Questions about fix reax/c/bond and fix reax/c/species commands

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


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


Ray (CCd) can likely answer these Qs.



The user sent me the same question off-line and this has been addressed, thanks.