I am a newbie in molecular dynamics. My basic study was to elucidate the growth process of nanoparticle evolution in which two bunches ( similar or different in size) of atomic aggregates of copper form a couple of nanoparticle and eventually coalesce to form a bigger nanoparticle. In this stepwise evolution, I want to calculate the change in their average binding energy throughout the time of development. Could it be possible to design and calculate the problem in LAMMPS? Which module is adequate for the calculation? Kindly share your views.
Hi Hirak,
This is possible in LAMMPS. Of course you will have to go through the documentation to figure out how to do it, and first learn the basics of LAMMPS. But once you get through the beginnings you can address your problem in one of multiple ways. My suggestions below correspond at least to one way of doing it. To help you a bit on your way:
If you only have a small number (2-4) of nanoparticles, you could consider defining separate groups for each nanoparticle. For example:
group particle1 type 1 2 3
group particle2 type 4 5 6
You don't have to use atom types to define groups. Indices and other information is also possible. See documentation.
Then you can compute and output the interaction energies between different groups.
compute interaction12 particle1 group/group particle2 kspace yes
if you refer to c_interaction12 you get the energy (where the 'c_' is added because you refer to a compute), while c_interaction12[1], c_interaction12[2], c_interaction12[3] are the forces in different directions.
The computed values change in time. I vaguely remember that there was some problem if you frequently want to print/dump the updated value of this compute, which I solved by defining a variable:
variable outint12 equal c_interaction12
Finally, use this variable to output your interaction energy every number (100 in this example) of timesteps:
fix printfix1 all print 100 "${outint12}" file interaction12out.txt screen no
I hope this will help you somewhat. Note that this is not the easiest thing to start with if you are unfamiliar with LAMMPS and with molecular dynamics in general.
Good luck
Thank you, Dr. Hartkamp, for such an elaborate reply. I do realize the simulation is going to be a hard nut to crack for me, but I can follow your instructions and will try to modify as per the requirements. Since I am just a new learner, it will take the time to go through the details. Support me with your views. Thanks again.
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