Dear Lammps Users:
Hello, I try to do some reactive md simulations and use fix reax/c/bond and species command to get the species information and bond connection table. When I check the connection table I found the molecule id of all atoms in the connection table are 0 but the species output file could show different number of species and molecules. It looks like weird and contradicting with each other. In the simulation, I use charge style which doesn’t include molecule id in the lammps data file. Does it result in this contradiction?
I also dumped the fix reax/c/species per-atom information which represents the molecule ID for each atom into the dump file. Then I visualize it using Ovito software. However, I found this command identify two atoms in a same molecule even the atoms are far away from each other. Is this normal in the lammps simulation? And is there some way to avoid this kind of thing?
Really appreciated if someone could help solve this problem. And I have attached the input file as following:
units real
dimension 3
boundary p p p
atom_style charge
pair_style reax/c NULL safezone 1.6 mincap 100
variable NVT_temp equal 3000
variable timestep_val equal 0.1
variable ensemble_style string NVT
read_data initial.data
variable t_damp equal 100*${timestep_val}
pair_coeff * * /home/sly1993/potential/ffield.reax.cho C O
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
mass 1 12.01
mass 2 16
compute eng all pe/atom
compute eatoms all reduce sum c_eng
reset_timestep 0
thermo 100
thermo_style custom step temp pe lx ly lz press pxx pyy pzz vol etotal
fix myQeQ all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
dump 1 all cfg 500 ./data/minimize.*.cfg mass type xs ys zs id q c_eng
dump_modify 1 element C O
minimize 1.00e-30 1.00e-30 100000 1000000
undump 1
reset_timestep 0
timestep ${timestep_val}
restart 5000 ./sav/restart.*
velocity all create ${NVT_temp} 8873445 mom yes rot no
fix 2 all nvt temp {NVT_temp} {NVT_temp} ${t_damp}
else quit
fix mySpecies all reax/c/species 1 1 100 species.out element C O position 1000 CO.pos
fix myBonds all reax/c/bonds 2000 bonds.reaxc
thermo 1000
thermo_style custom step temp pe lx ly lz press pxx pyy pzz vol etotal
dump 1 all cfg 2000 ./data/*.cfg mass type xs ys zs id q c_eng f_mySpecies
dump_modify 1 element C O