#-------------------------------------------------------------------------------
# Stage 1.1: Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units real
boundary p p p
atom_style full
atom_modify map array
pair_style lj/class2/coul/long 9.5
pair_modify mix sixthpower
pair_modify tail yes
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
special_bonds lj 0.0 0.0 1.0 coul 0.0 0.0 1.0
box tilt large
read_data structure.dat
Reading data file ...
orthogonal box = (0 0 0) to (28.375581 28.375581 28.375581)
1 by 1 by 3 MPI processor grid
reading atoms ...
1476 atoms
scanning bonds ...
3 = max bonds/atom
scanning angles ...
9 = max angles/atom
scanning dihedrals ...
20 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
1653 bonds
reading angles ...
2730 angles
reading dihedrals ...
4308 dihedrals
reading impropers ...
900 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
9 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.055 seconds
include parameters.dat
bond_coeff 1 1.0982 372.83 -803.45 894.32 # cp h
bond_coeff 2 1.417 470.84 -627.62 1327.6 # cp cp
bond_coeff 3 1.3912 447.04 -784.53 886.17 # cp nn
bond_coeff 4 1.3768 428.88 -738.24 1115 # cp o
bond_coeff 5 1.417 470.84 -627.62 1327.6 # cp cp
bond_coeff 6 1.3768 428.88 -738.24 1115 # cp o
bond_coeff 7 1.0012 465.86 -1066.2 1496.6 # h* nn
angle_coeff 1 118.9 61.023 -34.993 0 # cp cp cp
angle_coeff 2 117.94 35.156 -12.468 0 # cp cp h
angle_coeff 3 121.46 61.065 -21.617 0 # cp cp nn
angle_coeff 4 123.42 73.678 -21.679 0 # cp cp o
angle_coeff 5 120 65 0 0 # * cp_ *
angle_coeff 6 120 50 0 0 # * n_ *
angle_coeff 7 117.94 35.156 -12.468 0 # cp cp h
angle_coeff 8 118.9 61.023 -34.993 0 # cp cp cp
angle_coeff 9 118.9 61.023 -34.993 0 # cp cp cp
angle_coeff 10 123.42 73.678 -21.679 0 # cp cp o
angle_coeff 11 109.5 60 0 0 # * o_ *
angle_coeff 12 111.87 40.837 -15.667 0 # cp nn h*
dihedral_coeff 1 8.3667 0 1.1932 0 0 0 # cp cp cp cp
dihedral_coeff 2 0 0 3.9661 0 0 0 # cp cp cp h
dihedral_coeff 3 0 0 5.3826 0 0 0 # cp cp cp nn
dihedral_coeff 4 0 0 4.8498 0 0 0 # cp cp cp o
dihedral_coeff 5 0 0 1.8769 0 0 0 # h cp cp h
dihedral_coeff 6 0 0 2.25 0 0 0 # * cp_ n_ *
dihedral_coeff 7 0 0 2.25 0 0 0 # * cp_ n_ *
dihedral_coeff 8 0 0 1.3331 0 0 0 # h cp cp nn
dihedral_coeff 9 0 0 3.9661 0 0 0 # cp cp cp h
dihedral_coeff 10 8.3667 0 1.1932 0 0 0 # cp cp cp cp
dihedral_coeff 11 0 0 3.9661 0 0 0 # h cp cp cp
dihedral_coeff 12 0 0 1.7234 0 0 0 # h cp cp o
dihedral_coeff 13 8.3667 0 1.1932 0 0 0 # cp cp cp cp
dihedral_coeff 14 0 0 4.8498 0 0 0 # cp cp cp o
dihedral_coeff 15 0 0 1.8 0 0 0 # * cp_ o_ *
dihedral_coeff 16 0 0 1.219 0 0 0 # cp cp nn h*
