QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: Para_13 on January 19, 2011, 03:30

Title: Lattice surface structure
Post by: Para_13 on January 19, 2011, 03:30

I'm trying to create double bonds at the surface of the diamond lattice provided in the crystal cupboard. I thought it might be possible to drag and drop the template given in the crystal cupboard into the Molecular Builder but this is not the case. Is there any to do this?

Title: Re: Lattice surface structure
Post by: zh on January 19, 2011, 15:07

The bulk configuration cannot be manipulated by the "Molecular builder". The "Molecular builder" can manipulate a molecule configuration or  a sample imported from a xyz format file.

You can export the Cartesian coordinates of atoms of the surface cleaved from a bulk lattice and then manually write them into a file with XYZ format. After that, import this xyz file and use the "Molecular Builder" to create the double bonds.

Title: Re: Lattice surface structure
Post by: Para_13 on January 20, 2011, 08:12

Thanks, for the help :)

Also, is there a way to get this configuration with the double bonds at the surface from "Molecular Builder" to "Bulk Builder"?

Title: Re: Lattice surface structure
Post by: zh on January 21, 2011, 01:33

No. Once the atomic coordinates are obtained, one can manually build the bulk configuration with the original lattice constants.

Title: Re: Lattice surface structure
Post by: Para_13 on January 21, 2011, 03:44

Basically, I'm attempting to create a diamond bulk with the free carbon at the surface, double bonded to each other to create dimer rows and from that, calculate the work function. Is there no way to do this?

Title: Re: Lattice surface structure
Post by: zh on January 22, 2011, 07:34

Using VNL2008.10, I created a sample for the reconstructed C(001)(2x1) surface with a dimer in each topmost layer. The dimer was built by manually shifting atoms in the topmost layers.

Title: Re: Lattice surface structure
Post by: Para_13 on January 24, 2011, 03:19

Thanks. I think the dimer rows along the surface are only single bonded though. I have attached a lattice that I was hoping to use, but I am not sure how to create double bonds across the surface atoms. Is that possible?

       C======C
      /              \
    C                 C

Title: Re: Lattice surface structure
Post by: zh on January 24, 2011, 06:55

The so-called "single-bond" or "double-bond" are conceptual in chemistry, rather than the atomic coordination. For example, the N2 molecule is understood in chemistry to have triple bonds. The triple bonds in a N2 molecule do not mean that each N atom should be three-atom-coordinated.

Title: Re: Lattice surface structure
Post by: Para_13 on January 25, 2011, 05:03

Can you please elaborate on "manually shifting atoms"? I can shift them in "Bulk Builder" but that doesn't create a bond across the top layer. Is this achieved somewhere else?

Title: Re: Lattice surface structure
Post by: zh on January 25, 2011, 06:17

export the configuration into a script file, and then edit and adjust the atomic coordinates (x and y components) of the topmost layers.