1
General Questions and Answers / Re: Questions about potentials
« on: September 29, 2017, 04:14 »
You mean that "the sufficiently minimized" is the lowest energy of the system as possible as we can?
Show Posts
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
Pages: [1] 2
2
General Questions and Answers / Re: Questions about potentials
« on: September 28, 2017, 09:59 »
Moreover, I've a question about the phonon dispersion curve.
The attached file shows the phonon dispersion curve based on the atom structure (right side).
The ZA phonon branch has negative energy.
I wonder that it has negative energy although the optimization was performed.
Do you have any comments for that?
The system is consisted with C atoms. The C tersoff potential was used for the calculation of phonon dispersion and the optimization.
The attached file shows the phonon dispersion curve based on the atom structure (right side).
The ZA phonon branch has negative energy.
I wonder that it has negative energy although the optimization was performed.
Do you have any comments for that?
The system is consisted with C atoms. The C tersoff potential was used for the calculation of phonon dispersion and the optimization.
3
General Questions and Answers / Re: Questions about potentials
« on: September 28, 2017, 09:47 »
Thank you for reply!
Actually, we want to calculate the phonon dispersion of graphene with Pt and O atoms.
(you may notify our purpose if you see my previous posts)
I have tried some kinds of potentials that has C, O and Pt atoms that includes reaxFF.
But, they didn't work.
So, we just want to use C tersoff potential with changing the mass of some atoms to the mass of Pt or O atoms to know the tendency.
That is the reason why I ask some questions of changing mass of some atoms.
1) Is it possible to calculate the system what I'm mentioned? (C tersoff with changing the mass of some atoms)
2) Can the mass change affect the phonon dispersion?
Actually, we want to calculate the phonon dispersion of graphene with Pt and O atoms.
(you may notify our purpose if you see my previous posts)
I have tried some kinds of potentials that has C, O and Pt atoms that includes reaxFF.
But, they didn't work.
So, we just want to use C tersoff potential with changing the mass of some atoms to the mass of Pt or O atoms to know the tendency.
That is the reason why I ask some questions of changing mass of some atoms.
1) Is it possible to calculate the system what I'm mentioned? (C tersoff with changing the mass of some atoms)
2) Can the mass change affect the phonon dispersion?
4
General Questions and Answers / Re: Questions about potentials
« on: September 22, 2017, 01:26 »
I've got a question about changing the C atom mass with maintaining the bonds.
Can you tell me the way? Actually, I've changed the mass of C atoms through the C14 nanotube case.
However, I think the property of bonds between the C atoms are missing because the phonon dispersion has no branch of LA, TA, ZA.
I saw only horizontal lines in my phonon dispersion.
Thank you!
Can you tell me the way? Actually, I've changed the mass of C atoms through the C14 nanotube case.
However, I think the property of bonds between the C atoms are missing because the phonon dispersion has no branch of LA, TA, ZA.
I saw only horizontal lines in my phonon dispersion.
Thank you!
5
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.
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.
6
General Questions and Answers / Re: Questions about Geometry Optimization of Defective Graphene with Al atoms
« on: July 28, 2017, 08:51 »
I've tried to perform the molecular dynamics with the structure of the upper post (C-O-Pt-O)
(Not DFT calculation)
Well, the oxygen and platinum atoms are blown without binding.
The used potential was the LJ potential.
I need your help.
(Not DFT calculation)
Well, the oxygen and platinum atoms are blown without binding.
The used potential was the LJ potential.
I need your help.
7
General Questions and Answers / Re: Questions about Geometry Optimization of Defective Graphene with Al atoms
« on: July 13, 2017, 02:01 »
Thank you so much!
8
General Questions and Answers / Re: Questions about Geometry Optimization of Defective Graphene with Al atoms
« on: July 11, 2017, 02:34 »
Sorry for my post.
I'm not a native English speaker. So, I feel hardness to express.
Anyway, my purpose is to make a atomic structure as shown in the attached file.
At the C atom that has a broken bonding, I want to arrange the O, Pt, and O atoms with bondings and connections.
I'm not accustomed to use the interface of the Builder in the VNL.
Please let me know and I hope you understand my purpose.
I'm not a native English speaker. So, I feel hardness to express.
Anyway, my purpose is to make a atomic structure as shown in the attached file.
At the C atom that has a broken bonding, I want to arrange the O, Pt, and O atoms with bondings and connections.
I'm not accustomed to use the interface of the Builder in the VNL.
Please let me know and I hope you understand my purpose.
9
General Questions and Answers / Re: Questions about Geometry Optimization of Defective Graphene with Al atoms
« on: July 10, 2017, 03:53 »
Thank you for your reply.
I could obtain the structure what I wanted to.
However, now I'm trying to make a atomic structure of defective graphene with PtO2.
Based on the defective graphene layer, I want to attach a PtO2 to C atoms that has a dangling bond.
(I think the attached file will be helpful to understand what I want. The final structure will be C-O-Pt-O).
I hope you tell me about it!
I could obtain the structure what I wanted to.
However, now I'm trying to make a atomic structure of defective graphene with PtO2.
Based on the defective graphene layer, I want to attach a PtO2 to C atoms that has a dangling bond.
(I think the attached file will be helpful to understand what I want. The final structure will be C-O-Pt-O).
I hope you tell me about it!
10
General Questions and Answers / Re: Questions about Geometry Optimization of Defective Graphene with Al atoms
« on: June 27, 2017, 02:50 »
Sure, Thank you!
Please check the file attatched.
Please check the file attatched.
11
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!
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!
12
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.
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.
13
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.
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.
14
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?
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?
15
General Questions and Answers / Re: Calculation of thermal conductivity of a graphene layer
« on: April 3, 2017, 06:43 »
Thank you for your reply.
I performed the non-equilibrium momentum exchange simulation for 1 ns.
The time step was modified with 0.5 fs. And the log interval was 2000.
Still, we could see the increase of the temperature and the total energy.
(I think that the slope of the increase of the temperature is reduced when we compared to the 1 fs time step)
Please, see my attached files that contain the graph of the temperature and the total energy.
One of them is the case that we applied the 200 momentum exchange interval.
and the other is the case of the 400 momentum exchange interval.
1) Is it acceptable increase of the temperature in the graph? If not, I want you to give me some advise to fix them.
2) I expected the unbalance of the energy exchange between the heat source and the heat sink might cause this problem. Is there are method to obtain the heat flux at the heat source and the heat sink? and are there options at the heat source and the heat sink to modify the heat flux of each part?
I performed the non-equilibrium momentum exchange simulation for 1 ns.
The time step was modified with 0.5 fs. And the log interval was 2000.
Still, we could see the increase of the temperature and the total energy.
(I think that the slope of the increase of the temperature is reduced when we compared to the 1 fs time step)
Please, see my attached files that contain the graph of the temperature and the total energy.
One of them is the case that we applied the 200 momentum exchange interval.
and the other is the case of the 400 momentum exchange interval.
1) Is it acceptable increase of the temperature in the graph? If not, I want you to give me some advise to fix them.
2) I expected the unbalance of the energy exchange between the heat source and the heat sink might cause this problem. Is there are method to obtain the heat flux at the heat source and the heat sink? and are there options at the heat source and the heat sink to modify the heat flux of each part?
Pages: [1] 2