6
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Can anyone please help me transform $\ce{LiCoO2}$ hexagonal cell ($a \times a \times c$) to orthorhombic cell ($a \times a \sqrt{3} \times 1$) and hexagonal cell ($a \sqrt{3} \times a \sqrt{3}\times 1$)?Image of cell transformations from a hexagonal a x a x c cell

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9
  • 1
    $\begingroup$ Have you tried Edit -> Edit Data -> Unit cell option? From there you can change the unit cell as far as I know. $\endgroup$
    – PBH
    Dec 15, 2021 at 5:19
  • $\begingroup$ Thank you. I found transform function. But when I entered the transform matrix, it show something strange. I would appreciate if you can show me how to determine transformation matrix. $\endgroup$
    – Binh Thien
    Dec 15, 2021 at 6:06
  • 1
    $\begingroup$ Is this the required orthorhombic result? $\endgroup$
    – PBH
    Dec 15, 2021 at 15:14
  • 1
    $\begingroup$ I can do using two ways 1. In OVITO replicate in different direction and cut the periodic unit in orthogonal box. Method two simple using software called atomsk, just type this command "atomsk POSCAR1 -orthogonal-cell vasp" $\endgroup$ Dec 15, 2021 at 18:56
  • 2
    $\begingroup$ Replicate in Ovito and affine-transform only simulation box as required ,keep atoms inside new cell and delete rest, make sure not to include periodic atoms. You can talk this conversation in vasp chat group, chat.stackexchange.com/rooms/109983/vasp $\endgroup$ Dec 16, 2021 at 18:47

1 Answer 1

4
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structure 1
enter image description here
Method affine transformation of simulation box after replicating in X and Y in ovito enter image description here

OUTPUT: POSCAR

POSCAR file written by OVITO
1.0
        2.8428978920         0.0000000000         0.0000000000
        0.0000000000         4.9240398407         0.0000000000
        0.0000000000         0.0000000000        14.1456146240
   Li   Co    O
    6    6   12
Direct
     0.000000000         0.000000000         0.000000000
     0.500000461         0.166666663         0.333332985
     0.000000000         0.333333809         0.666666981
    -0.000000000         0.666667086         0.333332985
     0.499999958         0.500000436         0.000000000
     0.499999455         0.833334173         0.666666981
     0.000000000         0.333333809         0.166666998
    -0.000000000        -0.000000000         0.500000000
     0.500000461         0.166666663         0.833333019
     0.000000000         0.666667086         0.833333019
     0.499999455         0.833334173         0.166666998
     0.499999958         0.500000436         0.500000000
    -0.000000000        -0.000000000         0.239586996
     0.500000461         0.166666663         0.093745997
     0.500000461         0.166666663         0.572920049
    -0.000000000         0.333333809         0.427080019
    -0.000000000         0.333333809         0.906254011
    -0.000000000        -0.000000000         0.760412970
     0.000000000         0.666667086         0.093745997
    -0.000000000         0.666667086         0.572920049
     0.499999958         0.500000436         0.239586996
     0.499999455         0.833334173         0.427080019
     0.499999455         0.833334173         0.906254011
     0.499999958         0.500000436         0.760412970

structure2 enter image description here
Method affine transformation of simulation box after replicating in X and Y in ovito
enter image description here

OUTPUT: POSCAR

POSCAR file written by OVITO
1.0
        4.9240450859         0.0000000000         0.0000000000
        2.4620173651         4.2643450666         0.0000000000
        0.0000000000         0.0000000000        14.1456146240
   Li   Co    O
    9    9   18
Direct
     0.000000000         0.000000000         0.000000000
     0.333333430        -0.000000000         0.333332985
    -0.000000007         0.333333975         0.666666981
    -0.000000018         0.666666944         0.333332985
     0.666665892        -0.000000000         0.666666981
     0.333333114         0.333333891         0.000000000
     0.666666524         0.333333835         0.333332985
     0.333332722         0.666667838         0.666666981
     0.666666229         0.666667782         0.000000000
    -0.000000007         0.333333975         0.166666998
    -0.000000000        -0.000000000         0.500000000
     0.333333430        -0.000000000         0.833333019
    -0.000000018         0.666666944         0.833333019
     0.666665892        -0.000000000         0.166666998
     0.333332722         0.666667838         0.166666998
     0.333333114         0.333333891         0.500000000
     0.666666524         0.333333835         0.833333019
     0.666666229         0.666667782         0.500000000
     0.000000000        -0.000000000         0.239586996
     0.333333430        -0.000000000         0.093745997
     0.333333430        -0.000000000         0.572920049
    -0.000000007         0.333333975         0.427080019
    -0.000000007         0.333333975         0.906254011
    -0.000000000         0.000000000         0.760412970
    -0.000000018         0.666666944         0.093745997
    -0.000000018         0.666666944         0.572920049
     0.666665892        -0.000000000         0.427080019
     0.666665892        -0.000000000         0.906254011
     0.333333114         0.333333891         0.239586996
     0.666666524         0.333333835         0.093745997
     0.666666524         0.333333835         0.572920049
     0.333332722         0.666667838         0.427080019
     0.333332722         0.666667838         0.906254011
     0.333333114         0.333333891         0.760412970
     0.666666229         0.666667782         0.239586996
     0.666666229         0.666667782         0.760412970

Load POSCAR > show periodic image > affine transformation > manual selection > delete selected atoms >export as POSCAR

NOTE: During delete of extra atom outside simulation box don't include periodically equivalent atoms in boundaries

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4
  • $\begingroup$ Is it Ovito pro version? $\endgroup$
    – Binh Thien
    Dec 21, 2021 at 15:36
  • $\begingroup$ I am using old linux version 2.9 . $\endgroup$ Dec 21, 2021 at 17:21
  • $\begingroup$ I just downloaded version 3.6 on my macbook and I could not find periodic image and manual selection $\endgroup$
    – Binh Thien
    Dec 22, 2021 at 0:40
  • $\begingroup$ check option replicate $\endgroup$ Dec 24, 2021 at 14:26

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