Hello everyone. I want to take the whole advantage of the forum and ask masters of Lammps simulations about my question. I am studying silicon carbide oxidation under dry O2 gas conditions. It is expected that a part of the atoms in SiC surface will be separated from their initial crystallized positions. How am I supposed to calculate the number of C atoms out of the crystal, or other words, lost atoms in the system and the number of O atoms inside the SiC crystal? Is there any lammps command for that? Should I determine variables in my input script?
Here is my input code
LAMMPS Input file
SiC with O2 #name of the project
Intialization
units metal #picoseconds 10e-12 (eV, A, ps)
dimension 3
boundary p p f #periodic boundary conditions for x and y and fixed for z axis
atom_style charge #lmp data file must consist of charge
Atom Definition
read_data try.lmp
Settings
mass 1 28.086
mass 2 12.011
mass 3 15.999
reset_timestep 0
fix 1 all box relax/iso 0.0 vmax 0.001
velocity all create 298.15 4928459 rot yes mom yes dist gaussian
fix 2 all nvt temp 298.15 298.15 0.001 #set nvt ensemple
fix 3 all temp/berendsen 298.15 298.15 0.001 #set the beredsen control termostat
fix zwalls all wall/reflect zlo EDGE zhi EDGE #set a repeilsive boundary conditions for Z ort
pair_style reax/c NULL # set interatomic potential style
pair_coeff * * ffield20.reax Si C O # read in interatomic potential file
fix 4 all qeq/reax 1 0.0 10.0 1e-6 reax/c
thermo_style custom step temp epair etotal econserve press
thermo 500 #(every 500 timesteps – output thermo properties)
timestep 5.0e-4
neighbor 1.0 bin # define parameters for neighbor list
neigh_modify every 1 delay 10 check no # define parameters for neighbor list
thermo_modify lost ignore flush yes
Output
dump dumpXYZ all xyz 1 try.dump #write trajectory file in dump format (OVITO)
dump dmp all atom 100 dump.lammpstrj # write trajectory file in lammps trajectory format (VMD)
#dat file
thermo_style one
#thermo 100 #(every 100 timesteps – output thermo properties)
restart 100 file.restart #write executable wile of topology after 100 steps, which can be run as inticial topologu of atoms
#Minimization
min_style cg #(perfect crystal)
minimize 1e-10 1e-10 5000 5000
Run the simulation
run 2000000 #for 1 ns = 510e-42*10e6=1000ps