dimension 3
units real
atom_style full
boundary p p f 

variable t equal 240
variable t2 equal 500
variable zlo equal -1
variable zhi equal 800
variable xlo equal -1.5
variable xhi equal 56.5
variable ylo equal -1.5
variable yhi equal 56.5
variable latparam equal 3.92
variable xhi_a equal 56.8
variable yhi_a equal 56.8
variable cutoff equal 12.0 #Angstroms

####Pair_Potential#######

bond_style      harmonic
angle_style     harmonic
dihedral_style  charmm
improper_style  harmonic
pair_style      lj/cut/coul/long/gpu ${cutoff} 

#pair_style lj/charmm/coul/long/gpu 10 ${cutoff} ${cutoff}

kspace_style    pppm/gpu 1.0e-4
special_bonds amber
kspace_modify slab 3.0
#special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 1.0 angle yes dihedral yes
#pair_modify mix arithmetic tail no # eij = sqrt(ei*ej), dij = 0.5*(di+dj)

timestep 1

read_data data.lammps
include parm.lammps

change_box all x final ${xlo} ${xhi} units box
change_box all y final ${ylo} ${yhi} units box
change_box all z final ${zlo} ${zhi} units box

#Creating a Solid Platinum Wall

lattice	fcc ${latparam}
region Pt_solid block 0 ${xhi_a} 0 ${yhi_a} 0 19.6 units box
create_atoms 4 region Pt_solid

region fixed block 0 ${xhi_a} 0 ${yhi_a} 0 1.96 units box
group fixed region fixed

region phantom block 0 ${xhi_a} 0 ${yhi_a} 1.96 5.88 units box
group phantom region phantom

region solid block 0 ${xhi_a} 0 ${yhi_a} 5.88 19.6 units box
group solid region solid

neighbor 3 bin
neigh_modify delay 0 every 1 check yes

group pt type 4
set group pt charge 0
group ra type 1 2 3

group intre subtract all fixed 

fix zwalls all wall/reflect zlo EDGE zhi EDGE

min_style cg
minimize 1.0e-3 1.0e-5 100000 400000   # minimization beforehand is optional
write_data posss.data

reset_timestep 0


### Equilibration Period

velocity intre create ${t} 1234
fix freeze fixed setforce 0.0 0.0 0.0

fix 1 intre nve

fix 2 phantom langevin ${t} ${t} 100 498094

compute temp_ra ra temp
fix temp_ra ra ave/time 1 1000 1000 c_temp_ra file Temp_ra.txt

compute temp_Phant phantom temp
fix temp_Phant phantom ave/time 1 1000 1000 c_temp_Phant file Temp_Phantom.txt

compute temp_solid solid temp
fix temp_solid solid ave/time 1 1000 1000 c_temp_solid file Temp_Solid.txt


thermo	        10000
thermo_style custom step tpcpu temp pe ke etotal epair ebond eangle edihed press vol

dump 1 all custom 5000 tmp.dump mass id mol type x y z vx vy vz

run 500000

undump 1

unfix 2

# Setting the temperature of the substrate at a higher value.
fix 3 phantom langevin ${t2} ${t2} 100 498094

dump 2 all custom 5000 tmp2.dump mass id mol type x y z vx vy vz

run 1000000