improved shearing tutorial

docs/inputs/level2/nanosheared-electrolyte/Equilibration/input.lammps

@@ -21,7 +21,6 @@
 # ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠻⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣦⡀⠀⠈⠉⠛⠛⠓⠚⠋⠉⠁⠀⠀⠀⠀⠀⠀⠀
 # ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠙⠻⠿⣿⣿⣿⣿⡿⠟⠋⠀
 
-# Initialisation
 boundary p p p
 units real
 atom_style full
@@ -30,45 +29,24 @@ angle_style harmonic
 pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 12.0
 kspace_style pppm/tip4p 1.0e-4
 
-# System definition
 read_data ../Minimization/system.data
 
-# Simulation settings
 include ../PARM.lammps
+include ../GROUP.lammps
 
-# Define groups
-group gH2O type 1 2
-group gNa type 3
-group gCl type 4
-group gliquid type 1 2 3 4
-group gwall type 5
-region rtop block INF INF INF INF 0 INF
-region rbot block INF INF INF INF INF 0
-group gtop region rtop
-group gbot region rbot
-group gwalltop intersect gwall gtop
-group gwallbot intersect gwall gbot
+fix mynve all nve
+fix myber all temp/berendsen 300 300 100
+fix myshk H2O shake 1.0e-4 200 0 b 1 a 1
+fix myrct all recenter NULL NULL 0
+timestep 1.0
 
-# visualisation
 dump mydmp all atom 1000 dump.lammpstrj
-thermo 50
-variable walltopz equal xcm(gwalltop,z)
-variable wallbotz equal xcm(gwallbot,z)
+thermo 500
+variable walltopz equal xcm(walltop,z)
+variable wallbotz equal xcm(wallbot,z)
 variable deltaz equal v_walltopz-v_wallbotz
-fix myat1 all ave/time 10 10 100 v_deltaz file interwall_distance.dat
+fix myat1 all ave/time 100 1 100 v_deltaz file interwall_distance.dat
 
-# Dynamics
-fix mynve all nve
-compute tliq gliquid temp
-fix myber1 gliquid temp/berendsen 300 300 100
-fix_modify myber1 temp tliq
-compute twall gwall temp
-fix myber2 gwall temp/berendsen 300 300 100
-fix_modify myber2 temp twall
-fix myshk gH2O shake 1.0e-4 200 0 b 1 a 1
-fix myrct all recenter NULL NULL INIT
-
-timestep 1.0
-run 20000
+run 30000
 write_data system.data