Messages

1

General Questions and Answers / Re: Ask the building of air or specific gas environment

« on: April 7, 2018, 00:27 »

Hi,

I have a question to make a N2 molecule.

Nitrogen is N2 in air not N.

When I want to make N2 molecule, how to define the bonding between N and N?

Thanks,

Jaeyoung

2

General Questions and Answers / Re: Ask the building of air or specific gas environment

« on: April 4, 2018, 23:00 »

Hi, Petr Khomyakov

Yes, I did the clean interface.

As you mentioned, I want some foreign atoms or molecules at graphene-Cu interface.

This is because graphene was physically transferred on the Cu substrate in my experiment.

I suspect that there may be the air gap between graphene and Cu because I did not heat my sample.

I already finished the vacuum condition which means the clean Cu surface.

If I'm followed by your direction, can I export the final structure ( graphene/gap having gas molecules/Cu) to LAMMPS data file?

Thanks,

Jaeyoung Jeong

3

General Questions and Answers / Ask the building of air or specific gas environment

« on: April 4, 2018, 21:50 »

Hi,

I'm VNL user and working on thermal transport.

I wonder whether I can make air or specific gas environment with VNL.

I made graphene on Cu substrate. There is a gap between graphene and Cu.

I know that there is vacuum gap between graphene and Cu when I build this structure by VNL.

Can I apply air or a specific gas(ex. N2 molecules) environment in this gap when I build this structure by VNL?

I want to compare vacuum condition with air condition when I calculate heat transfer between graphene and Cu with MD.

I'd really appreciate it if you give me any comments.

Thanks,

Jaeyoung Jeong

4

General Questions and Answers / Re: Optimize the structure of materials

« on: March 8, 2018, 15:58 »

Hi,

Thanks, Petr Khomyakov

5

General Questions and Answers / Run LAMMPS with an exported LAMMPS input file

« on: March 8, 2018, 01:04 »

Hi,

I tried to run LAMMPS with LAMMPS input file which was exported by VNL academic version.

I build graphene on Cu structure with their unit cells.

I have two questions.

First one is the interface distance between two materials.

After I made the interface of two materials like the first picture,  the smallest interatomic distance was 27A and z value was 0.

If I want to make the interface with 3A between two materials, is it correct to put -24.0 as z value as the first picture?

My second question is the primitive vector value like the second picture.

With this structure having negative B-Y value, LAMMPS input file showed an error because it yhi value is smaller than ylo value as shown the 2nd.

I'd really appreciate it if you give me some comments to solve this problem.

Thanks,

Jaeyoung Jeong

6

General Questions and Answers / Optimize the structure of materials

« on: March 7, 2018, 18:54 »

Hi,

I'm working on MD simulation with LAMMPS.

I'm building some materials structure with VNL academic version.

While MD simulation with LAMMPS, NPT, NVE and thermal equilibrium steps were conducted before calculating.

If I make a material structure with VNL and it is exported to LAMMPS input file, do I need to optimize the material's structure before exporting LAMMPS input file?

If I have to do it,  please let me know its process.

I'd really appreciate it.

Thanks,

Jaeyoung Jeong

7

General Questions and Answers / Re: Define Nitrogen gas molecule bonding

« on: February 22, 2018, 17:38 »

Thank you so much

8

General Questions and Answers / Re: Define Nitrogen gas molecule bonding

« on: February 21, 2018, 19:58 »

Hi,

Thank you for a reply.

Can you let me know where I can set the distance?

I can find the distance value but I don't know where I can set it at VNL.

Thanks,

Jaeyoung

9

General Questions and Answers / Define Nitrogen gas molecule bonding

« on: February 20, 2018, 20:12 »

Hi,

I want to put N2 gas molecules between graphene and Cu substrate.

I have tried to use molecule builder on VNL.

When I make two mono-nitrogen atoms as attached pictures, I tried to define the bonding between two nitrogen atom because nitrogen gas is N2 but I could not.

I will run MD simulation with this geometry. For running MD, I will use LAMMPS and define interatomic potential for each material and N2 gas.

In this case, do I need to make the bond of nitrogen atoms for N2 or I can put mono-nitrogen atom into the interface?

I'd appreciate if you let me know that.

Thanks,

Jaeyoung Jeong

 

10

General Questions and Answers / Encapsulation polymer within CNT

« on: January 30, 2018, 20:47 »

Hi,

I want to put a polymer material to CNT inside.

Can I build such structure VNL?

If I can do it, please give me tutorial or direction for that.

Thanks,

Jaeyoung

11

General Questions and Answers / Re: Export a problem of grpahene structure

« on: January 29, 2018, 21:30 »

Thanks Petr Khomyakov

12

General Questions and Answers / Re: Export a problem of grpahene structure

« on: January 26, 2018, 17:01 »

Hi,
Thanks, Peter Khomyakov.

I have one more question.

When I set A lattice vector to (a,0,0), do I need to change in A row? or need to change B and C  also?

I changed in A lattice vector as a below-attached file. is this right?

Thanks,

Jaeyoujng

13

General Questions and Answers / Export a problem of grpahene structure

« on: January 25, 2018, 18:59 »

Hi,

I tried to export a graphene structure to LAMMPS format.

First, I made graphene unit cell from a database and made its supercell with 10x10.

When I tried to export this structure to LAMMPS format but there was an error like "LAMMPS Exporter can only handle cells with zero yx,zx,zy components.

I attached a file also.

How can I figure it out?

Thanks,

Jaeyoung Jeong

14

General Questions and Answers / Re: Phonon dispersion with supercell

« on: August 24, 2017, 23:48 »

Hi, Petr Khomyakov

If I can only use the unit cell of graphene having two atoms to calculate the phonon dispersion and DOS, do you mean that there is not any big different between the phonon dispersion for two atoms and that for many atoms?

Finally, I want to check the phonon dispersion of graphene on Cu as function of distance between both materials.
In this case also, can I only use unit cells for both materials? Do I need to increase the number of repetitions for calculating the dynamical matrix to increase accuracy?

I don't use any defects, doping, ripples.

Because I only use VNL for academic version, there is BZ folding when I use many atoms to calculate phonon band structure.
Finally, the phonon dispersion is so many straight lines.

For VNL academic version, is there any method to avoid BZ folding?

Thanks,

JY

15

General Questions and Answers / Phonon dispersion with supercell

« on: August 21, 2017, 20:56 »

Hi,

I'm currently working on phonon calculation.

I'm using VNL for acedemic user.

I can have phonon dispersion and phonon density of state for two atom in unit cell.

I wonder whether I can obtain phonon dispersion and phonon density of state results for graphene supercell having many atoms not only two atom in unit cell.

Thanks,

JY