#prime simulation settings

units          lj
atom_style     full
boundary       p p f

#Simulation box description

region simulation_box block 0 40 0 40 0 120
create_box 6 simulation_box bond/types 1 extra/bond/per/atom 2 extra/special/per/atom 5

#mass assignment
mass * 1.0

#lattice definition
lattice sc 1.0

#substrate insertion in the above mentioned box
region xy block EDGE EDGE EDGE EDGE 0.0 1.0 side in units box 
create_atoms 1 region xy units box
group substrate region xy
set type 1 charge -0.1
fix 2 substrate setforce 0.0 0.0 0.0

#substrate insertion in the above mentioned box
#region xyhi block EDGE EDGE EDGE EDGE 119.0 120.0 side in units box 
#create_atoms 1 region xyhi units box
#group substrate2 region xyhi
#fix 4 substrate2 setforce 0.0 0.0 0.0
#The fix wall below replaces the actual substrate2 to cover the top of the simulation box.

fix wallhi all wall/lj93 zhi 119.0 1.5 1.0 2.5 units box
fix_modify wallhi energy yes

#polymer insertion in the above mentioned box
#The insertions are carried out in specific regions to avoid overlapping and bond atoms missing error

molecule pe_positive pe_positive.tmp
molecule counter_ion_positive counter-ion_positive.tmp
molecule coion co-ion.tmp
molecule pe_negative pe_negative.tmp
molecule counter_ion_negative counter-ion_negative.tmp
region simuboxp block 0.0 EDGE 0.0 EDGE 20.0 40.0  side in units box
region simuboxn block 0.0 EDGE 0.0 EDGE 20.0 40.0  side in units box  
region boxcp block 0.0 EDGE 0.0 EDGE 42.0 82.0 side in units box
region boxcn block 0.0 EDGE 0.0 EDGE 84.0 114.0 side in units box
region box block EDGE EDGE EDGE EDGE 115.0 118.0 side in units box
create_atoms 0 random 30 145678 simuboxp mol pe_positive 789145 units box
create_atoms 0 random 900 568745 boxcp mol counter_ion_positive 456879 units box
create_atoms 0 random 320 125478 box mol coion 456854 units box

write_data basic_setup.polymer

group mobile type 2 3 4
group pe type 2
group cionpe1 type 3

#The group mobile consists of pe1 its counter-ion and co-ion(to neutralize the charged substrate)

#communication error
#comm_modify mode single cutoff 10.0 vel yes


#force field parameters
#bond coefficient

pair_style lj/cut/coul/long 2.5 15.0
pair_modify    shift yes
bond_style     fene
special_bonds  fene
bond_coeff * 15 2.0 1.0 1.0
kspace_style pppm 0.0001
kspace_modify slab 3.0
dielectric 1.0

#polymer and solvent-interaction pair coefficients definition
#The interaction parameters of the polymer-substrate-counterions- coions(to neutralize substrate)

pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
pair_coeff 1 3 1.0 1.0 1.12
pair_coeff 1 4 1.0 1.0 1.12
pair_coeff 1 5 1.0 1.0 2.5
pair_coeff 1 6 1.0 1.0 1.12
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 2 3 1.0 1.0 1.12
pair_coeff 2 4 1.0 1.0 1.12
pair_coeff 2 5 1.0 1.0 2.5
pair_coeff 2 6 1.0 1.0 1.12
pair_coeff 3 3 1.0 1.0 1.12
pair_coeff 3 4 1.0 1.0 1.12
pair_coeff 3 5 1.0 1.0 1.12
pair_coeff 3 6 1.0 1.0 1.12
pair_coeff 4 4 1.0 1.0 1.12
pair_coeff 4 5 1.0 1.0 1.12
pair_coeff 4 6 1.0 1.0 1.12
pair_coeff 5 5 1.0 1.0 2.5
pair_coeff 5 6 1.0 1.0 1.12
pair_coeff 6 6 1.0 1.0 1.12
#pair_coeff * * 1.0 1.0 2.5

#Run settings
timestep       0.01
run_style      verlet 
neighbor       0.3 bin
#neigh_modify   one 10000 check yes once no cluster no binsize 10000

#minimization
min_style cg
minimize 1e-12 1e-12 50000 10000

#thermo_style	custom step atoms temp epair etotal press
#thermo          100
#thermo_modify	temp add lost/bond ignore lost warn
#thermo_style one
#thermo_modify lost ignore

