fix phonon for graphene

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Dear Prof.Kong
How are you. Great appreciation to you for providing us codes freely.

As I calculated the dispersion of graphene(qusi-2D), the command fix phonon in 
lammps cannot work. But it is work for  supercell of bulk silicon(3D)

The stucture of graphene supercell consist of 192 atoms with a 1.4nm thick 
vacuum layer.This supercell is obtained by expanding the unit cell of 4 atoms 
by 6*8*1,in which "1" denotes the thickness direction. 3D periodical boundary 
conditions are applied in MD by lammps. AIREBO potential is used to describe 
the interation in graphene.

The map file for dispersion calculation is produced by the code 'latgen',in 
which the lattice type option "7" is used. I already check the atom 
coordination and the atom ID by latgen to make sure that they are the same to 
those used in lammps. 

However, the command fix phonon cannot work, exits with error message: mpirun 
noticed that process rank 1 with PID 16586 on node mez508.ust.hk exited on 
signal 11 (Segmentation fault).

Do you have comments and sugesstions? Attached please find the input files (in 
file and structure file) of lammps and map file by latgen for your test.

Best regards

Youdi

Original issue reported on code.google.com by kuangzha...@gmail.com on 7 Jan 2014 at 4:49

Attachments:

• grapbre192.lammps05
• grapbre.in
• map.in

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I noticed your report, but I am pretty busy recently. Will probably get back to 
you within two weeks. thanks.

Original comment by kon...@gmail.com on 8 Jan 2014 at 7:23

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It is fine. Many thanks for your endeavour.

Original comment by kuangzha...@gmail.com on 8 Jan 2014 at 7:33

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Dear Prof.Kong
Very sorry. We just find that the fix phonon cannot work well just because
our server has some problems.
This comand still works well for graphene.

Original comment by kuangzha...@gmail.com on 8 Jan 2014 at 8:45

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very good.

Original comment by kon...@gmail.com on 8 Jan 2014 at 11:48

• Changed state: Done

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Dear Prof.Kong
I just use the input files above to calculate the dispersion curve of graphene 
but i got such a graph,can you help me?

Original comment by 404422...@qq.com on 13 Jun 2014 at 3:37

Attachments:

• pdisp.eps
• disp.dat
• gra.bin.300001
• in.disp
• plot.dis

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And I tried  to calculate the curve of a 2d squre lattice ,and compare the 
result with the book Solid State Theory by Zhengzhong Li. I'll be glad to see 
it be modified and become  an example of FixPhonon,thank you ! 

Original comment by 404422...@qq.com on 13 Jun 2014 at 3:43

Attachments:

• 2D-squre.rar