Here is my script. Can anyone be kind enough to direct me where I made the mistake?

# heat layers

region hot_end block INF INF INF INF 0 6.805

region cold_end block INF INF INF INF 156.506 163.311

region hot block INF INF INF INF 0 20

region cold block INF INF INF INF 141 161.946

region fixed_heat_source_side block INF INF INF INF 0 12

region fixed_heat_sink_side block INF INF INF INF 151 161.946

group hot region hot

group cold region cold

group fixed_heat_source_side region fixed_heat_source_side

group fixed_heat_sink_side region fixed_heat_sink_side

group end union fixed_heat_source_side fixed_heat_sink_side

group moving subtract all end

velocity all create $t 87287 dist gaussian

compute Thot hot temp

compute Tcold cold temp

# 1st equilibration run

fix 1 all nvt temp $t $t 0.5

thermo 1000

thermo_modify lost ignore flush yes

run 100000

unfix 1

reset_timestep 0

# 2nd equilibration run

fix 2 all nve

fix hot_langevin hot langevin ${thi} ${thi} 0.5 59804 tally yes

fix cold_langevin cold langevin ${tlo} ${tlo} 0.5 287859 tally yes

#velocity end set 0.0 0.0 0.0

#fix set_end end setforce 0.0 0.0 0.0

fix_modify hot_langevin temp Thot

fix_modify cold_langevin temp Tcold

variable tdiff equal c_Thot-c_Tcold

thermo_style custom step temp c_Thot c_Tcold f_hot_langevin f_cold_langevin v_tdiff etotal

thermo 1000

thermo_modify lost ignore flush yes

run 1000000

# 3rd thermal conductivity calculation

# reset langevin thermostats to zero energy accumulation

unfix hot_langevin

unfix cold_langevin

fix hot_langevin hot langevin ${thi} ${thi} 0.5 59804 tally yes

fix cold_langevin cold langevin ${tlo} ${tlo} 0.5 287859 tally yes

velocity end set 0.0 0.0 0.0

fix set_end end setforce 0.0 0.0 0.0

fix_modify hot_langevin temp Thot

fix_modify cold_langevin temp Tcold

fix ave all ave/time 1 200000 200000 v_tdiff ave running

thermo 10000

thermo_style custom step temp c_Thot c_Tcold f_hot_langevin f_cold_langevin v_tdiff etotal

thermo_modify lost ignore flush yes

compute ke all ke/atom

variable KB equal 8.625e-5

variable temp atom c_ke/1.5/${KB}

# Define spatial bins along the z-axis for temperature profiling

compute myChunk all chunk/atom bin/1d z lower 0.01 units reduced

fix 4 all ave/chunk 1 200000 200000 myChunk v_temp file profile.langevin ave running

run 5000000

More Fnu Asrafuzzaman's questions See All
Similar questions and discussions