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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 supercellgeometry 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.But how can we say that our calculations have periodicity in x direction. thanking in advancesanjeev
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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 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 dimensionsx= 10, y=50, z=50, for this I set.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 directionsThanking in advance.Sanjeev 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, 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 Re: How to apply periodic boundary conditions ( No.4 ) Date: 2019/02/08 23:03 Name: Kylin  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) methodCheers,Kylin

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