# Default script for simulating Nafion membrane with or without electrodes
# Testing for temperature (giving weird numbers)
clear
units              si
dimension          3
boundary           p p p
atom_style         molecular

thermo             100
comm_modify        vel yes
neighbor           3e-9 bin
neigh_modify       one 5000
                  
variable           filename index nafion.data
variable           T equal 300
variable           Seed equal 1234
variable           R equal 8.14e-10
variable           Nsteps equal 5e3
variable           timestep equal 2e-13
                  
pair_style         dpd ${T} ${R} ${Seed}
bond_style         harmonic
read_data          ${filename}

minimize           1.0e-10 1.0e-10 10000 10000           # energy tol, force tol, maxiter, maxeval
                  
velocity           all create ${T} ${Seed}
reset_timestep     0
timestep           ${timestep}
fix                1 all nvt temp ${T} ${T} 1     # Tstart, Tstop, Tdamp
run                ${Nsteps}
                   
print              "All done."