#prime simulation settings

units          lj
atom_style     full
boundary       p p f
processors     2 2 *

#Simulation box description

region simulation_box block 0 40 0 40 0 40
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 0.0 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 39.0 40.0 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


#polymer insertion in the above mentioned box

molecule pe_positive pe_positive.tmp
molecule counter_ion_positive counter-ion_positive.tmp
molecule coion co-ion.tmp
region simubox block EDGE EDGE EDGE EDGE 15.0 25.0  side in units box 
region box block EDGE EDGE EDGE EDGE 1.0 39.0 side in units box
create_atoms 0 random 30 789586 simubox mol pe_positive 256897 units box
create_atoms 0 random 900 568745 box mol counter_ion_positive 456879 units box
create_atoms 0 random 160 458789 box mol coion 754214 units box

#communication error
#comm_modify mode single cutoff 10.0 vel yes


#force field parameters
#bond coefficient

pair_style lj/cut/coul/long 2.5 10.0
pair_modify    shift yes
bond_style     fene
special_bonds  fene
bond_coeff * 30 1.5 1.0 1.0
kspace_style pppm 0.00001
kspace_modify slab 3.0
dielectric 1.0

#polymer and solvent-interaction pair coefficients definition
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 2.5
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 2.5
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






#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-24 1e-24 50000 10000



#thermo_style one
#thermo_modify lost ignore

#NVT fix
fix 3 all nve
fix 1 all 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 	   50000 restart_cdepo1/poly.restart
write_data after_min_40l.polymer

run 10000

write_data 06_05_2022_40l.polymer

#Deposition step 2
#polymer insertion in the above mentioned box

molecule pe_negative pe_negative.tmp
molecule counter_ion_negative counter-ion_negative.tmp
region simubox block EDGE EDGE EDGE EDGE 15.0 25.0  side in units box 
region box block EDGE EDGE EDGE EDGE 1.0 39.0 side in units box
create_atoms 0 random 30 789586 simubox mol pe_negative 256897 units box
create_atoms 0 random 900 568745 box mol counter_ion_negative 456879 units box

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 	   50000 restart_cdepo2/poly.restart

#NVT fix
fix 3 all nve
fix 1 all langevin 1 1 2.0 48279 

run 10000

write_data 06_05_2022_40l_depo2.polymer