# This is the control script for LAMMPS.
echo both
log 2.1_Initialize.out
#-------------------------------------------------------------------------------
# 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
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
group fixed subtract all movable
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
#-------------------------------------------------------------------------------
# Stage 2.2: Minimization
#-------------------------------------------------------------------------------
min_style cg
min_modify dmax 0.05 line quadratic
reset_timestep 0
thermo_style custom step fmax fnorm press vol v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy pe v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz
dump sci all custom 1000 2.2.xyz id mol type q xs ys zs
thermo 100
fix 2_2_qeq all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
minimize 0.0 1.0 1000 10000
undump sci
unfix 2_2_qeq
log 2.3_Velocities.out
#-------------------------------------------------------------------------------
# Stage 2.3: Set the initial velocities for $T
#-------------------------------------------------------------------------------
velocity all create 300 72489 dist gaussian mom yes rot no
log 2.4_NPT.out
#-------------------------------------------------------------------------------
# Stage 2.4: NPT integration for 100 ps with a timestep of 1 fs
# Temperature 300 K
# Pressure 0 atm
#-------------------------------------------------------------------------------
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo ${Nthermo}
fix 1 movable npt temp 300 300 100 iso 0 0 100 drag 0 mtk yes nreset 2000
fix 2 movable ave/time 1 9999 10000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1
fix 3 movable ave/time 10 1 10 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt
fix 4 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
restart 100000 2.4.restart
dump sci all custom 10000 2.4.xyz id mol type q xs ys zs
timestep 1
run 100000
undump sci
restart 0
dump sci all custom 100000 2.4.xyz id mol type q xs ys zs
run 0
undump sci
unfix 1
unfix 2
unfix 3
unfix 4