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Dear commuitors

I've been tried to calculate graphene with adsorbate

molecules. During the calculation, i have a questions about

difference between initial strcuture and relaxed structure of

graphene.

I obtained very different relaxed graphene structure as

compared to initial structure when i checked with viewer

program.

Is it wrong?? or right??

The cartesian coordinates of initial and relaxed structure are

following as

The unitcell vetor is

1.00000000000000
8.521686509137260 -4.919998000000000 0.0000000000000000
0.000000000000000 9.8399960000000000 0.0000000000000000
0.000000000000000 0.0000000000000000 27.2389000000000000


initial structure

C 2.15130000 1.21870000 6.55800000
C 8.54260000 -2.47130000 6.55800000
C 8.54260000 4.90870000 6.55800000
C 7.83240000 6.13870000 6.55800000
C 1.44120000 9.82870000 6.55800000
C 1.44120000 2.44870000 6.55800000
C 3.57160000 1.21870000 6.55800000
C 7.83240000 -1.24130000 6.55800000
C 7.83240000 3.67870000 6.55800000
C 6.41210000 6.13870000 6.55800000
C 2.15130000 8.59870000 6.55800000
C 2.15130000 3.67870000 6.55800000
C 4.28170000 -0.01130000 6.55800000
C 8.54260000 -0.01130000 6.55800000
C 6.41210000 3.67870000 6.55800000
C 5.70200000 7.36870000 6.55800000
C 1.44120000 7.36870000 6.55800000
C 3.57160000 3.67870000 6.55800000
C 1.44120000 4.90870000 6.55800000
C 3.57160000 8.59870000 6.55800000
C 5.70200000 4.90870000 6.55800000
C 8.54260000 2.44870000 6.55800000
C 6.41210000 -1.24130000 6.55800000
C 4.28170000 2.44870000 6.55800000
C 5.70200000 -0.01130000 6.55800000
C 7.83240000 1.21870000 6.55800000
C 5.70200000 2.44870000 6.55800000
C 4.28170000 7.36870000 6.55800000
C 2.15130000 6.13870000 6.55800000
C 4.28170000 4.90870000 6.55800000
C 6.41210000 1.21870000 6.55800000
C 3.57160000 6.13870000 6.55800000

optimized structure

C 2.15130 1.21870 6.55800
C 0.02091 2.44870 6.55800
C 0.02091 -0.01130 6.55800
C 7.83240 -3.70130 6.55800
C 1.44120 -0.01130 6.55800
C 1.44120 2.44870 6.55800
C 3.57160 1.21870 6.55800
C 7.83240 -1.24130 6.55800
C 7.83240 3.67870 6.55800
C 6.41210 -3.70130 6.55800
C 2.15130 -1.24130 6.55800
C 2.15130 3.67870 6.55800
C 4.28170 -0.01130 6.55800
C 0.02091 4.90870 6.55800
C 6.41210 3.67870 6.55800
C 5.70200 -2.47130 6.55800
C 1.44120 7.36870 6.55800
C 3.57160 3.67870 6.55800
C 1.44120 4.90870 6.55800
C 3.57160 -1.24130 6.55800
C 5.70200 4.90870 6.55800
C 0.02091 7.36870 6.55800
C 6.41210 -1.24130 6.55800
C 4.28170 2.44870 6.55800
C 5.70200 -0.01130 6.55800
C 7.83240 1.21870 6.55800
C 5.70200 2.44870 6.55800
C 4.28170 -2.47130 6.55800
C 2.15130 6.13870 6.55800
C 4.28170 4.90870 6.55800
C 6.41210 1.21870 6.55800
C 3.57160 6.13870 6.55800

All carbon atoms were relaxed

I need you guys help. please help me to understand

e.g. atoms 2 and 3 crossed the (virtual) cell boundary, that's why it looks weird to you.

Cheers,

alex

alex// you mean that is there no problem??

alex// you mean that is there no problem??

Yes, exactly. Example:
atom # 2, x=8.54, the lattice vector a = 8.52. So your x is translational symmetric to the new x'=0.02, which is in the first unit cell ...

Cheers,

alex

Thank you for your helping!! your comment is very helpful to me Thank you!

best wishes

Sunwoo Kang