hcp (111)

[Johannes Panagiotopoulos]

Having the hcp with the the (111) along the  z-axis is somewhat limiting. For instance, cylindrical nanowires of hexagonal Co  grow with the c-axis along their length. It would take some flexibility in either the cylinder or the hcp commands...

[Muftah Al-Mahdawi]

For that you need to use the ucf file to define your custom crystal. Please refer to previous posts about ucf and the definition document sent by Evans in the mailing list.

On 2015年07月31日 23:18, Johannes Panagiotopoulos wrote:

Having the hcp with the the (111) along the  z-axis is somewhat limiting. For instance, cylindrical nanowires of hexagonal Co  grow with the c-axis along their length. It would take some flexibility in either the cylinder or the hcp commands...

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[Johannes Panagiotopoulos]

Dear Muftah thank you for your quick reply. 

I have prepared a file for hcp Cobalt with the c-axis along the z-direction but it seems that  the "Unit cell vectors" info is ignored and the output is as if it was just a unit matrix.

Has anyone else tried something similar?

This is what I use:

# Unit cell size:

2.5031 2.5031 4.0605

# Unit cell vectors: 

1.00 0.000 0.0 

-0.5 0.866 0.0 

0.00 0.000 1.0 

# Atoms num, id cx cy cz mat lc hc 

2

0 0.333333 0.666667 0.2500 0 0 0

1 0.666667 0.333333 0.7500 0 0 0

[Muftah Al-Mahdawi]

Dear Johannes,

I found that hexagonal unit vectors do not work as expected with ucf. First you need to generate a new  cubic unit cell with orthogonal vectors. You can do this with cif2cell tool (you can get the cif file from any crystallographic database). The transformation you need from hexagonal to cubic is (2x+y,2y,z). the command for this is
cif2cell orig.cif --no-reduce --supercell=[[2,1,0],[0,2,0],[0,0,1]] -p cif -o cubic.cif
Then you can use the new lattice constants and atom positions  from cubic.cif into ucf file with (1,0,0),(0,1,0),(0,0,1) unit vectors.
The difficulty comes with filling the interactions part of ucf file with the increased number of atoms. For a single species, this can be on a spreadsheet program. For more, you need more automation. Please refer to gen_nbrs_example.py script I sent before.

Dear Richard,
Sorry I did not report this before, because I did not follow it throughly. System generation from non-orthogonal unit cell (hexagonal or rhombohedral) does not work as expected. So we need to generate a cubic unit cell to make it work properly.

Best wishes,
Muftah

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Crossing-Correlation Spin Electronics Lab (Sahashi group).
Dept. of Electronic Engineering, Tohoku University.

Research Center for Rare Metal and Green Innovation (RaMGI),
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[richard....@gmail.com]

Dear Johannes, Muftah,

Yes - I apologize that non-orthogonal cells do not function correctly yet - I am working on fixing that part. However in general it would be better to enable an arbitrary particle or crystal orientation in the code with a single command, so I will take this as a feature request and will look at implementing that in the near future. 

All the best,

Richard

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[Muftah Al-Mahdawi]

Dear Richard,
It is my personal opinion, but as it is now, it works perfect enough. We can generate orthogonal cells easily with usually known transformations. I think it would be better to work on tutorials/scripts/codes that can generate the ucf file, and leave this part for the user. It might be difficult to catch up with all combinations of shapes and crystal systems.
Best wishes,
Muftah