Hello everyone,
I am new to using the compute chunk/atom command in LAMMPS and would appreciate some guidance.
I am simulating the bombardment of Kapton with atomic oxygen (AO) using the ReaxFF potential to study how AO interacts with Kapton. In my setup, Kapton is positioned at the bottom of the simulation cell, and I have extended the z-dimension to allow the addition of atomic oxygen for bombardment.
During the simulation, I observe the formation of various molecules such as OH, H₂O, O₂, carbon chains, CO, CO₂, and others. I now want to identify and count all the molecules generated during the reaction using LAMMPS, rather than relying solely on visualization.
Based on my understanding of the compute chunk/atom
documentation, this command can assign an ID to each molecule. To achieve my goal, I included the following lines in my script:
Temperature Profile Across z-Direction
compute Temp_cc1 all chunk/atom bin/1d z lower 2
compute tempChunk all temp/chunk Temp_cc1
fix avgTemp all ave/time 1000 1 1000 c_tempChunk file temp_profile.dat
Tracking Desorbed Gases
region region_desorbtion block INF INF INF INF 55 198 units box
group At_desorbed dynamic all region region_desorbtion every 500
compute mol_cc1 At_desorbed chunk/atom molecule
compute countMol At_desorbed count/chunk mol_cc1
compute idMol At_desorbed property/atom mol
fix saveMolCount all ave/time 1000 1 1000 c_countMol file desorption_gases.dat
fix saveMolID all ave/time 1000 1 1000 c_idMol file desorption_mol_IDs.dat
However, I encounter the following error:
ERROR: Compute chunk/atom molecule for non-molecular system (src/compute_chunk_atom.cpp:312)
Last command: compute mol_cc1 At_desorbed chunk/atom molecule
I am unsure if I am using compute chunk/atom molecule
correctly. Could someone help me understand what I might be doing wrong? Any advice would be greatly appreciated!
Thank you!