Messages

1096

General Questions and Answers / Re: I-V curves for 2D materials

« on: April 4, 2017, 12:40 »

There are a couple of issues with your calculations.

1. Two of the three electron transport calculations are done for perfect, infinite system. For that, please have a look at my replies to this forum discussion, http://quantumwise.com/forum/index.php?topic=4970.msg21537#msg21537.

2. One of your calculations assumes a scatter (molecule) on top of the 2D material in the central region. This molecule seems to be quite decoupled from the substrate, so it is not surprising that you see no difference in electron transmission, compared to perfect system calculations. I guess in your case the current essentially goes through the substrate. Since the current is carried by charge carriers near the Fermi level, the electronic structure of your material at and near the Fermi energy should be altered by the molecule adsorbed on the surface in order to affect the electron transmission through the central region. Apparently, it is not the case for the system as you have designed it. 

1097

Scripts, Tutorials and Applications / Re: Graphene_MoS2 interface with electrode

« on: April 4, 2017, 10:07 »

If you want to study the in-plane electron transport, the C-axis should be parallel to the graphene-MoS2 plane because the C-axis is a transport direction in ATK by default. As far as I can see in the script, this requirement is not met in your setup.

Moreover, the C-axis (transport direction) should be orthogonal to the A and B axes (cross section plane), or in other words the electron transport direction is to be orthogonal to the cross section area of the device assumed in ATK to be given by the AB plane. It means that when you match the graphene and MoS2 sheets in the Interface builder plugin, you should chose a matching in-plane supercell that has a rectangular shape. 

 

1098

General Questions and Answers / Re: the *.py files in tutorial "Bi2Se3 topological insulator"

« on: April 1, 2017, 15:20 »

This is not a python problem. I have been able to save the trouble files in Chrome and Firefox with no problem by simply right clicking on the file link and then doing Save link as. Clicking on the file link also allowed me opening the script in the browser directly, and saving it by right clicking.  You may restart your browser, and give it a try once again.

1099

General Questions and Answers / Re: Longitudinal and transverse directions for effective mass in MoS2

« on: March 31, 2017, 18:15 »

This is the paper where you can find the symmetry k-points and lines for the Brillouin zone of all the 14 Bravais lattices, see  Computational Materials Science 49 (2010) 299–312. The effective masses are usually calculated at the symmetry k-points along the symmetry lines.

1100

General Questions and Answers / Re: Building interfaces in VNL

« on: March 29, 2017, 15:03 »

The VNL interface builder reports interface strain components and mean strain value (as specified in the previous post) for a chosen supercell structure.

I do not know what these 2-3% in the literature refer to. It may for example refer to the mismatch for the two surfaces matched with the minimal in-plane unit cells.  This is something one should evaluate first to see how lattice-matched your structures are; this can be done simply by comparing the in-plane lattice constants of the two surfaces. Some materials do not grow on top of each other if the lateral strain is too large.

I would say the individual components have real physical meaning, whereas their average is not uniquely defined, and more meant to give an overall idea of how far the interface is from being perfectly lattice-matched.   

Strain can be positive and negative, depending on whether the structure is compressed or stretched in certain directions.

1101

General Questions and Answers / Re: Building interfaces in VNL

« on: March 29, 2017, 09:45 »

- Are the parameters that I added to my first post  good enough?

I guess noone can say whether your parameters are good enough or not. You should actually study it by choosing other generated interface structures to find out how sensitive physical properties of your system to interface strain.

- How do I connect the way VNL build interfaces with the procedure explained in this paper: J. Mater. Chem., 2012, 22, 22063 , at page 22064 (The Interface model construction)

I would say that is the same procedure, except that the interface builder does not fully relax the interface structure; it may do some separation distance optimization using classical MD, provided there exist corresponding classical potentials. After the structure is built, you may however optimize it by means of other ATK tools. 

- In section 2.1.2, commensurability of two phases is explained. Is this the same way that VNL calculate the mismatch?(I mean in eq. 2)

As I said the interface builder provides geometrical construct of interfaces, so it does not use an equation such as Eq. 2, where there are some non-geometrical (energy) parameters. The interface builder uses mean strain = (e11+e22+e12)/3 as a measure for the interface matching quality. Having mean strain = 0 corresponds to  perfectly matched surfaces.

