr!!)
> axes should be: m n z
> z-rotation vector: 1.0000 1.0000 0.0000
> y-rotation vector: 0.0000 0.0000 -1.0000 0
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.0000000 0.7071068 0.7071068 1.0000000 0.0000000 0.0000000
> 0.0000000-0.7071068 0.7071068 0.0000000 1.0000000 0.0000000
> 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4
> 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6
> 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 4 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 16 ISYM: 2 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -5
> Fe5 operation # 1 1
> Fe5 operation # 2 -1
> Fe5 operation # 13 m n -110
> Fe5 operation # 19 2 || -110
> pointgroup is 2/m (neg. iatnr!!)
> axes should be: 2 || z, m n z
> z-rotation vector: -1.0000 1.0000 0.0000
> y-rotation vector: 0.0000 0.0000 1.0000 0
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.0000000-0.7071068-0.7071068 1.0000000 0.0000000 0.0000000
> 0.0000000-0.7071068 0.7071068 0.0000000 1.0000000 0.0000000
> -1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 2 0 2 2 -2 2 4 0 4 2 -4 2 4 4 -4 4 6 0 6 2 -6 2 6 4 -6
> 4 6 6 -6 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 5 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 8 ISYM: 4 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -6
> O 6 operation # 1 1
> O 6 operation # 13 m n -110
> pointgroup is m (neg. iatnr!!)
> axes should be: m n z
> z-rotation vector: -1.0000 1.0000 0.0000
> y-rotation vector: 0.0000 0.0000 -1.0000 0
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.0000000-0.7071068-0.7071068 1.0000000 0.0000000 0.0000000
> 0.0000000-0.7071068 0.7071068 0.0000000 1.0000000 0.0000000
> -1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4
> 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6
> 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 6 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 16 ISYM: 2 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -7
> O 7 operation # 1 1
> O 7 operation # 12 m n 110
> pointgroup is m (neg. iatnr!!)
> axes should be: m n z
> z-rotation vector: 1.0000 1.0000 0.0000
> y-rotation vector: 0.0000 0.0000 -1.0000 0
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.0000000 0.7071068 0.7071068 1.0000000 0.0000000 0.0000000
> 0.0000000-0.7071068 0.7071068 0.0000000 1.0000000 0.0000000
> 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4
> 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6
> 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 7 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 16 ISYM: 2 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -8
> O 8 operation # 1 1
> O 8 operation # 12 m n 110
> pointgroup is m (neg. iatnr!!)
> axes should be: m n z
> z-rotation vector: 1.0000 1.0000 0.0000
> y-rotation vector: 0.0000 0.0000 1.0000 0
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.0000000 0.7071068 0.7071068 1.0000000 0.0000000 0.0000000
> 0.0000000-0.7071068 0.7071068 0.0000000 1.0000000 0.0000000
> 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4
> 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6
> 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 8 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 16 ISYM: 2 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
>
> ATOM: -9
> O 9 operation # 1 1
> O 9 operation # 13 m n -110
> pointgroup is m (neg. iatnr!!)
> axes should be: m n z
> z-rotation vector: -1.0000 1.0000 0.0000
> y-rotation vector: 0.0000 0.0000 1.0000 0
> WARNING: LOCAL ROTATION MATRIX CHANGED
> LOCAL ROT MATRIX: NEW OLD
> 0.0000000-0.7071068-0.7071068 1.0000000 0.0000000 0.0000000
> 0.0000000-0.7071068 0.7071068 0.0000000 1.0000000 0.0000000
> -1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000
> lm: 0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4
> 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6
> 6
> ==============================================
> ---------- ERROR ------------------
> ERROR: (multiplicity of atom 9 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT: 16 ISYM: 2 NSYM 8
> ERROR: Check your struct file with x sgroup
> ---------- ERROR ------------------
> 0.006u 0.003s 0:00.01 0.0% 0+0k 0+136io 0pf+0w
>
> Also I have worked on the same structure by creating 1x1x1 supercell
> which ran quiet well. Kindly help me solve this problem
>
> Thanking you,
> Riyajul Islam
> _______________________________________________
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--
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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