[Wien] [SPAM?] Re: [SPAM?] Re: Regarding supercell
Riyajul Islam
riyajul80 at gmail.com
Thu Jul 12 15:13:14 CEST 2018
When I run x symmetry I get the same error as I mentioned earlier.
On 12 July 2018 at 18:42, Riyajul Islam <riyajul80 at gmail.com> wrote:
> On 12 July 2018 at 18:40, Riyajul Islam <riyajul80 at gmail.com> wrote:
>> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Wien mailing list
>>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>> SEARCH the MAILING-LIST at:
>>>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>>>>
More information about the Wien
mailing list