LAMMPS (5 Oct 2016)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.

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
Lattice spacing in x,y,z = 1.41421 2 2

region         mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box     1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
  1 by 1 by 1 MPI processor grid
mass           * 1.0
create_atoms   1 box
Created 1000 atoms

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

pair_style lj/cubic
pair_coeff * * 1.0 0.8908987

# Relax box dimensions

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
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.84754
  ghost atom cutoff = 1.84754
  binsize = 0.923769 -> bins = 8 11 11
Memory usage per processor = 3.65406 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz 
       0            0   -6.2937539   -6.2937539   -2.7722431   -2.7722431   -2.7722431    7.0710677    9.9999999    9.9999999 
     100            0   -6.3319018   -6.3319018  -0.75971321  -0.75971321  -0.75971321    7.0003571    9.8999999    9.8999999 
     134            0   -6.3344257   -6.3344257 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13    6.9780266    9.8684199    9.8684199 
Loop time of 0.0817621 on 1 procs for 134 steps with 1000 atoms

100.3% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = force tolerance
  Energy initial, next-to-last, final = 
         -6.2937539309     -6.33442568056     -6.33442568056
  Force two-norm initial, final = 3395.29 5.83329e-10
  Force max component initial, final = 1960.27 3.42093e-10
  Final line search alpha, max atom move = 1 3.42093e-10
  Iterations, force evaluations = 134 137

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.066955   | 0.066955   | 0.066955   |   0.0 | 81.89
Neigh   | 0.001004   | 0.001004   | 0.001004   |   0.0 |  1.23
Comm    | 0.0014298  | 0.0014298  | 0.0014298  |   0.0 |  1.75
Output  | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 |   0.0 |  0.02
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.01236    |            |       | 15.11

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0

# Define initial velocity

velocity        all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.84754
  ghost atom cutoff = 1.84754
  binsize = 0.923769 -> bins = 8 11 11

# Start Run #1

log log.nodrag
