Messages

136

General Questions and Answers / Re: Mimicking decomposition of Silicon on 6H-SiC(000-1)

« on: September 15, 2015, 10:33 »

Yes, in this case it (0001) and (000-1) distinguish between a C-terminated surface and a Si-terminated surface. So, in simple words, whether you use the top or the bottom surface of the slab.

137

General Questions and Answers / Re: Mimicking decomposition of Silicon on 6H-SiC(000-1)

« on: September 14, 2015, 13:39 »

Not a really straightforward way, but you can do it all in a python script. I have attached an example script that uses a classical potential.
Please consider it only an example, and review and adapt the parameters (configuration, calculator, thermostat, equilibration time, evaporated atoms, etc.) as needed.

The script employs an equilibration simulation, and then a loop over all atoms that should be removed. In each cycle, the respective atom is removed, a new configuration is generated, the indices are updated, and an MD simulation is run.

138

General Questions and Answers / Re: Imaginary frequencies/ ASR

« on: September 14, 2015, 09:46 »

Imaginary/negative frequencies can have several reasons, generally mean that the system can gain energy by displacement along this mode. Possible reasons for this can be:
-  The structure is not at a local minimum. In this case an accurate geometry optimization will remove the negative frequencies.
- The structure is at a saddle point. In this case, try small random displacements, followed by a geometry optimization to break the symmetry.
- Although phonon calculations are in general possible for strained cells, in some cases,  especially for 1D- or 2D-materials, an additional cell optimization might help to remove saddle points and the resulting imaginary frequencies.

If you encounter negative frequencies (or non-negative frequencies in general) in the accoustic branches at the gamma point, then the translational invariance is violated, as the system energy would change by a translation of the entire system. This is typically caused by a problem with the accuracy of the calculation.
If you are using classical potentials then you might try increasing the "Maximum interaction range" parameter in case you have long-ranged potentials (especially for atk2014).
For DFT you may try to increase the accuracy parameters, such as mesh cutoff, tolerance, etc.
As it is not always possible to increase the accuracy until all these non-zero frequencies have vanished, you can enforce the acoustic sum rule, by checking the ASR box in the DynamicalMatrix parameters. Then the dynamical matrix is shifted to correct the ASR at the gamma point.
Note that this doesn't correct negative frequencies at finite q-points.

You may also take a look at the Phonon tutorials http://www.quantumwise.com/publications/tutorials/itemlist/category/94-phonons-and-thermal-properties .

139

General Questions and Answers / Re: Building 6H-SiC Question

« on: September 11, 2015, 14:50 »

BTW. We'll soon have a brand new tutorial on vapor deposition simulations on the SiC(0001) surface..

140

General Questions and Answers / Re: Building 6H-SiC Question

« on: September 11, 2015, 14:47 »

The bond stub is still there, so it looks as if the structure is still intact, only that the one silicon atom is outside the box. Try repeating the cell in A- and B-direction, or using Bulk Tools > Wrap to wrap the atoms inside the box, and check if the bonds still is broken.
I don't see any of these problems when I use the cif-file structure and do the same cleaving operations.

I've been reading,


Ogasawara N, Norimatsu W, Irle S, Kusunoki M. Growth mechanisms and selectivity for graphene or carbon nanotube formation on SiC (0001¯): A density-functional tight-binding molecular dynamics study. Chemical Physics Letters [serial online]. March 18, 2014;595-596:266-271. Available from: ScienceDirect, Ipswich, MA. Accessed September 11, 2015.

They use 5x5x.5 unit cells, I wonder if that is a coincidence?

I guess that's just the choice the authors made to obtain a supercell of a suitable size.

141

General Questions and Answers / Re: questions regarding to tutorial of Isotope impurity effect on a single-wall carb

« on: September 11, 2015, 09:03 »

We have quite a lot of predefined potentials for SiC. You can simply use one of those. Send your SiC configuration to the ScriptGenerator, add a New Calculator, double-click it to open its settings, and select ATK-Classical, a list of possible potentials will be available. I'd recommend you use one of the Tersoff potentials, e.g. Tersoff_SiC_2005 or Tersoff_SiC_1989.

142

General Questions and Answers / Re: Building 6H-SiC Question

« on: September 11, 2015, 08:56 »

In the diagram the structure looks similar to " 6H SiC Example.png " in my original post. I'm guessing the structure in Jakse was not really meant to represent the physical appearance of the material from one face, but perhaps just a 2-d representation of the stacking sequence?

Yes, you are right. From the picture in the paper it could be both 6H-SiC or 2H-Sic.

Guessing from the side view in your picture " 6H SiC Example.png", it might rather be 2H-SiC (cf. attached picture), but it is not 6H-SiC.

143

General Questions and Answers / Re: Building 6H-SiC Question

« on: September 10, 2015, 13:12 »

I'm confused, doesn't 6H-SiC have 12 atoms in a unit cell? There's only 6 in the coordinates you gave for 6H.

If you import the .cif file, attached in my previous post, into the Builder (via Add > From Files), you will see that it has 12 atoms, although the cif file has only 6 coordinates. The remaining coordinates are deduced from the symmetry.

Also, different sources seem to get different structures for the unit cell, is there more than one?

The two structures in the pictures might be equivalent within periodic boundary conditions, but it is really difficult to tell just from the flat picture.

