# Kyle Rego

################################################################## Initialization
clear
units metal

variable howmany equal 100 # how often thermodynamics is outputted, and how many timesteps per frame in dump.

# distance Angstroms
# energy eV
# time picoseconds
# mass grams/mol

dimension 3

boundary p p p

atom_style molecular

newton on

# Load the atoms
read_data 3200nanotube.data

################################################################### Potentials

pair_style airebo/morse 3.0
pair_coeff * * CH.airebo-m C

#################################################################### Settings

neighbor 2 bin
neigh_modify delay 0 every 1 one 10000 check yes

# updating neighbor list every timestep

thermo ${howmany} # output thermodynamics every howmany timesteps

# relax the system
minimize 0.0001 0.0001 1000 1000

compute peratom all stress/atom NULL
compute px all reduce sum c_peratom[1]
variable stressperatom atom (c_peratom[1]+c_peratom[2]+c_peratom[3])/3

group mid2800 id 201:3000

compute en mid2800 pair airebo/morse
variable REBO     equal c_en[1]
variable LJ       equal c_en[2]
variable TORSION  equal c_en[3]

compute energ all pair airebo/morse
variable REBO2    equal c_energ[1]
variable LJ2      equal c_energ[2]
variable TORSION2  equal c_energ[3]


###################################################################### Equilibration

timestep 0.0005 # 1 femtoseconds 

thermo_style custom step time temp c_px pe fmax v_REBO v_LJ v_TORSION v_REBO2 v_LJ2 v_TORSION2 v_REBO2
dump 1 all custom ${howmany} nanotube.lammpstrj id x y z v_stressperatom
dump_modify 1 sort id


###################################################################### Simulation

velocity all create 10 12345

fix 1 all nve
fix 2 all temp/rescale 1 10 10 0.01 0.01
run 5000 # anneal at simulation temperature for 5000 timesteps
#
#unfix 1
#unfix 2
#
#reset_timestep 0
#fix 1 all nve
#fix 2 all temp/berendsen 10 10 0.025
#
#run 45000

print "Done"