Commit before merge.

atom_modify sort 0 1.0

# Pair interactions require lists of neighbours to be calculated

neighbor 1.0 bin

neigh_modify every 1 delay 0 check yes

neighbor 3.0 bin

neigh_modify every 30 delay 0 check yes

read_data data.duplex2

variable ekin equal c_ekin

variable epot equal c_epot

variable etot equal c_erot+c_ekin+c_epot

fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes

fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen no file oxdna_thermo.dat

#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz

#dump_modify out sort id

thermo 100000

dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz

dump_modify out sort id

# dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"

run 1000000