##########################################################
#------------Variables and cell--------------------------#
##########################################################

clear
units           metal         #eV,atomic charge,angstroms,ps,kelvin,bars,g/mol
dimension 3
boundary p p p
atom_style full 

#processors * * * grid numa
fix csinfo all property/atom i_CSID
read_data coordinates.lammps fix csinfo NULL CS-Info	#File name read in containing coordinates etc.

group lithium type 1
group cores type 2 4 6 8
group shells type 3 5 7 9

#neighbor 2.0 bin
comm_modify vel yes

variable T1 equal 1		#Sets temperature of the system
variable Timer equal step*dt

#########################################################
#---------- Pair styles and electrostatics--------------#
#########################################################

pair_style buck/coul/long 8.0       #A, rho, C
pair_coeff * * 0.0            1.000      0.00  
pair_coeff 1 9 632.1018       0.2906     0.0000
pair_coeff 3 9 1582.5000      0.2882     0.00000
pair_coeff 5 9 1397.6300      0.3211     0.00000
pair_coeff 7 9 1329.8200      0.3087     0.00000
pair_coeff 9 9 22764.0000     0.1490     65.0000

bond_style harmonic
bond_coeff 1  93.7   0.0
bond_coeff 2  196.3  0.0
bond_coeff 3  95.0   0.0
bond_coeff 4  65.0   0.0

kspace_style ewald 1e-03		#Ewald precision

########################################################
# -------------- Run Minimization ---------------------#
########################################################
 
reset_timestep 0 
timestep 0.001
thermo 1			#prints data every x steps
#compute 1 all pe/atom
#dump 1 all custom 1 patom.dump id mol type pe/atom
thermo_style custom step etotal temp enthalpy &
             fmax lx ly lz vol press 
min_style cg 
minimize 1e-25 1e-25 5000 10000 


########################################################
# -------------- Relax Cell ---------------------------#
########################################################

reset_timestep 0 
timestep 0.001
fix 1 all box/relax aniso 1.0 vmax 0.003
thermo 1 
thermo_style custom step enthalpy fmax lx ly lz vol press 
min_style cg 
minimize 1e-25 1e-25 5000 10000 
unfix 1

########################################################
# ------------- Run NPT T1-----------------------------#
########################################################


reset_timestep 0
timestep 0.01
compute         mymsd lithium msd com yes
variable        msdx equal "c_mymsd[1]"
variable        msdy equal "c_mymsd[2]"
variable        msdz equal "c_mymsd[3]"
variable        msdtot equal "c_mymsd[4]"
fix             msdT1 lithium ave/time 1 1 10000 v_msdx v_msdy v_msdz v_msdtot file msd${T1}
fix             3 all npt temp ${T1} ${T1} 0.01 aniso 0.0 0.0 10
thermo_style custom step v_Timer cpu temp etotal fmax lx ly lz vol press 
thermo 1
dump dynamics all xyz 5000 dynamics.xyz		#Prints dynamixs file every x steps
run             10000000
unfix 3
unfix msdT1