[Wien] [SPAM?] Re: [SPAM?] Re: Regarding supercell
Riyajul Islam
riyajul80 at gmail.com
Thu Jul 12 15:10:52 CEST 2018
On 12 July 2018 at 18:40, Riyajul Islam <riyajul80 at gmail.com> wrote:
> On 12 July 2018 at 18:39, Riyajul Islam <riyajul80 at gmail.com> wrote:
>> On 12 July 2018 at 18:36, Riyajul Islam <riyajul80 at gmail.com> wrote:
>>> These are the structure files. I'm still having the same problem in symmetry.
>>>
>>> On 12 July 2018 at 07:01, Gavin Abo <gsabo at crimson.ua.edu> wrote:
>>>> The FAQ page [
>>>> http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html ] says you
>>>> can also use special labels.
>>>>
>>>> Probably, if you set all equivalent atoms as nonequivalent atoms in
>>>> StructGen using the special labels it will keep the 2x2x2 supercell that you
>>>> see in XCrySDen. However, more nonequivalent atoms should increase
>>>> computation time. So you may want to use less special labels if possible to
>>>> reduce the cells as much as possible during initialization (with the help of
>>>> x nn, x sgroup, and x symmetry).
>>>>
>>>> On 7/11/2018 7:35 AM, Riyajul Islam wrote:
>>>>
>>>> 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
>>>>
>>>>
>>>> _______________________________________________
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