dihedral_coeff 17 0 0 2.25 0 0 0 # * cp_ n_ *
improper_coeff 1 7.1794 0 # cp cp cp cp
improper_coeff 2 4.8912 0 # cp cp cp h
improper_coeff 3 10 0 # * cp_ * *
improper_coeff 4 0.1 0 # * n_ * *
improper_coeff 5 10.786 0 # cp cp cp nn
improper_coeff 6 4.8912 0 # cp cp cp h
improper_coeff 7 13.042 0 # cp cp cp o
improper_coeff 8 0.1 0 # * n_ * *
angle_coeff 1 bb 68.286 1.417 1.417 # cp cp cp
angle_coeff 2 bb 1.0795 1.417 1.0982 # cp cp h
angle_coeff 3 bb 46.951 1.417 1.3912 # cp cp nn
angle_coeff 4 bb 48.475 1.417 1.3768 # cp cp o
angle_coeff 5 bb 0.0 1.3912 1.3768 # * cp_ *
angle_coeff 6 bb 0.0 1.3912 1.3912 # * n_ *
angle_coeff 7 bb 1.0795 1.417 1.0982 # cp cp h
angle_coeff 8 bb 68.286 1.417 1.417 # cp cp cp
angle_coeff 9 bb 68.286 1.417 1.417 # cp cp cp
angle_coeff 10 bb 48.475 1.417 1.3768 # cp cp o
angle_coeff 11 bb 0.0 1.3768 1.3768 # * o_ *
angle_coeff 12 bb 4.5393 1.3912 1.0012 # cp nn h*
angle_coeff 1 ba 28.871 28.871 1.417 1.417 # cp cp cp
angle_coeff 2 ba 20.003 24.218 1.417 1.0982 # cp cp h
angle_coeff 3 ba 39.404 73.655 1.417 1.3912 # cp cp nn
angle_coeff 4 ba 58.479 107.68 1.417 1.3768 # cp cp o
angle_coeff 5 ba 0.0 0.0 1.3912 1.3768 # * cp_ *
angle_coeff 6 ba 0.0 0.0 1.3912 1.3912 # * n_ *
angle_coeff 7 ba 20.003 24.218 1.417 1.0982 # cp cp h
angle_coeff 8 ba 28.871 28.871 1.417 1.417 # cp cp cp
angle_coeff 9 ba 28.871 28.871 1.417 1.417 # cp cp cp
angle_coeff 10 ba 58.479 107.68 1.417 1.3768 # cp cp o
angle_coeff 11 ba 0.0 0.0 1.3768 1.3768 # * o_ *
angle_coeff 12 ba 38.57 16.552 1.3912 1.0012 # cp nn h*
dihedral_coeff 1 mbt 27.599 -2.312 0 1.417 # cp cp cp cp
dihedral_coeff 2 mbt 0 -1.1521 0 1.417 # cp cp cp h
dihedral_coeff 3 mbt 0 -0.5693 0 1.417 # cp cp cp nn
dihedral_coeff 4 mbt 0 4.8255 0 1.417 # cp cp cp o
dihedral_coeff 5 mbt 0 4.8228 0 1.417 # h cp cp h
dihedral_coeff 6 mbt 0.0 0.0 0.0 1.3912 # * cp_ n_ *
dihedral_coeff 7 mbt 0.0 0.0 0.0 1.3912 # * cp_ n_ *
dihedral_coeff 8 mbt 0 2.2883 0 1.417 # h cp cp nn
dihedral_coeff 9 mbt 0 -1.1521 0 1.417 # cp cp cp h
dihedral_coeff 10 mbt 27.599 -2.312 0 1.417 # cp cp cp cp
dihedral_coeff 11 mbt 0 -1.1521 0 1.417 # h cp cp cp
dihedral_coeff 12 mbt 0 5.5432 0 1.417 # h cp cp o
dihedral_coeff 13 mbt 27.599 -2.312 0 1.417 # cp cp cp cp
dihedral_coeff 14 mbt 0 4.8255 0 1.417 # cp cp cp o
dihedral_coeff 15 mbt 0.0 0.0 0.0 1.3768 # * cp_ o_ *
dihedral_coeff 16 mbt 0 3.2085 0 1.3912 # cp cp nn h*
dihedral_coeff 17 mbt 0.0 0.0 0.0 1.3912 # * cp_ n_ *
dihedral_coeff 1 ebt -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 # cp cp cp cp
dihedral_coeff 2 ebt 0 -6.8958 0 0 -0.4669 0 1.417 1.0982 # cp cp cp h
