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lammps/examples/hugoniostat/in.hugoniostat
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in.hugoniostat
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# 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
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
# 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
# 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 10.0 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 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
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} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
#dump id all atom 500 dump.hugoniostat
#dump 2 all image 500 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
run 10000
# Start Run #2
log log.drag
clear
read_restart restart.equil
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term on
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
run 10000
# Start Run #3
log log.nhchains
clear
read_restart restart.equil
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
run 10000
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