[Wien] [SPAM?] Re: [SPAM?] Re: Regarding supercell
Gavin Abo
gsabo at crimson.ua.edu
Thu Jul 12 03:31:10 CEST 2018
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
> <mailto: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 <mailto: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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