# This file creates a small arrangement of spheres, and controls the 
# stresses when loaded by periodic boundaries.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


# Initialisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
units		si # This means m, kg, s for base units.
boundary	p p p
atom_style	sphere
atom_modify  map array # new thing for adnan
dimension	3
newton		off
echo         both
comm_modify  vel yes 


# Create particles ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_data	Thornton_Lattice_96_Spheres.lj


# Pre-fix settings ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
neighbor	0.00005 bin # ~5% of the diameter of the largest particle
neigh_modify	delay 0 
pair_style      gran/shm/history 29.17e9 0.2 0.1
pair_coeff	* *
timestep	auto
run_style	verlet

compute 	1 all pair/local p1 p2 p3 p4 p5 p6 p7 p8 p9 p10 p11 p12 p13 p14
compute 	conn all coord/gran 
compute 	aveconn all reduce ave c_conn 

# compute 	2 all coord/atom cutoff 0.00005 # original commands
# Slightly > 1 (max) diameter

dump		1 all local 100000 postliu_contact/dump*.contact c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7] c_1[8] c_1[9] c_1[10] c_1[11] c_1[12] c_1[13] c_1[14]

fix             1 all multistress 0.5 1000 x stress 100000 y stress 100000 z stress 100000 units box

variable 	step equal step
variable 	xxstress equal f_1[1]
variable 	yystress equal f_1[2]
variable 	zzstress equal f_1[3]
variable 	xystress equal f_1[4]
variable 	xzstress equal f_1[5]
variable 	yzstress equal f_1[6]
variable	xlength equal lx
variable	ylength equal ly
variable	zlength equal lz

variable        coordNum equal c_aveconn

fix 		2 all print 20000 "${step} ${xxstress} ${yystress} ${zzstress} ${xystress} ${xzstress} ${yzstress} ${xlength} ${ylength} ${zlength}" file mean_stresses_iso.txt screen no

fix		3 all nve/sphere

fix 		4 all print 20000 "${step} ${coordNum}" file trial_coord.txt screen no

fix          5 all momentum/gran  

dump         2 all custom 20000 postliu_connectivity/dump*.connectivity id c_conn x y z diameter

dump         3 all atom 20000 postliu_atom/dump*.atom
dump_modify  3 scale no

dump         4 all custom 20000 postliu_stress/dump*.stress id diameter c_1_stress[1] c_1_stress[2] c_1_stress[3] c_1_stress[4] c_1_stress[5] c_1_stress[6]

dump         5 all custom 20000 postliu_velocity/dump*.all_velocities id diameter x y z vx vy vz omegax omegay omegaz fx fy fz


#========================================================================================


restart		100000 restart_file

#=========================================================================================
run		1000000