[lammps-users] Count the no of Hexagons formed

Dear LAMMPS users,
I have a system that has a rectangular-shaped Nickel slab with the close-packed (111) facet is used to represent the Ni substrate, where elemental B and N are deposited initially for hBN nucleation and growth. There is a vacuum of 90 Å above and below the slab. My MD simulations are based on the reactive force-field (ReaxFF).

After some time hBN started to form on Ni. Now I want to count the no of Hexagonal Boron Nitride formed at different timesteps. I apply the “fix reax/c/species” command to write out the chemical species information and position. Some of the species no and position information are…

species no:

Timestep No_Moles No_Specs Ni711B195N176 N2 BN2 B3N4

2160700 12 4 1 8 2 1

Timestep No_Moles No_Specs Ni711B195N176 N2 BN2 B3N4

2160800 12 4 1 8 2 1

Timestep No_Moles No_Specs Ni711B195N176 N2 BN2 B3N4

2160900 12 4 1 8 2 1

Timestep No_Moles No_Specs Ni711B195N176 N2 BN2 B3N4

2161000 12 4 1 8 2 1

position information:
Timestep 2160000 NMole 12 NSpec 4 xlo 0.000000 xhi 29.902100 ylo 0.000000 yhi 25.895978 zlo -90.000000 zhi 98.138300
ID Atom_Count Type Ave_q CoM_x CoM_y CoM_z
1 1082 Ni711B195N176 0.00138046 0.98646879 0.03824521 0.51390987
2 2 N2 -0.07266975 0.44197726 0.64339168 0.81661106
3 3 BN2 -0.03554126 0.09058079 0.52365953 0.77143264
4 2 N2 -0.07253215 0.37591636 0.14331396 0.16636233
5 2 N2 -0.07227347 0.71566886 0.96067929 0.06603779
6 2 N2 -0.07251231 0.85086040 0.47660773 0.14296617
7 2 N2 -0.07252321 0.74308687 0.58817416 0.75162154
8 2 N2 -0.07250826 0.23374582 0.60694378 0.86754275
9 7 B3N4 -0.01726345 0.50114156 0.99889054 0.82769784
10 2 N2 -0.07252778 0.67474114 0.22499860 0.65720111
11 2 N2 -0.07246968 0.34383525 0.75025528 0.09368131
12 3 BN2 -0.03538444 0.70466055 0.89759370 0.22696317

From these informations by “fix reax/c/species” command how can I count the no of Hexagonal Boron Nitride formed??

Thanks

fix reax/c/species does exactly what the documentation says: it groups atoms into molecular clusters based on the bond order information and the provided (or default) cutoffs.
it doesn’t know anything about hexagons. if you want to count those automatically, you’ll have to implement your own algorithm and postprocess the data provided.

axel.