## Input data file for polarizable water ##

variable dataname index data_polwater.txt
variable simuname index polwater.txt
variable chh equal 0.4238
variable cho equal -2*v_chh

############ Initialization ##################################

units		real
boundary	p p p
atom_style	full
log			log.${simuname}
read_data	${dataname}

#### Pair, bond and angle coefficients ###
#### Uses SPC/E water model ##############
	
pair_style	lj/cut/coul/cut 9.2 9.2
#kspace_style ewald 1.0e-1
pair_coeff 1 1 0.1553 3.166
pair_coeff * 2 0 0
pair_coeff 3 3 0.130 2.156  
pair_coeff 4 4 0.130 2.156 

bond_style	harmonic
bond_coeff	1 350.0 1.000

angle_style harmonic
angle_coeff 1 100.0 109.47

##### Neighbor Criteria and Minimization ####

neighbor		0.01 bin
neigh_modify 	every 1 delay 0 check yes

thermo_style	custom step temp etotal ke pe vol press
thermo			100
min_style       sd
minimize		1e-10 1e-10 1000 100000

##### Velocity Initialization and Energy minimization II ####

velocity all create 300 554856 mom yes dist gaussian

min_style       sd
minimize		0 0 1000 100000

timestep		1.0

## Fixing Groups and Charges ####
group 		oxy type 1
group 		hyd type 2

fix ch_hyd hyd adapt 0 atom charge v_chh  
fix ch_oxy oxy adapt 0 atom charge v_cho 

group		water type 1 2

dump		1	all custom 1000 dump.xyz  id type x y z vx vy vz q
dump        2   all xyz 1000 jmol.xyz 
dump        for all custom 1000 for.xyz id fx fy fz


## Thermal annealing I ##
fix         2 water shake 0.0001 20 10000 b 1 a 1
fix 		tannealI all npt temp 300.0 1000.0 100.0 iso 0.0 0.0 1000.0
unfix tannealI
unfix 2
run         10000

## Thermal annealing II ##
fix 		tanealII all nve
fix         2 water shake 0.0001 20 10000 b 1 a 1

run 10000
unfix tanealII
unfix 2


## Thermal annealing III ##

fix			4 all nvt temp 1000.0 1000.0 200
fix         5 water shake 0.0001 20 10000 b 1 a 1
run         5000
unfix 4
unfix 5

fix			4 all nvt temp 300.0 300.0 200
fix         5 water shake 0.0001 20 10000 b 1 a 1
fix         3 all deform 1 x final 0.0 18.6 y final 0.0 18.6 z final 0.0 18.6 units box remap v
run         15000
unfix 4
unfix 5
unfix 3

## Thermal annealing IV ##

fix			4 all nve
fix         5 water shake 0.0001 20 10000 b 1 a 1
run         10000
unfix 4
unfix 5

fix			6 all nvt temp 300.0 300.0 200
fix         7 water shake 0.0001 20 10000 b 1 a 1
run         15000
dump_modify	1 sort id
write_restart           equil.restart.*