units metal
atom_style full
boundary p p p
timestep 0.0001 # 0.1 fs

read_data methane-box-8.data

# DISCLAIMER: This potential mixes parameters from methane and silane
# potentials and is NOT intended to be a realistic representation of either
# system.  It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials,
# including the use of separate 'special_bonds' settings.

pair_style hybrid/overlay lj/cut 8.0 quip

# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0,
# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut
special_bonds lj/coul 0.999999999 0.999999999 0.999999999

# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
# Coulomb interactions omitted for simplicity
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
pair_coeff 1 2 lj/cut 0.0019295487 2.95
pair_modify shift no
# change exclusion settings for lj/cut only: exclude bonded pairs
pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0

# Intramolecular
# Tell QUIP to pretend this is silane (which is covered by the parameter file)
pair_coeff * * quip sw_example.xml "IP SW" 14 1
bond_style none
angle_style none

fix 1 all nve

# Include diagnostics that allow us to compare to a pure QUIP run
compute equip all pair quip
compute evdw all pair lj/cut
compute vir all pressure NULL virial

thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip
thermo 1

# dump 1 all custom 1 dump.molecular id type x y z fx fy fz
# dump_modify 1 sort id

run 10