####
# The LAMMPS input script for
# making a liquid structure with a specified temperature & pressure.
#

clear





######################
## MANUAL INPUTS     ##
######################

# title
variable	title string test
variable	jumpTarget string "test.txt"


# log and mkdir
shell mkdir ./dumps
shell mkdir ./logs
shell mkdir ./custom
shell mkdir ./dumps/${title}/
shell mkdir ./logs/${title}/
shell mkdir ./custom/${title}/
log ./logs/${title}/${title}(SETUPS).log




# potential
variable	pairStyle string tersoff
variable	potentialFilename string "./Si89.tersoff"
variable	potentialLabel string Si(C)

# supercell (z-axis must equal to c-axis)
variable	dataFilename string "./Si_tetrahedron_isolated.txt"




##########################
## SUBSIDIARY INPUTS     ##
##########################



log ./logs/${title}/${title}(MAIN).log
##########################
## initial setups       ##
##########################

timestep	0.001
units		metal
dimension	3

atom_style	atomic
atom_modify 	map array
boundary	p p p

read_data	${dataFilename}

pair_style	${pairStyle}
pair_coeff	* * ${potentialFilename} ${potentialLabel}


compute		temp1 all temp
compute		virialPres all pressure temp1 virial
compute		pePerAtom all pe/atom pair
compute		kePerAtom all ke/atom
compute		avePePerAtom all reduce ave c_pePerAtom 
compute		aveKePerAtom all reduce ave c_kePerAtom 

thermo		100
thermo_style	custom step c_avePePerAtom pe enthalpy c_aveKePerAtom temp press vol density 


dump		simpleDump all custom 1 ./dumps/${title}/${title}_simpleDump.txt id type x y z c_pePerAtom c_kePerAtom
run		0
undump		simpleDump