################################
###########VARIABLES############
################################


variable		n index 11	#number of beads
variable		d index 1	#distance between beads
variable		preang index 50	#an angle between the ends of the chain
variable		r equal 36/PI	#radius of a circle

variable		b equal $n*$d+1
variable		ang equal ${preang}/(v_n-1)


################################
###########SIMULATION BOX#######
################################

boundary		p p p

atom_style		full
atom_modify		sort 0 5. map array
units			lj

#processors		1 * *

region		universe block 0 2 0 1 0 11 
create_box		1 universe

mass			1 1

variable		t loop $n

label			one

variable		m equal v_t-$n/2.0-0.5
variable		x equal $r-$r*cos(v_ang*$m*PI/180)
variable		z equal $r*sin(v_ang*$m*PI/180)+$r*sin(v_ang*5*PI/180)


create_atoms		1 single $x 0.5 $z 
next			t
jump			SELF one

set			group all mol 1

change_box		all boundary s m s
change_box		all boundary p p p x final 0 1.6 y final 0 1.6 z final 0 11

compute			chunks all chunk/atom molecule

replicate		15 15 9

velocity		all create 0.2 53252 mom yes rot yes

neigh_modify		exclude molecule/intra all

################################
###########POTENTIAL############
################################

pair_style		lj/cut $(2^(1/6))
pair_coeff		* * 1 1
pair_modify		shift yes


variable w equal $(density)
variable k equal density/11
variable s equal step


thermo_style		custom step time press etotal density cpuremain ndanger v_k lx ly lz
thermo			1000
timestep		0.01

dump			dump all custom 100000 dump_initial.lammpstrj id element xu yu zu
dump_modify		dump element A format float %6.3f sort id


fix			dt all dt/reset 1 0.0 0.01 0.005 
neigh_modify		every 1 check yes delay 0
comm_modify		cutoff 5.0

fix extra all print 1000 "$(step) $(etotal) $(press) $(vol) $(density) $(lx) $(ly) $(lz)" file initial_data.txt screen no title "TIMESTEP PRESSURE VOLUME DENSITY LX LY LZ"

fix			rigid all rigid/npt/small molecule temp 1.0 1.0 1.0 iso 1.0 1.0 1.0
compute      density_num_1   all   chunk/atom   bin/1d   z   lower   1 units box

fix         4   all   ave/chunk   1000  1  1000   density_num_1   density/mass   file   initial_density_mass_bin_1.txt 


run			70000000