# 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 deform-mod.data

displace_atoms all move -12 0 0 # optional

pair_style reaxff NULL safezone 3.0 mincap 150

pair_coeff * * ffield.reax.CHOFe Si O H

fix myqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400

group grpSi type Si

group grpO type O

group grpH type H

variable qSi equal charge(grpSi)/count(grpSi)

variable qO equal charge(grpO)/count(grpO)

variable qH equal charge(grpH)/(count(grpH)+1e-10)

variable vq atom q

thermo 200

thermo_style custom step temp etotal press vol v_qSi v_qO v_qH

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 adiam H 1.0 &

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 decorate-Si.histo mode vector

fix myhis2 grpO ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file decorate-O.histo mode vector

fix myhis3 grpH ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file decorate-H.histo mode vector

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

fix mynvt all nvt temp 300.0 300.0 100

timestep 0.5

label loop

variable a loop 10

variable seed equal 35672+${a}

create_atoms 3 random 2 ${seed} NULL overlap 2.6 maxtry 50

run 2000

next a

jump SELF loop