Topics

1

General Questions and Answers / Questions about potentials

« on: September 18, 2017, 07:01 »

I want to calculate the phonon dispersion curve of graphene with O atoms.

That means I need a potential that can explain C-O bonding.

In ATK, some reaxFF support the C-O bonding.

But, I obtained the incorrect phonon dispersion using reaxFF.

i) If there are possible to obtain the phonon dispersion using reaxFF, please let me know.

ii) Is it possible to use airebo potential? Actually, I know the parameter about the airebo potential.

iii) If possible, I want you to recommend some potentials that can support C-O bonding.

Thank you.

2

General Questions and Answers / Questions about Geometry Optimization of Defective Graphene with Al atoms

« on: June 26, 2017, 08:11 »

Hi, everybody.
I've tried to simulate the atomic structure of the defective graphene with Al atoms to obtain the phonon dispersion curve of the defective graphene with Al atoms. The Al atoms will be located in the middle of the defects.
(I think the figure that is attached will be helpful.)

However, whenever I optimized the geometry of the defective graphene with Al atoms, the result is different  with the atomic structure of the attached figure.

How can I realize the atomic structure of the defective graphene with Al atoms? and Is
it OK that I use the potential combined with tersoff and the Lennard-Jones potential for this case? Please help me!
In addition, sometimes the atom are blown up. I mean that the atom are not binded.
Please let me know!

3

General Questions and Answers / Questions about Eigenvectors

« on: May 24, 2017, 12:49 »

I have calculated the eigenvectors of a graphene layer for phonon.
Successfully, I could obtain the eigenvector of the graphene layer at certain wave vectors.
(using the class of vibrational modes)
The output is arrays (that contains six elements) with six lines.
(Please, see the attached file)

I think the six lines is related on the phonon modes.
However, I don't know what the elements indicate.

In my opinion, for the graphene case, there are two eigenvector e1, e2.
Then, the six elements are e1x e1y e1z e2x e2y e2z.
Is that the correct? Please let me know about the eigenvector output.

4

General Questions and Answers / About trajectory files

« on: May 17, 2017, 07:30 »

Hello, everybody!

I have calculated the phonon lifetime of a graphene layer using molecular dynamics by the normal mode analysis.

Because the highest phonon frequency of the graphene layer is approximately 70 THz, we choose the log interval with 10 steps and 0.5 fs time steps. and the total integration time is 1 ns. That is, the size of the trajectory file can be large.

And the normal mode analysis is required the trajectory file that contains atomic positions at each time.

Here, I have some questions.
1) Is it possible to make the simulation faster? It spends a lot of time to perform the molecular dynamics.

2) Can we make the trajectory file compactly? Actually, I just want the atomic positions at each time step except other information. The trajectory file (.nc) has informations such as force, mass, velocity and so on.

3) Which platform is more faster? Windows vs. Linux? or no difference? Please let me know

Thank you so much.

5

Installation and License Questions / Questions about License

« on: May 17, 2017, 06:05 »

We have installed the ATK-VNL 2016 in a windows system with a license.

Now, we are trying to install the ATK-VNL 2016 in a linux system (Ubuntu).

Can we use the same license in the linux system?
(We are not going to use the license at the same time)

If possible, where can i find the installation file and manual?

6

General Questions and Answers / Calculation of thermal conductivity of a graphene layer

« on: March 9, 2017, 07:38 »

Hello, everyone. I have tried to figure out the thermal conductivity of a graphene layer with the unit of “W/mK” (not W/K) using NEMD methods.

The structure is a graphene nanosheet which has the size of 12 nm × 9 nm. The total number of the carbon atoms is approximately 2240.

For the equilibrium, the structure was optimized and simulated using Nose-Hoover thermostat at 300 K. In this simulation, the time step was 1 fs and the whole process time was 4 ns. The thermostat timescale was 100 fs. The reservoir temperature and final temperature were 300 K. The tersoff_C_2010 potential was applied.

The non-equilibrium simulation was then performed using Nose-Hoover thermostat at 300 K with the same condition of the equilibrium simulation (ex. time and temperature). Also, The heat source and heat sink were set at the left side and right side of the structure. Using the non-equilibrium momentum exchange in ATK, I want to make the temperature gradient in the area between the heat source and heat sink. Then, I will calculate the thermal conductivity of the graphene layer.

I have several questions about the simulation.
1)    I know that the nanosheet is 2D and periodic in the y and z directions. Is it required to set the periodic boundary condition for the top and bottom side additionally? If the boundary condition is periodic, there are no scattering effects related on the phonon or electrons because the top and bottom side are not terminated anymore, Right? I expect for the case; there are no dependencies on the width of the structure for the thermal conductivity. I want to know about this.

2)    For the non-equilibrium momentum exchange, should we set the fixed boundary at the left and right side of the structure besides the heat sink and source?

3)     For the Nose-Hoover thermostat, the temperature gradient can be generated using reservoir temperature. Is there are no problem to obtain the thermal conductivity of the graphene layer although some synchronization issues are between the heat source and sink.

4)    I read a several papers about NEMD for the calculation of the thermal conductivity by LAMMPS. In that case, the method is similar methods kinds of setting the different reservoir temperature on both sides for the Nose-Hoover thermostat.

5)    Please comment about the procedure of simulation, some notes and missing point and so on.