# Variables
################################################################################
variable POTENTIAL_PATH	string	"/home/yoelk/LAMMPS/lammps-27May10/potentials"
variable OUT_FOLDER		string	"checkpoints"
variable NAME			string	"Di_300K-512[001]"
variable RANDOM_SEED	equal	4928459
variable TIME_STEP		equal	0.0001 # In picoseconds

# Init
################################################################################
units metal
timestep ${TIME_STEP}
boundary	p p p
newton on
atom_style	atomic
neighbor 1.0 bin
atom_modify sort 0 12.0
read_data	${NAME}.xyzlmps
pair_style airebo 3.0 0 0
pair_coeff * * ${POTENTIAL_PATH}/CH.airebo C  
mass 1 12.0107

# Simulation
################################################################################
variable TOTAL_TIME					equal	10 # In picoseconds
variable TOTAL_TIME_STEPS			equal	${TOTAL_TIME}/${TIME_STEP}

group GROUP_FIX_SET_PLACE id 10 200 500

# Dump the whole sample's positions
dump DUMP_ALL all custom ${DUMP_ALL_FREQUENCY} ${OUT_FOLDER}/${NAME}_Checkpoint*.xyz_all id type x y z
dump_modify DUMP_ALL first no

thermo_style custom step temp etotal ke pe press
thermo ${DUMP_ALL_FREQUENCY}

# Run
################################################################################
variable TS1						equal	${TOTAL_TIME_STEPS}/10

variable TEMP equal 4000.0
velocity all create ${TEMP} ${RANDOM_SEED} dist gaussian units box mom yes rot yes
fix FIX_ALL_NPT all npt temp ${TEMP} ${TEMP} 1.0 iso 1.0 1.0 10.0 mtk yes
	run	${TS1}
unfix FIX_ALL_NPT

fix FIX_ALL_NVE all nve
	run	${TS1}
unfix FIX_ALL_NVE