My knowledge in solid state physics is limited. I'm trying to build 6H-SiC to run tests on the surfaces. I'm not sure if I'm doing this correctly. I start with the Hexagonal SiC in the data base, it consists of 4 atoms. I repeat it and then move atoms around to get the structure of the 6H-SiC unit cell (12 atoms) by going off schematics I've found from various sources. Then I repeat the 6H-SiC structure 5X5X1. I attached images of two of my stash items with the unit cell and the 5X5X1, I also attached two images I looked off of to help me.

Basically my question is...is this right?

If you take the unit cell from the .cif file and cleave the (0001) surface (using the Surface (Cleaver) plugin, and selecting a carbon atom as the topmost terminating atom) then you get the surface as in the picture (see attached figure). Then you can start introducing the modifications.

144

General Questions and Answers / Re: Tremolox Package

« on: September 2, 2015, 15:04 »

You are right, the parameters for EAM and ReaxFF are in stored in separate files. These files are shipped with VNL, so you don't need to generate anything, and you can just use the predefined potentials as they are.

In case you want to modify the predefined EAM or ReaxFF-potentials, you find the files,  if you go into the directory where VNL is installed, and then search for the filename from here. They will be in a subdirectory. You should never directly modify any of these files, as the corresponding predefined potential will be changed or lost without any notice!!!
Instead you should make a copy of this file in the same directory and modify the copied file.
If you then want to employ this new potential file, you simply have to specify the new file name instead of the old one in the EAMsetflPotential constructor (or ReaxFF constructor).
Still, you should be extremely careful when you make any changes in the VNL-installation directory!!

145

General Questions and Answers / Re: Tremolox Package

« on: September 2, 2015, 09:20 »

For most of the potentials, the parameters for the predefined potentials are in the source code itself.
You can, however, easily access and modify the parameters, by setting up a calculator with the desired potential in the Script Generator, and then setting "Script detail" in the "Global IO" settings of the Script Generator to "Show Defaults". If you then send the script to the Editor, a detailed python script with all potential functions and parameters is generated, where the parameters can easily be modified.
See also the tutorial "Adding, combining, and modifying classical potentials" (http://www.quantumwise.com/publications/tutorials/item/848-adding-combining-and-modifying-classical-potentials).

146

General Questions and Answers / Re: Tremolox Package

« on: August 31, 2015, 12:53 »

Generating new potential parameters is a generally a very difficult procedure and it is far from being a black-box procedure. Although, we are working on a tool that will facilitate fitting of new potentials, the current version of VNL does not include such functionality. If there is no parameter set for the desired combination of elements available in the literature, you need to do the fitting yourself.
The common approach is the following: First you generate reference training configurations of your system and calculate representative properties using a higher-level method (e.g. DFT), or use experimental values. These can be lattice constants, elastic constants, energy-displacement curves, atomic forces upon displacement, NEB-energy-curves etc. The reference date should resemble the situation you are finally interested in, as close as possible, so when you are interested in elastic properties, elastic constants should be reproduced by the potential, if you are interested in surface reactions, then bond breaking barriers (e.g. via NEB) should be included in the training set etc. Then you have to choose a potential form which might suit the general material class, e.g. embedded atom for metals and alloys, Tersoff for covalent crystals, or ionic potentials for oxides. Ideally, you can start from combing existing potentials, then you fit some or all potential parameters by hand or using an optimization algorithm (e.g. from numpy/scipy) until the reference properties calculated with the new parameter set match the reference properties sufficiently.
However, you should be aware that fitting potentials requires quite some experience in using classical potentials at the first place.

147

General Questions and Answers / Re: EMTCalculator Parameters for Carbon?

« on: August 28, 2015, 09:00 »

That is nothing to worry about.
ATK-Classical actually comprises 3 calculators: TremoloX, Brenner, and EMT, the last two essentially for historic reasons. When you open the New Calculator widget and select ATK-Classical, VNL checks all of these 3 calculators if they have potentials for the current configuration. If one of these 3 doesn't have parameters for the required elements, then this info message is shown, but hat doesn't mean that there are no parameters available in general.
In your case you can still choose the e.g. the suggested Tersoff potential (from the TremoloXCalculator) without any problem, and simply ignore that message.

148

General Questions and Answers / Re: Building 6H-SiC Question

« on: August 10, 2015, 09:08 »

It looks right, but it's difficult to tell exactly just from the picture.
I have attached a .cif file of the SiC-6H (http://rruff.geo.arizona.edu/AMS/minerals/Moissanite) structure to which you can compare your structure.

149

General Questions and Answers / Re: Ph.-DOS /transmission eigen values

« on: July 17, 2015, 09:03 »

1) An instead of using finite temperature difference between the phonon occupancies of the reservoirs, the differential ( n_L (T_L) - n_R(T_R) ) / (T_L - T _R) is evaluated as dn(T)/dT at the specified temperature.

2) As it says in the manual M is a diagonal matrix with matrix elements corresponding to the masses of the atoms.

150

General Questions and Answers / Re: Local Struct. / Projected Local DOS

« on: July 7, 2015, 09:15 »

(3) The PartialCharges are zero if the classical potential you selected does not use coulomb interactions to model the electrostatics of the system. In this case no partial charges on the atoms are defined and that is what the PartialCharges analysis object tells you.