[Wien] [SPAM?] Re: [SPAM?] Re: Regarding supercell
Riyajul Islam
riyajul80 at gmail.com
Thu Jul 12 15:09:23 CEST 2018
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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