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I'm doing geometry optimization of bilayer h-BN, a 72-atom supercell (6x6x1) with vacuum thickness of 20 Å, and I set the parameters in INCAR as below:

ISTART = 0 #begin from scratch\
ICHARG = 2 #initial charge density\
LREAL = Auto\
ISMEAR = 0\
SIGMA = 0.02\
ENCUT = 400\
PREC = Normal\
ISIF = 3 #change of cell\
ISPIN = 1 #spin\
NSW = 500 #maximun ion step\
IBRION = 2 #conjugate gradient algorithm\
POTIM = 0.5  #step size of ion\
EDIFF = 1E-6 #standard of electronic convergence\
EDIFFG = -0.01 #standard of ion step convergence\
IVDW = 12 #vdw_D3\
LWAVE = .FALSE.\
LCHARG = .FALSE.\
ALGO = Fast

But interestingly, the vacuum layer disappeared, why it comes like that? And how should I maintain the vacuum layer during relaxing?

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    $\begingroup$ When you say 'disappeared', what do you exactly mean? as you are using ISIF=3 the cell shape will be relaxed for sure in all directions including where you have added the vacuum level, usually it will change slightly but not to totally vanish! However, there is a hack for avoiding the relaxation in certain directions, you can refer to the first answer of similar question I had before mattermodeling.stackexchange.com/q/12043/1554 $\endgroup$ Jan 22 at 10:23
  • $\begingroup$ This is due to the full structure relaxation option (ISIF=3). I’ve observed similar situations with 2D slabs with vacuum. The answer to your question has been already posted (mattermodeling.stackexchange.com/questions/11878): Situations where ISIF=3 is NOT acceptable: • Calculations with vacuum (slabs or molecules). This is the most important one. Especially in slab calculations, allowing the cell volume to change will almost always result in your vacuum being reduced to zero (cell becomes periodic). $\endgroup$
    – Victor
    Apr 3 at 14:16

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