[Wien] [SPAM?] Re: Regarding supercell
Riyajul Islam
riyajul80 at gmail.com
Wed Jul 11 15:35:41 CEST 2018
At first I made a supercell of MnFe2O4 and then I replaced Mn with Ca and
changed Z.
On Wed, 11 Jul 2018, 7:03 pm Laurence Marks, <L-marks at northwestern.edu>
wrote:
> 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
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>>
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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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