Dear LAMMPS Community,
Greetings!
I am performing ReaxFF MD simulation on a simulation box initially containing oxygen molecule and lithium atom. However, when simulation proceeds, oxygen reacts with lithium forming various products such as Li2O, LiO2, and Li2O2 etc. I wanna calculate the number of time evolution of oxygen, lithium and their corresponding products. When I try to define Group for Li2O2 in input script, it shows following error;
“ERROR: Group command requires atom attribute molecule (src/group.cpp:207)”
Kindly guide me how to define Groups for all the products, and how to calculate their time evolution? Below is the input script;
REAXff
-------------------- Init Section ----------------------
units real
boundary p p p
atom_style charge
pair_style reax/c lmp_control
-------------------- Atom Definition Section ------------
read_data datafile.txt
#replicate 6 6 8
group oxygen type 1 # C
group Li type 2 # Li
group Li2O2 molecule 1 2
#--------------------- Pair Coefficients ------------------------
pair_coeff * * ffield.reax.LIS C Li
-------------------- Settings Section -------------------
neighbor 2 bin
neigh_modify every 10 delay 0 check no
timestep 0.1
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
-------------------- MSD Section -------------------
compute msdli Li msd
variable twopoint_li equal c_msdli[4]/6/(stepdt+1.0e-6)
#fix 3 lithium vector 10000 c_msdli[4]
#variable fitslope equal slope(f_3)/4/(10dt)
-------------------- Run Section (NVT: diffusion)------------------------
fix 3 all nvt temp 300.0 300.0 500.0
thermo 100
thermo_style custom step time etotal temp press vol density c_msdli[4] v_twopoint_li
dump 1 all atom 100 MD1-NVT*.lammpstrj
#restart 30000 MD.restart
run 1000
write_data data.out