# Simple virus model.
#

units lj
dimension 3
boundary f f f

atom_style angle
pair_style lj/cut 4.0
pair_modify shift yes
bond_style harmonic
angle_style harmonic

neigh_modify binsize 5.0

read_data init.data

group NC    type 1
group rest  type 2 3 4
group CA    type 3


timestep 0.0001
variable R equal "ramp(v_R0,v_R1)"

variable RF equal ${R1}
variable Rw equal "v_RF - 0.5"

print "**** R scales from ${R0} to ${R1} and wall is at ${Rw} ****"

variable rr   atom "sqrt( x*x + y*y + z*z )"
compute  ravg CA reduce ave v_rr

region my_sphere sphere 0 0 0 v_Rw side out
fix wall all wall/region my_sphere lj126 1.0 1.0 1.1225


variable U equal pe
variable epair equal epair
fix U all ave/time 2000 1 2000 v_U v_R v_epair
variable t equal time
variable ravg equal c_ravg

variable T equal 0.25

variable pU equal f_U[1]
variable pE equal f_U[3]

fix out all print 2000 "$t    ${pU}    $R    ${ravg}    ${pE}" file thermo.${DATA}.dat screen no

fix step1 rest nvt temp $T $T 1.0
fix step2 NC   nvt/manifold/rattle 1e-4 10 sphere v_R temp $T $T 1.0

special_bonds lj 0 0 0

angle_coeff 1 250.0 180.0

thermo_style custom time step pe v_pU ke etotal epair temp v_R
thermo 10000



compute pe         all pe/atom
fix     pe_avg     all ave/atom 100 50 5000 c_pe


dump traj_all   all  custom 5000 virus.dump id type x   y   z f_pe_avg

run 2500000
unfix out

fix step1 rest nvt temp $T $T 1.0
fix step2 NC   nvt/manifold/rattle 1e-4 10 sphere ${R1} temp $T $T 1.0

run 1000000