# Python script (License CC BY 4.0)

# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer

# The DOI will be added upon publication

# Find more on GitHub: https://github.com/lammpstutorials

units real

atom_style full

read_data relax.data

pair_style reaxff NULL safezone 3.0 mincap 150

pair_coeff * * reaxCHOFe.inc 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 200

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 deform-Si.histo mode vector

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

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

fix mynvt all nvt temp 300.0 300.0 100

timestep 0.5

run 5000

fix mydef all deform 1 x erate 5e-5

run 25000

write_data deform.data