#NVT fix for the group mobile previously defined

fix 3 mobile nve
fix 1 mobile langevin 1 1 2.0 48279 

shell              mkdir img_cdepo1
dump               1 all image 250000 img_cdepo1/*.jpg type type view 90 90 size 1000 1000 zoom 2

shell		   mkdir restart_cdepo1
restart 	   1000 restart_cdepo1/poly.restart

write_data after_min_40l.polymer

#compute cc pe cluster/atom 1.2
#compute layers1 pe chunk/atom bin/1d z 0.0 0.25 units box

#fix den pe ave/chunk 100000 1 100000 layers1 density/number file density_n.txt
#dump unad pe custom 500000 dump.myunad.txt* id mol type q x y z 



thermo 1000
run 10000
write_data 06_05_2022_40l.polymer
#Rinsing step after depo 1

region cube block EDGE EDGE EDGE EDGE 3.0 119.0 side in units box
region cubec block EDGE EDGE EDGE EDGE EDGE 119.0 side in units box
delete_atoms porosity pe cube 1.0 482793 bond yes
delete_atoms porosity cionpe1 cubec 1.0 482793 bond yes
#Deposition of second layer
create_atoms 0 random 30 478589 simuboxn mol pe_negative 5478256 units box
create_atoms 0 random 900 214489 boxcn mol counter_ion_negative 426589 units box
create_atoms 0 random 360 568745 boxcp mol counter_ion_positive 456879 units box
group simurun type 3 5 6
group pe2 type 5
group cionpe2 type 6
#Group "mobile2" consists of Polyelectrolyte-2 with its counter-ions
#Group "between_sub" consists of all particles except the substrate

fix wallhi all wall/lj93 zhi 119.0 1.5 1.0 2.5 units box
fix_modify wallhi energy yes

#minimization
min_style cg
minimize 1e-12 1e-12 50000 10000

#NVT fix
fix 4 simurun nve
fix 5 simurun langevin 1.0 1.0 2.0 48279

shell              mkdir img_cdepo2
dump               2 all image 250000 img_cdepo2/*.jpg type type view 90 90 size 1000 1000 zoom 2



shell		   mkdir restart_cdepo2
restart 	   1000 restart_cdepo2/poly.restart

write_data 06_05_2022_40l_aftermin_depo2.polymer

compute layers2 pe2 chunk/atom bin/1d z 0.0 0.25 units box
fix den2 pe2 ave/chunk 1000 1 1000 layers2 density/number file density_n_2.txt
dump unad2 pe2 custom 1000 dump.myunad2.txt* id mol type q x y z 

thermo 100
run 10000

write_data after_deletion2.pol
#Taking out the unadsorbed polymeric layer 2
region cube2 block EDGE EDGE EDGE EDGE 4.0 119.0 side in units box
region cubec2 block EDGE EDGE EDGE EDGE EDGE 119.0 side in units box
delete_atoms porosity pe2 cube2 1.0 482793 bond yes
delete_atoms porosity cionpe2 cubec2 1.0 482793 bond yes

write_data after_deletion_3.pol

#deposition of third layer
create_atoms 0 random 30 458975 simuboxp mol pe_positive 145256 units box
create_atoms 0 random 900 256365 boxcp mol counter_ion_positive 254369 units box
create_atoms 0 random 30 256321 boxcn mol counter_ion_negative 458742 units box
group mobile type 2 3 4
group pe type 2
group cionpe1 type 3

write_data basic_set_up_3.pol

fix wallhi all wall/lj93 zhi 119.0 1.5 1.0 2.5 units box
fix_modify wallhi energy yes

#minimization
min_style cg
minimize 1e-12 1e-12 50000 10000

#NVT fix
fix 3 mobile nve
fix 1 mobile langevin 1.0 1.0 2.0 48279

shell              mkdir img_cdepo3
dump               3 all image 250000 img_cdepo3/*.jpg type type view 90 90 size 1000 1000 zoom 2



shell		   mkdir restart_cdepo3
restart 	   1000 restart_cdepo3/poly.restart

write_data 06_05_2022_40l_aftermin_depo3.polymer

#compute layers3 pe chunk/atom bin/1d z 0.0 0.25 units box
#fix den3 pe ave/chunk 1000 1 1000 layers3 density/number file density_n_3.txt
#dump unad3 pe custom 1000 dump.myunad3.txt* id mol type q x y z 

thermo 100
run 500000
write_data data_after_3_insertion.pol