MoS2 nanotubes

[kalewu]

Dear Sir,

Now I am using the ATK 12.8.2. I want to build MoS2 nanotube, And I follow the instructions (http://www.quantumwise.com/publications/tutorials/builder/177-mos2-nanotubes). However, I can not get the MoS2 tube.

I just check my results and find that everything is good until I opened "Bulk Tools>Lattice Parameters" and selected "Cartesian" coordinates (9th step). I just find the lattice parameters in my model is different from the ones shown in the video(http://www.youtube.com/watch?v=t2_nlrW3_Qk&feature=youtu.be).

What is wrong?

Thanks in advance.

[zh]

It is quite obvious that you may make wrong action or setup in the construction of orthorhombic supercell of MoS2 monolayer from a hexagonal unit cell. Please check the part at 2.22/5.24 of that video carefully.

[kalewu]

Thanks for your reply. I am sure that I just follow the instructions and video as Nanna did. What I used is the ATK 12.8.2, while Video used the ATK 12.2. Maybe it is caused by the different version?

[zh]

Yes, it is caused by different version. In the ATK12.8.2, several parameters should be adjusted because the two primitive unit vectors in xy planes of hexagonal MoS2 are taken along the lines with an angle of +/-60 degree with respect to the X axis.

In the supercell conversion from a hexagonal primitive unit cell to an  orthorhombic supercell:
      A  B  C
A': 1   1   0
B': 1  -1   0
C'  0   0   1

In the step of repeating orthorhombic supercell, the repetition number is chosen along at the A direction with "A=20".

Additional step is needed: "Swap Axes". You may try the options  in both  the  "swap the unit cell axes" and "swap the coordinate system axes" so that the lattice parameters is the same with those shown in the video.

[Anders Blom]

Thanks for raising the issue, and thanks ZH for providing the details. To be slightly more correct, the transformation is better made as

Code

     A  B  C
A':  1  1  0
B': -1  1  0
C'   0  0  1

to avoid making a left-handed cell. We'll look into fixing the tutorial to clarify things. It can be noted that the "A'=2A+B" version also gives an orthorhomic cell, just not aligned along the xyz axes. Another way to align the cell is therefore to use the original transformation and then go to Lattice Parameters and select "SimpleOrthorhomic" as the lattice (with "Keep Fractional coordinates"). Also, whether or not to repeat along A or B, and how to swap the axes, depends on whether you are making an armchair or zigzag tube.

[kalewu]

Yes, it is caused by different version. In the ATK12.8.2, several parameters should be adjusted because the two primitive unit vectors in xy planes of hexagonal MoS2 are taken along the lines with an angle of +/-60 degree with respect to the X axis.

In the supercell conversion from a hexagonal primitive unit cell to an  orthorhombic supercell:
      A  B  C
A': 1   1   0
B': 1  -1   0
C'  0   0   1

In the step of repeating orthorhombic supercell, the repetition number is chosen along at the A direction with "A=20".

Additional step is needed: "Swap Axes". You may try the options  in both  the  "swap the unit cell axes" and "swap the coordinate system axes" so that the lattice parameters is the same with those shown in the video.

Thank you very much.

[kalewu]

Thanks for raising the issue, and thanks ZH for providing the details. To be slightly more correct, the transformation is better made as

Code

     A  B  C
A':  1  1  0
B': -1  1  0
C'   0  0  1

to avoid making a left-handed cell. We'll look into fixing the tutorial to clarify things. It can be noted that the "A'=2A+B" version also gives an orthorhomic cell, just not aligned along the xyz axes. Another way to align the cell is therefore to use the original transformation and then go to Lattice Parameters and select "SimpleOrthorhomic" as the lattice (with "Keep Fractional coordinates"). Also, whether or not to repeat along A or B, and how to swap the axes, depends on whether you are making an armchair or zigzag tube.

Thanks