Removed some stuff

# This script reproduces the damped and undamped

# stress trajectories in Fig. 1 in

# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)

units           lj

boundary        p p p

atom_style	atomic

# Set up FCC lattice with z axis along <110>

lattice                fcc 1.4142136 &

                       orient x 0 0 1 &

                       orient y 1 -1 0 &

                       orient z 1 1 0

region         mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice

create_box     1 mycell

mass           * 1.0

create_atoms   1 box

# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987

pair_style lj/cubic

pair_coeff * * 1.0 0.8908987

fix             3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100

thermo          100

thermo_style	custom step temp pe etotal pxx pyy pzz lx ly lz 

min_modify      line quadratic

minimize	0.0 1.0e-6 10000 100000

# Define initial velocity

velocity        all create 0.01 87287 mom yes rot yes dist gaussian

write_restart restart.equil

# Start Run #1

log log.nodrag

clear

read_restart restart.equil

neighbor        0.2 bin

neigh_modify    every 1 delay 0 check yes

timestep        0.001

reset_timestep 0

# Pzz = 40.0, drag/damping term off

fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0 

# Specify reference state from paper, times 1000 atoms

fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519

# Add fix energy to ouput etotal

fix_modify myhug energy yes 

# Define output

variable dele  equal f_myhug[1] # energy delta [temperature]

variable us    equal f_myhug[2] # shock velocity [distance/time]

variable up    equal f_myhug[3] # particle velocity [distance/time]

variable pzz   equal pzz  # axial stress

variable tau equal (pzz-0.5*(pxx+pyy)) # shear stress

variable time equal dt*step

thermo          10

thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up

fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'

run		10000

# Start Run #2

log log.drag

clear

read_restart restart.equil

neighbor        0.2 bin

neigh_modify    every 1 delay 0 check yes

timestep        0.001

reset_timestep 0

# Pzz = 40.0, drag/damping term on

fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 

# Specify reference state from paper, times 1000 atoms

fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519

# Add fix energy to ouput etotal

fix_modify myhug energy yes 

# Define output

variable dele  equal f_myhug[1] # energy delta [temperature]

variable us    equal f_myhug[2] # shock velocity [distance/time]

variable up    equal f_myhug[3] # particle velocity [distance/time]

variable pzz   equal pzz  # axial stress

variable tau equal (pzz-0.5*(pxx+pyy)) # shear stress

variable time equal dt*step

thermo          10

thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up

fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'

run		10000

# Start Run #3

log log.nhchains

clear

read_restart restart.equil

neighbor        0.2 bin

neigh_modify    every 1 delay 0 check yes

timestep        0.001

reset_timestep 0

# Pzz = 40.0, drag/damping term off, Nose-Hoover chains

fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0

# Specify reference state from paper, times 1000 atoms

fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519

# Add fix energy to ouput etotal

fix_modify myhug energy yes 

# Define output

variable dele  equal f_myhug[1] # energy delta [temperature]

variable us    equal f_myhug[2] # shock velocity [distance/time]

variable up    equal f_myhug[3] # particle velocity [distance/time]

variable pzz   equal pzz  # axial stress

variable tau equal (pzz-0.5*(pxx+pyy)) # shear stress

variable time equal dt*step

thermo          10

thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up

fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'

run		10000