#Input script for LAMMPS, simulating a bead tethered to a surface with a semi-flexible polymer tether.

# bb_radius: 5e-09
# fb_radius: 1.014e-09
# sb_radius: 1.014e-09

###----------VARIABLES: MAIN----------###
variable quote string "'" 
variable lj_eps equal 2.07097278e-20
# 2.07e-20 J equals 5.00 kT (T = 300.0 K)

###----------INITIALIZATION----------###
units	si
boundary	p p f
dimension	3
atom_style	hybrid angle sphere
log	"LOG\TEST3045_log.log" 

restart 13570 "RESTARTS\TEST3045_restart*.restart" 

###-----------PAIR INFO----------###
pair_style	lj/cut 2.390170685669979e-09

read_data	TEST3045_df.df
echo screen

###----------NEIGHBOUR SETTINGS-----------#
neighbor	9e-09 bin
neigh_modify	every 1000 delay 0 check yes one 1000

###----------BOND INFO-----------###
bond_style	harmonic

bond_coeff	1 0.005725949892552008 6.014e-09 
bond_coeff	2 0.0503545233593595 2.028e-09 
bond_coeff	3 0.0503545233593595 2.028e-09 

###-----------PAIR COEFFS----------###
pair_coeff	1 1 2.07097278e-20 1.0500000000000001e-08 1.1785851507248418e-08
pair_coeff	1 2 2.07097278e-20 6.314700000000001e-09 7.0880110964591985e-09
pair_coeff	1 3 2.07097278e-20 6.314700000000001e-09 7.0880110964591985e-09
pair_coeff	2 2 2.07097278e-20 2.1294e-09 2.390170685669979e-09
pair_coeff	2 3 2.07097278e-20 2.1294e-09 2.390170685669979e-09
pair_coeff	3 3 2.07097278e-20 2.1294e-09 2.390170685669979e-09
pair_modify shift yes

###----------ANGLE INFO----------###
angle_style	harmonic
angle_coeff 1 2.2701047780769226e-21 180
# 2.27E-21 J/rad^2 equals 0.55 kT/rad^2 (T = 300.0 K)

###----------GROUP INFO----------###

group fb type 1
group sb type 2
group bb type 3

###----------VELOCITIES----------###
velocity all create 300.0 1231
velocity	fb zero linear

###----------FIX COMMANDS BEFORE MINIMIZATION----------###
fix id_fix1 bb langevin 300 300 1.2337164750957855e-10 1231 angmom 3.333333
fix id_fix2 fb langevin 300 300 9.25550716157487e-14 1231
fix id_fix3 sb langevin 300 300 9.25550716157487e-14 1231
fix top all wall/reflect zhi EDGE
fix lowwall all wall/reflect zlo EDGE
#fix bblow bb wall/reflect zlo 5e-09 #wall/reflect not compatible with rigid body styles
fix zeroforce fb setforce 0 0 0
velocity fb zero linear
fix	newton0 sb nve
fix	newton1 fb nve
fix	newton2 bb nve/sphere
velocity fb zero linear
fix zeroforce fb setforce 0 0 0

###----------MINIMIZATION----------###
timestep	5e-15
minimize 4.1419e-22                 4.1419e-22                 10000000                 10000000

###----------TIMESTEP----------###
timestep	1e-13

###-------THERMO OUTPUT--------###
thermo_style custom step temp etotal ke pe
thermo 2475

###----------RUNS & DUMP ----------###
variable maxRunsPerDump equal 2000000000.0
variable totalRuns equal 2713943
variable noSubRuns equal ceil(${totalRuns}/${maxRunsPerDump})
variable remainingRuns equal ${totalRuns}

variable i loop ${noSubRuns}
variable pathStr string DMPS\TEST3045
print ${noSubRuns}
label loop
if "${remainingRuns}>${maxRunsPerDump}" then &
 "dump	$i all custom 2475 ${quote}${pathStr}_dump$i.dump${quote} id type x y z vx vy vz fx fy fz" &
 "dump_modify $i sort id pad 12" &
 "run ${maxRunsPerDump}" &
 "variable remainingRuns equal ${remainingRuns}-${maxRunsPerDump}" &
 "undump $i" &
 "next i" &
elif ${remainingRuns}<=0 &
 "undump $i" &
 "variable remainingRuns equal 0" & 
 "jump TEST3045_input.in end" &
else &
 "dump	$i all custom 2475 ${quote}${pathStr}_dump$i.dump${quote} id type x y z vx vy vz fx fy fz" &
 "dump_modify $i sort id pad 12" &
 "run ${remainingRuns}" &
 "variable remainingRuns equal 0" &
 "jump TEST3045_input.in end" 
jump TEST3045_input.in loop
label end