I’m not sure exactly what your system is. It sounds like you either have Si
with graphene or you have a SiC with graphene. Each system will be treated
differently. If you have Si with graphene, then you need a separate potential
for Si and Graphene as they are separate materials. To capture the interactions
between these materials, you can use a Lennard-Jones potential. The GPUMD lines
might look like:
potential Si_Tersoff_1989.txt 0
potential Graphene_Lindsay_2010_modified.txt 1
potential my_lennard_jones_parameters.txt 0 1
For this case, it is important to make sure your xyz.in file orders atoms by
If your two materials are SiC and graphene, then the situation is a little bit
more complicated. Here there are still two materials and two many body
potentials must be defined, but we need to distinguish the carbon atoms in SiC
and graphene. To do this, we must use groups in the xyz.in file. For example Si
can be group 0, C atoms part of SiC can be part of group 1, and graphene atoms
can be part of group 2. These groups will be part of group method 0. We can
assign the potentials correctly using a special keyword. The potential
definitions might look like this:
potential_definition group 0
potential SiC_Tersoff_1989.txt 0 1
potential Graphene_Lindsay_2010_modified.txt 2
potential my_lennard_jones_parameters.txt 0 1 2
Now, it is important to order the atoms in your xyz.in by the group that you’re
defining your potentials by.
Finally, take special care in defining the parameters for the Lennard-Jones
potential. If the potential_definition is by group, then the definitions in
that file must also be by group. Hopefully this helps but, if I misunderstood
your structure, let me know and I’ll try again.
Also, if you are familiar with Python, you can use a package that I made to
help with GPUMD input and output files (here it would be LJ potential and
xyz.in file): https://github.com/AlexGabourie/thermo. ;
From: gpumd-bounce@xxxxxxxxxxxxx <gpumd-bounce@xxxxxxxxxxxxx> On Behalf Of "???"
Sent: Thursday, September 26, 2019 6:43 PM
Subject: [gpumd] How can I set the potential command when I want to use two
potentials which contain same atom?
Thank you to Zheyong Fan for using this good GPUMD program.
Today, I have question again.
When I use GPUMD for EMD calculation of graphene with Si doped material,
Suppose that I can set the potential command in run.in file like below:
But if I want the situation with potential
'Graphene_Lindsay_2010_modified.txt' which describes the C-C bonds,
Is it right to set the command like that?:
How can I set the potential command in GPUMD?
(For example, when I use LAMMPS I set it like:
pair_style hybrid/overlay tersoff tersoff
pair_coeff * * tersoff 1 SiC.tersoff Si C
pair_coeff * * tersoff 2 Graphene_Lindsay_2010_modified.tersoff NULL C )