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lammps/examples/USER/qtb/methane_qtb/methane_qtb.in
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## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 &
a1 3.9783624 0 0 &
a2 0 3.9783624 0 &
a3 0 0 3.9783624 &
&
basis 0.5 0.5 0.5 &
basis 0.663 0.663 0.663 &
basis 0.337 0.337 0.663 &
basis 0.663 0.337 0.337 &
basis 0.337 0.663 0.337
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reax 10.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initilization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 100
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 3000 #750 fs
unfix methane_qtb
unfix scapegoat_qtb
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