Hello everyone,
I have simulated 252 atoms of graphene and functinonalized graphene with -OH groups. I deformed the simulation box in zigzag direction of graphene with fix deform command. Then I plotted the x,y,z coordinates in MATLAB and found out that my graphene sheet is moving in the simulation box although I am pulling along uniaxial mode. They were not supposed to move rather stretch. I remapped the atomic coordinated also. I am using PBC in all directions. Here's a part of my code:
# Applying axial and shear strain by fix deform
fix 8 all nvt temp ${temp} ${temp} 5.0 drag 1
fix 9 all deform 1 x erate ${erate1} units box remap x
Is there anything I have to do to keep the atoms fix in the box without using set force 0? Any suggestions will be helpful
In your first line you are time-integrating all atoms available in your simulation cell. You should use a group excluding your graphene atoms in your fix nvt line.
Hello Baris,
I think you are asking me to grouping C atoms and (O+H) atoms separately. I am not sure how to do that. Currently this is what I have in the script:
-3.05 17.85 xlo xhi
-12.80 15.60 ylo yhi
26.0 40.0 zlo zhi
group graphene type 1
group oxygen type 2
group ho type 3
What changes should I make here? I can't group oxygen and ho together. Can you please help me to understand how to do it?
There are many ways of doing this in lammps. You should go through the lammps manual.
For example, you can combine two or more groups into a new one using group union, also subtract one or more groups from another one using group subtract, etc.
And make sure that the atoms that you do not want to move should not be in the group you use in your fix nvt line.
baris.
Hello Baris,
I changed the group ID in fix NVT so that graphene atoms don't move. This is what I did:
#------------ define groups ------------------xxx
group graphene type 1
group oxygen type 2
group ho type 3
group hydroxyl type 2 3
group mobile subtract all graphene
# Applying axial and shear strain by fix deform
fix 8 mobile nvt temp ${temp} ${temp} 5.0 drag 1
fix 9 all deform 1 x erate ${erate1} units box remap x
But as I am applying strain along ZZ direction, the graphene sheet kept on stretching without fracture upto 0.5 strain (because I am running 50000 steps) which is unrealistic because pristine graphene breaks around 0.28 strain. And the stress also goes upto 192 GPa (because of the steps). If I had run longer steps I would have gotten much higher stress and strain. So, something is definitely not right. But, when I am doing fix all, the results seem reasonable but the graphene sheet travels through space which I don't like. Do you think it's reasonable that the sheet is moving?
Hi Baig,
If your graphene travels as a whole as you apply your strain, your graphene layer may not be periodic in the direction of strain. I advise you to make sure this fact. Once you fix this, I think you should include all atoms in your fix nvt and fix deform lines.