Removed some stuff

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6921 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/hugoniostat/in.nphug

@@ -0,0 +1,159 @@
+# 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
+