- In fig. 1,  the steps leading to an interface model are shown.  Does VNL do all of these steps?  if yes,  how step 3  is done with VNL?

See my reply to your first question. In step 3, the interface builder uses two surfaces (cleaved in a separate Builder plugin, see http://docs.quantumwise.com/tutorials/ag_au_interface/ag_au_interface.html for more details) to match them in different ways. 

1102

General Questions and Answers / Re: Can't open the results of PLOS

« on: March 28, 2017, 09:22 »

You have to redo all the calculations in ATK-2016 to be able to view the PLDOS.

1103

General Questions and Answers / Re: missing bonds after optimization

« on: March 27, 2017, 22:32 »

In the Builder, you may select Graphics->Properties->Atoms, and then increase Fuzz factor until you see "missing bonds" in your structure.

1104

General Questions and Answers / Re: Geometrical Optimization

« on: March 27, 2017, 16:13 »

I think you can do it in two steps. First, geometry optimization for bulk GaN, and then surface calculation with electrode and its extension constrained as Fixed. In this calculation, pseudo-hydrogen atoms with fractional charges, which are used to passivate the GaN surface, may and probably should be constrained as Rigid, not Fixed.   

1105

General Questions and Answers / Re: Can't open the results of PLOS

« on: March 27, 2017, 15:21 »

In addition to my previous post, if you did the device calculation and transmission spectrum analysis in one version of ATK, e.g., ATK-2015, and then generated PLDOS in a newer version, e.g., ATK-2016, that would have created a problem such as that you have reported.

1106

General Questions and Answers / Re: Can't open the results of PLOS

« on: March 27, 2017, 13:38 »

Could you enclose the original python script(s) where you did the device calculation and transmission spectrum analysis?

1107

General Questions and Answers / Re: How to extract the contribution of an atom in the supercell energy band?

« on: March 27, 2017, 12:31 »

This feature is not available in ATK-2016 or older versions, but it will be available in ATK-2017.

1108

General Questions and Answers / Re: Building interfaces in VNL

« on: March 27, 2017, 11:56 »

What exactly do you mean by "weird" regarding the structure you have enclosed? I see nothing obviously wrong with it.

I am not sure I fully understood your second question. The interface builder allows you to match two structures by rotating them with respect to each other (i.e., by choosing different shapes and dimensions of lateral unit cells). This process is automated and produces a set of interface structures with different strain configurations corresponding to particular choices of the lateral unit cells I have mentioned in the previous sentence. This is fully geometrical procedure, and it is up to you to decide on which ones suit your needs.

In general, one usually aims at structures with no or minimal strain. In practice, one may want to avoid dealing with huge structures, and in this case one should tolerate some strain in the interface structure. But that is really up to you to decide what is good for a particular problem of your study. For Li|Li3N, I would perhaps allow some strain on the metal side, i.e., in Li, and this is what you have done.  You may certainly consider an interface structure with less strain, but you will then likely need to enlarge your lateral unit cell size. 

If you only do ion optimization of your interface structure, the macroscopic strain will not change for the final structure. Otherwise, you have to use in-plane lattice parameters of the final interface structure to recalculate the strain tensor.

1109

General Questions and Answers / Re: Why am I getting a small bandgap in density of states of graphene?

« on: March 24, 2017, 19:29 »

As you may see in my original post, I have not suggested reading the entire paper, but a rather tiny Appendix, which has all the information about the k-meshes that can be adopted for accurate calculation of graphene's DOS (not for self-consistent calculation).  The choice of the mesh is up to you, as you are the master of your research. As I said in the original reply, the k-grid should include the K-symmetry point since this is where the conduction and valence bands touch, and the DOS has a gap because the k-mesh is too coarse as pointed out by zh.   

1110

General Questions and Answers / Re: MGGA and DFT-U

« on: March 24, 2017, 15:46 »

In addition, MGGA and GGA+U are both meant to get more accurate band gap and band widths for semiconductor materials. I think it would not make sense to mix the two approaches, unless there is a good argument for doing so.