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How to apply periodic boundary conditions
Date: 2019/01/17 18:23
Name: sanjeev

I am new to openmx. I am trying to reproduse some papers on graphene published by "openmx".
I want to know how to apply periodic boundary conditions in different direction, which keywords will control this.

Now suppose in a paper published by Lou &Lee, (J. phys.chem, c, 2009,113, 21213). He stated that "we adopted a supercell
geometry where the length of a vacuum region along the nonperiodic direction (y- direction) was 20 A, and the lattice constant along the
periodic direction (x direction) wa 3.11 A.

I can control the dimension of the supercell by the keywords like given below.

<Atoms.UnitVectors
0.000 0.000 4.88
20.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>


But how can we say that our calculations have periodicity in x direction.

thanking in advance

sanjeev
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Re: How to apply periodic boundary conditions ( No.1 )
Date: 2019/01/18 01:25
Name: Naoya Yamaguchi

Hi,

OpenMX always considers periodic boundary conditions along a-, b-, and c-axes except some methods, such as NEGF and ESM. For example, slab calculations are usually performed by inserting a vacuum region with an enough width to remove influence of image cells through "Atoms.UnitVectors" as you said.

Regards,
Naoya Yamaguchi
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Re: How to apply periodic boundary conditions ( No.2 )
Date: 2019/01/18 13:53
Name: sanjeev


Dear Yamaguchi,

Thank you very much for your reply. But still my doubt is not clear.
In the above mentioned paper the author has mentioned that he made Y & Z directions nonperiodic.
My question is that, How he made Y & Z nonperiodic and X as periodic. while, openmx consider all x,y,z
directions as periodic.

Now suppose I want to simulate graphene fragments with a supercell dimensions
x= 10, y=50, z=50, for this I set.


<Atoms.UnitVectors
10.000 0.000 0.000
0.000 50.000 0.000
0.000 0.000 50.000
Atoms.UnitVectors>

it means I have created a vacuum in Y & Z directions, but how it mean that my calculations is periodic in x direction only.

It is right if I say that my calculations are periodic in all x,y,z directions

Thanking in advance.

Sanjeev




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Re: How to apply periodic boundary conditions ( No.3 )
Date: 2019/01/19 02:01
Name: Naoya Yamaguchi

Dear Sanjeev,

>My question is that, How he made Y & Z nonperiodic and X as periodic. while, openmx consider all x,y,z
>directions as periodic.

Now I read the paper and I guess that they did band calculations using OpenMX 3.4 (or 3.5) and inserted a vacuum region, for example:
Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
3.11 0.0 0.0
0.0 L 0.0
0.0 0.0 L
Atoms.UnitVectors>
, where L>20.

>Now suppose I want to simulate graphene fragments with a supercell dimensions
>x= 10, y=50, z=50, for this I set.

I think it is right for calculations of one-dimensional materials such as nanoribbons.

Regards,
Naoya Yamaguchi
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Re: How to apply periodic boundary conditions ( No.4 )
Date: 2019/02/08 23:03
Name: Kylin  <Kylincaster@foxmail.com>

Dear all,
The periodicity in OpenMX calculation is automatically determined and straightforwardly shown in the screen log files as "The system is molecule|chain|slab|bulk" will be displayed as in the screen log file, representing 0D|1D|2D and 3D system respectively. So be careful to check periodicity in our calculation which was determined by PAOs cut-off (Rc) and dimensions of box sizes. It becomes non-periodic only with 2Rc > box_size.

Moreover, the calculation of Uele was based on FFT which is only valid for 3D periodicity box which may induce some problems with the low dimensional material studies. So a large interlayer vacuum spacing is necessary or taking the effective screening medium (ESM) method


Cheers,

Kylin



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