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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7497 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-01-10 01:54:14 +00:00
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LAMMPS (10 Jan 2012)
# 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:167)
Memory usage per processor = 2.80047 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 -4.4422116e-13 -4.919366e-13 -4.9777247e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.082279 on 1 procs for 134 steps with 1000 atoms
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 5.78407e-10
Force max component initial, final = 1960.27 3.42777e-10
Final line search alpha, max atom move = 1 3.42777e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0646594 (78.5855)
Neigh time (%) = 0.00100803 (1.22514)
Comm time (%) = 0.00203061 (2.46796)
Outpt time (%) = 2.09808e-05 (0.0254996)
Other time (%) = 0.01456 (17.6959)
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
# Start Run #1
log log.nodrag

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LAMMPS (10 Jan 2012)
# 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 2 by 2 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:167)
Memory usage per processor = 2.77702 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 -4.5540246e-13 -4.9541511e-13 -5.0200254e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0306363 on 4 procs for 134 steps with 1000 atoms
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 5.85569e-10
Force max component initial, final = 1960.27 3.45689e-10
Final line search alpha, max atom move = 1 3.45689e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0165715 (54.0909)
Neigh time (%) = 0.000261545 (0.85371)
Comm time (%) = 0.00607055 (19.8149)
Outpt time (%) = 2.06828e-05 (0.0675108)
Other time (%) = 0.00771207 (25.173)
Nlocal: 250 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250 ave 6350 max 4305 min
Histogram: 1 0 0 0 2 0 0 0 0 1
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
# Start Run #1
log log.nodrag