in.molecular
65b295e826aalammm-devel

in.molecular
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			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 ommitted 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