#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------

units			real
boundary		p p p
atom_style		full


box                     tilt large
read_data               structure.dat
Reading data file ...
  orthogonal box = (0 0 0) to (12.5214 12.5214 10.6652)
  2 by 4 by 2 MPI processor grid
  reading atoms ...
  216 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.002 seconds

pair_style              reax/c NULL checkqeq no safezone 10.0 mincap 1000
pair_coeff              * * parameters.dat C N O Si

variable		R		equal 0.00198722
variable		sysvol		equal vol
variable		sysmass		equal mass(all)/6.0221367e+023
variable		sysdensity	equal v_sysmass/v_sysvol/1.0e-24
variable		coulomb		equal ecoul+elong
variable		etotal		equal etotal
variable		pe		equal pe
variable		ke		equal ke
variable		evdwl		equal evdwl
variable		epair		equal epair
variable		ebond		equal ebond
variable		eangle		equal eangle
variable		edihed		equal edihed
variable		eimp		equal eimp
variable		lx		equal lx
variable		ly		equal ly
variable		lz		equal lz
variable		Nthermo		equal 0
variable		cella		equal lx
variable		cellb		equal sqrt(ly*ly+xy*xy)
variable		cellc		equal sqrt(lz*lz+xz*xz+yz*yz)
variable		cellalpha	equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc))
variable		cellbeta	equal acos(xz/v_cellc)
variable		cellgamma	equal acos(xy/v_cellb)
variable		p		equal press
variable		pxx		equal pxx
variable		pyy		equal pyy
variable		pzz		equal pzz
variable		pyz		equal pyz
variable		pxz		equal pxz
variable		pxy		equal pxy
variable		sxx		equal -pxx
variable		syy		equal -pyy
variable		szz		equal -pzz
variable		syz		equal -pyz
variable		sxz		equal -pxz
variable		sxy		equal -pxy
variable		fmax		equal fmax
variable	        fnorm		equal fnorm
variable		time equal step*dt+0.000001
variable		surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz)

thermo_style		custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo_modify		flush yes


#
# Set up the fixed and movable groups
#

group		    	movable union all
216 atoms in group movable
group		    	fixed subtract all movable
0 atoms in group fixed

compute 		sum_f1 movable reduce sum fx fy fz
variable 		sum_fx equal c_sum_f1[1]
variable 		sum_fy equal c_sum_f1[2]
variable  		sum_fz equal c_sum_f1[3]
log			2.2_Minimization.out