units real 
dimension 3 
boundary p p p 
atom_style charge 

# ---------- Create Atoms --------------------- 
read_data     data_right_middle_left.FC

group PssPedot id <= 14112
group water id >= 14113
# ---------- Define Interatomic Potential --------------------- 
pair_style hybrid/overlay   reax/c NULL checkqeq no  reax/c NULL checkqeq no 
#pair_style hybrid/overlay   reax/c NULL checkqeq no safezone 16 mincap 1000 reax/c NULL checkqeq no safezone 16 mincap 1000 
#lj/cut/coul/cut 10.0  
#coul/cut 10.0 
pair_coeff * * reax/c 1 ffield_Castro_CombFlame C C O H S C O O H H S NULL NULL
pair_coeff * * reax/c 2 ffield.protein NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL H O 

pair_coeff 4 12 none 
pair_coeff 9*10 12 none 
pair_coeff 1*2 12 none
pair_coeff 6 12 none
pair_coeff 3 12 none
pair_coeff 7*8 12 none
pair_coeff 5 12 none
pair_coeff 11 12 none
pair_coeff 4 13 none 
pair_coeff 9*10 13 none
pair_coeff 1*2 13 none
pair_coeff 6 13 none
pair_coeff 3 13 none
pair_coeff 7*8 13 none
pair_coeff 5 13 none 
pair_coeff 11 13 none

#pair_coeff 4 12 lj/cut/coul/cut  0.02 2. 
#pair_coeff 9*10 12 lj/cut/coul/cut  0.02 2. 
#pair_coeff 1*2 12 lj/cut/coul/cut  0.055 3.
#pair_coeff 6 12 lj/cut/coul/cut  0.055 3.
#pair_coeff 3 12 lj/cut/coul/cut   0.063 2.6
#pair_coeff 7*8 12 lj/cut/coul/cut   0.063 2.6
#pair_coeff 5 12 lj/cut/coul/cut  0.063 3.
#pair_coeff 11 12 lj/cut/coul/cut  0.063 3. 
#pair_coeff 4 13 lj/cut/coul/cut  0.063 2.6 
#pair_coeff 9*10 13 lj/cut/coul/cut  0.063 2.6 
#pair_coeff 1*2 13 lj/cut/coul/cut  0.173 3.6
#pair_coeff 6 13 lj/cut/coul/cut 0.173 3.6 
#pair_coeff 3 13 lj/cut/coul/cut  0.2 3.2 
#pair_coeff 7*8 13 lj/cut/coul/cut  0.2 3.2
#pair_coeff 5 13 lj/cut/coul/cut  0.2 3.6 
#pair_coeff 11 13 lj/cut/coul/cut  0.2 3.6 
#kspace_style pppm 1.0e-4
#dielectric 1000.
neighbor 2.10 bin # build the neighbor list with bin style (~N/P)
neigh_modify delay 100 check yes  
#fix 12 PssPedot qeq/reax 1 0.0 10.0 1.0e-6 reax/c 
#fix 13 water qeq/reax 1 0.0 10.0 1.0e-6 reax/c 



dump	10 all xyz 1000 dump.xyz 
#dump mydump all custom 10000 dump.pedot id type q x y z
#dump_modify mydump sort id


# ---------- Run Minimization --------------------- 

fix 5 PssPedot setforce 0.0 0.0 0.0
velocity    water create 100 1234 dist gaussian mom yes rot yes



fix            2  all nvt temp 100 100 1.                                                                                                             
thermo 1000 
thermo_style custom step temp pe lx ly lz press
timestep	0.1
run 50000
unfix 2
unfix 5

fix            2  all npt temp 100 1000 1. iso 0.1 0.1 1000.                                                                                                            
thermo 1000 
thermo_style custom step temp pe lx ly lz press
timestep	0.2
run 100000
unfix 2


fix            2  all npt temp 1000 1000 1. iso 0.1 0.1 1000.                                                                                                            
thermo 1000 
thermo_style custom step temp pe lx ly lz press
timestep	0.2
run 1000000