molecule add

Hi all;

I have been tryin to add methane molecule at random position nearby a graphene for a while. I am aware of that adding molecule has been discussed before.

Unfortunately, I could find a way to add methane to my box containing graphene. I have ended up molecules have been fragmented throughout the box. I do not understand why methane has been fragmented.

I am using AIREBO potential to represent C-H interaction.

Any help will be greatly appreciated. Thanks for your time and help.

Here is my input and data files for graphene and methane, respectively.

–ipek

Hi all;

I have been tryin to add methane molecule at random position nearby a
graphene for a while. I am aware of that adding molecule has been discussed
before.
Unfortunately, I could find a way to add methane to my box containing
graphene. I have ended up molecules have been fragmented throughout the box.
I do not understand why methane has been fragmented.
I am using AIREBO potential to represent C-H interaction.
Any help will be greatly appreciated. Thanks for your time and help.
Here is my input and data files for graphene and methane, respectively.

the input your provide is incomplete, has lots of confusing commented
out parts and has blatant syntax errors and conceptual mistakes (you
apply time integration to atoms in overlapping groups multiple times).

so before asking for help, you should make it easier to help you and
please do the following:

strip down your inputs to the absolute minimum, take out all lines
that need not be there (whether commented out or not), correct all
syntax and concept error and provide:
- a complete data file for your graphene structure.
- an input script that demonstrates running MD successfully with the
graphene only
- a second input that adds the methane deposition to the previous
input and the corresponding (cleaned up) molecule file.
to keep file size small, you can combine all files into a tar.gz or zip archive.

then we can look at the second input file, compare to the first and
comment on how to address the issues in your simulation.

thanks for your cooperation,
      axel.

Hi Axel;

You are absolutely right.Why i did not pay attention to other lines in my input is that my problem starts at the very beginning.

here I am enclosing my tar file for your help. As you see in my input, I just want to see my initial geometry after adding methane molecules. I do not want to do anything for now. Because I am trying to be sure for the initial geometry.

Although I do not implement any minimization or something similar in my input, methane seems fragmented.

Since I am using AIREBO potential, I do not have to put any paramaters for bonding scheme. But I do not still figure out why this fragmentation occurs.

Thanks for your kindly warning in previous email. I hope that this email is much more clear for your valuable guidance.

Regards,

ipek

lammps_forum.tar (950 KB)

Hi Axel;

You are absolutely right.Why i did not pay attention to other lines in my
input is that my problem starts at the very beginning.
here I am enclosing my tar file for your help. As you see in my input, I
just want to see my initial geometry after adding methane molecules. I do
not want to do anything for now. Because I am trying to be sure for the
initial geometry.
Although I do not implement any minimization or something similar in my
input, methane seems fragmented.
Since I am using AIREBO potential, I do not have to put any paramaters for
bonding scheme. But I do not still figure out why this fragmentation occurs.

i don't see any "fragmentation". what i see is that you create you
methane molecule so that it overlaps with the graphene. of course,
that will lead to divergence.

axel.

in addition, you really should follow the path that i suggested and
test the graphene layer by itself. that by itself does have a
diverging energy, so you need to correct that first. also, your
methane molecule geometry looks very whacky.

since you already mentioned GI-GO, i just have to repeat it and remind
you that it applies to *everything*. the problem doesn't start with
the molecule addition, but way before.

axel.