# LAMMPS Input File
# Licensed under CC BY 4.0
# A Set of Tutorials for the LAMMPS Simulation Package (LiveCoMS, 2025)
# By Simon Gravelle, Cecilia M. S. Alvares, Jacob R. Gissinger, and Axel Kohlmeyer
# Please cite doi.org/10.33011/livecoms.6.1.3037
# Find more on GitHub: https://github.com/lammpstutorials

units real
atom_style full

read_data silica.data

mass Si 28.0855
mass O 15.999

pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * ffield.reax.CHOFe Si O
fix myqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400

group grpSi type Si
group grpO type O
variable qSi equal charge(grpSi)/count(grpSi)
variable qO equal charge(grpO)/count(grpO)
variable vq atom q

thermo 100
thermo_style custom step temp etotal press vol v_qSi v_qO
dump viz all image 100 myimage-*.ppm q &
  type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
dump_modify viz adiam Si 2.6 adiam O 2.3 backcolor white &
  amap -1 2 ca 0.0 3 min royalblue 0 green max orangered

fix myhis1 grpSi ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file relax-Si.histo mode vector
fix myhis2 grpO ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file relax-O.histo mode vector

fix myspec all reaxff/species 5 1 5 relax.species element Si O

velocity all create 300.0 32028
fix mynpt all npt temp 300.0 300.0 100 aniso 1.0 1.0 1000
timestep 0.5

run 5000

write_data relax.data nofix