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Crystal structure with a molecule
Date: 2022/08/25 04:40
Name: ELIE ALBERT   <>

Dear all,

I am trying to study the energetics of a molecule on top of a boron nitride monolayer. What is the best way to simulate this structure in OPENMX?

Do we run a "Cluster" calculation or the consider the whole system periodic, and thus run the usual "Band" calculation?

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Re: Crystal structure with a molecule ( No.1 )
Date: 2022/08/25 16:21
Name: T. Ozaki


You can model your system by a slab model which consists of a slab of boron nitride monolayer with
the in-plane periodicy and a molecule placed on the monolayer. Of course you need to insert the vaccum
in between the copied slabs to avoid the interaction between the slabs.
If the in-plane unit cell vectors are long enough, you can perform the gamma point calculation.
In this case, even if you set "Band", OpenMX automatically reset from "Band" to "Cluster" for the eigenvalue solver
by taking account of the computational efficiency, while keeping the periodicity.
Note that only the operations by real variables are performed in the "Cluster" solver, leading to the efficient calculation.


Re: Crystal structure with a molecule ( No.2 )
Date: 2022/08/25 21:05

Dear Prof. Ozaki,

Thank you for the valuable information. When "Band"is automatically reset to "Cluster", would I still be able to compute the whole band structure and DOS of the system?

Re: Crystal structure with a molecule ( No.3 )
Date: 2022/08/25 23:21
Name: T. Ozaki


The k-points and k-paths can be independently set for DOS and band structure calculations, respectively.
So, one can calculate the band structure and DOS of the system even using the "Cluster" solver.
However, you need to be sure that the bands are almost dispersionless when the "Cluster" solver is employed
for the periodic system. That's why we need to take a large super cell in order to guarantee the dispersionless.


Re: Crystal structure with a molecule ( No.4 )
Date: 2022/08/26 03:30

Dear prof. Ozaki,

Once again, thanks for the clarification

A final question though: how do you determine the in-plane lattice unit vectors of the system crystal+ molecule?

I formed the molecule from an XYZ file and when I have changed it to an OPENMX format, the code automatically assigned an 18A distance along the three directions. Here I can just use the gamma point.

However, I am inclined to use the same lattice vectors of the orthogonal boron nitride structure for the combined system: BN + molecule (and thus a larger k-grid must be used). My goal is to check what new states appear, when you include the molecule compared to the BN monolayer on its own.
Re: Crystal structure with a molecule ( No.5 )
Date: 2022/08/26 03:41

Just a quick update,

Actually, when I use the same lattice vectors of BN to the system BN + molecule, the molecule part seems strange, as if part of it was detached..Probably the best solution is use large in-plane lattice vectors.

Re: Crystal structure with a molecule ( No.6 )
Date: 2022/08/26 12:06
Name: T. Ozaki


This seems to be your very first trial for such a calculation.
The way you did leads to an improper structure having damgling bonds and/or breaking the periodicity.
Please try the following way.

Take a unit cell with orthogonal unit cell vectors such as


System.CurrrentDirectory ./ # default=./
System.Name hBN4
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

# Definition of Atomic Species

Species.Number 2
B B7.0-s2p2d1 B_PBE19
N N6.0-s2p2d1 N_PBE19

# Atoms

Atoms.Number 4
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
1 B 1.2522487 7.9528563 0.0000 1.5 1.5
2 N 2.5045013 7.2298680 0.0000 2.5 2.5
3 B 2.5044987 5.7838957 0.0000 1.5 1.5
4 N 1.2522513 5.0609074 0.0000 2.5 2.5
Atoms.UnitVectors.Unit Ang # Ang|AU
2.5045 0.0000000 0.000
0.0000 4.3379212 0.000
0.0000 0.0000000 15.0000


and drad and drop the dat file to the OpenMX Viewer.

(2) Secify "Supercell 10 x 6 x 1" which should be properly chosen depending on the size of your molecule.

(3) Save "OMX (xyz)". Then, you can get "abc.dat" which contains the supercell of hBN and the proper lattice vectors keeping the periodiciy.

(4) You can add the xyz coordinates of molecule by modifying "Atoms.SpeciesAndCoordinates" in the abc.dat.



Re: Crystal structure with a molecule ( No.7 )
Date: 2022/08/26 10:58

Dear professor Ozaki,

I really appreciate the time and effort to respond.

thanks for the valuable information. Will do as instructed


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