##################################################################################################################
# Nipun Goel
# Ph.D.
# February 7, 2021
# setup MD calculation to equilibrate and evaluate strengthening in dislocation fault system
##################################################################################################################

# Variable definitions
variable initTemp equal 1.0          	# desired temperature
variable initPress equal 0.0          # desired pressure
variable equilTime equal 10000        	# number of increment to equilibrate the temperature
variable runTime equal 50000   	# number of increment to calibrate the velocity

##################################################################################################################

# System Initialization

processors	* * *

units		metal
dimension	3
atom_style	atomic

#read_restart	/home/jeff/nipun/strengthening/0K/mu_calculation/potential_test/CoCr/co0p0cr1p0/l03162021l_sgmc_NPT_0K_200000.rst
read_data	/home/jeff/nipun/strengthening/0K/mu_calculation/potential_test/CoCr/co0p0cr1p0/l03162021l_sgmc_NPT_0K_emin_pure.data

#replicate	2 1 6
timestep	0.001

group grp_Co type 1
group grp_Cu type 2
group grp_Cr type 3
group grp_Fe type 4
group grp_Ni type 5
#group grp_W type 6
#group grp_Al type 7

velocity        all create ${initTemp} 61578932

# Defining Interatomic Potential
pair_style	eam/alloy
pair_coeff	* * /home/jeff/nipun/lammps-29Oct20/potentials/CoCuCrFeNiWAl.set Co Cu Cr Fe Ni W Al
neighbor        1.0 bin
neigh_modify    every 1 delay 1 check yes

#####################################################
# Computes #
#####################################################

compute		eng all pe/atom
compute		eatoms all reduce sum c_eng
compute		c1 all stress/atom NULL

#####################################################
# Fixes #
#####################################################

fix		f1 all ave/atom 20 50 1000 c_c1[1]
fix		f2 all ave/atom 20 50 1000 c_c1[2]
fix		f3 all ave/atom 20 50 1000 c_c1[3]

#####################################################
# Equilibration: Isobaric-Isothermal Ensemble	(NPT) #
#####################################################

fix		fix_npt1 all npt temp ${initTemp} ${initTemp} 0.2 iso ${initPress} ${initPress} 1.0
fix		SGMC all atom/swap 10 100 61236050 ${initTemp} semi-grand yes types 1 3 mu 0.0 1.0


thermo		100
thermo_style	custom step temp pe ke etotal vol press pxx pyy pzz pxy pyz pxz c_eatoms
thermo_modify	flush yes

restart	10000 /home/jeff/nipun/strengthening/0K/mu_calculation/potential_test/CoCr/co0p0cr1p0/l03162021l_sgmc_NPT_0K_*.rst
dump		dump1 all custom 2000 /home/jeff/nipun/strengthening/0K/mu_calculation/potential_test/CoCr/co0p0cr1p0/l03162021l_sgmc_NPT_0K_*.xyz  id type x y z f_f1 f_f2 f_f3 c_c1[1] c_c1[2] c_c1[3]

dump_modify	dump1 element Co Cu Cr Fe Ni W Al

run		${runTime}

unfix fix_npt1