dihedral_coeff 3 ebt 0 -6.5404 0 0 -7.3477 0 1.417 1.3912 # cp cp cp nn
dihedral_coeff 4 ebt 0 0.2655 0 0 4.8905 0 1.417 1.3768 # cp cp cp o
dihedral_coeff 5 ebt 0 -0.689 0 0 -0.689 0 1.0982 1.0982 # h cp cp h
dihedral_coeff 6 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.417 1.3912 # * cp_ n_ *
dihedral_coeff 7 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3912 # * cp_ n_ *
dihedral_coeff 8 ebt 0 -2.6482 0 0 -1.6402 0 1.0982 1.3912 # h cp cp nn
dihedral_coeff 9 ebt 0 -6.8958 0 0 -0.4669 0 1.417 1.0982 # cp cp cp h
dihedral_coeff 10 ebt -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 # cp cp cp cp
dihedral_coeff 11 ebt 0 -0.4669 0 0 -6.8958 0 1.0982 1.417 # h cp cp cp
dihedral_coeff 12 ebt 0 -1.5867 0 0 4.2641 0 1.0982 1.3768 # h cp cp o
dihedral_coeff 13 ebt -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 # cp cp cp cp
dihedral_coeff 14 ebt 0 0.2655 0 0 4.8905 0 1.417 1.3768 # cp cp cp o
dihedral_coeff 15 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.417 1.3768 # * cp_ o_ *
dihedral_coeff 16 ebt 0 -3.7281 0 0 0.2849 0 1.417 1.0012 # cp cp nn h*
dihedral_coeff 17 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0012 # * cp_ n_ *
dihedral_coeff 1 at 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 2 at 0 2.5014 0 0 2.7147 0 118.9 117.94 # cp cp cp h
dihedral_coeff 3 at 0 9.0901 0 0 -6.0882 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 4 at 0 10.015 0 0 1.7404 0 118.9 123.42 # cp cp cp o
dihedral_coeff 5 at 0 2.4501 0 0 2.4501 0 117.94 117.94 # h cp cp h
dihedral_coeff 6 at 0.0 0.0 0.0 0.0 0.0 0.0 121.46 120 # * cp_ n_ *
dihedral_coeff 7 at 0.0 0.0 0.0 0.0 0.0 0.0 120 120 # * cp_ n_ *
dihedral_coeff 8 at 0 2.9813 0 0 0.2787 0 117.94 121.46 # h cp cp nn
dihedral_coeff 9 at 0 2.5014 0 0 2.7147 0 118.9 117.94 # cp cp cp h
dihedral_coeff 10 at 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 11 at 0 2.7147 0 0 2.5014 0 117.94 118.9 # h cp cp cp
dihedral_coeff 12 at 0 1.8729 0 0 2.5706 0 117.94 123.42 # h cp cp o
dihedral_coeff 13 at 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 14 at 0 10.015 0 0 1.7404 0 118.9 123.42 # cp cp cp o
dihedral_coeff 15 at 0.0 0.0 0.0 0.0 0.0 0.0 123.42 109.5 # * cp_ o_ *
dihedral_coeff 16 at 0 1.2616 0 0 0.7744 0 121.46 111.87 # cp cp nn h*
dihedral_coeff 17 at 0.0 0.0 0.0 0.0 0.0 0.0 120 111.87 # * cp_ n_ *
dihedral_coeff 1 aat 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 2 aat -4.8141 118.9 117.94 # cp cp cp h
dihedral_coeff 3 aat 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 4 aat -21.025 118.9 123.42 # cp cp cp o
dihedral_coeff 5 aat 0.3598 117.94 117.94 # h cp cp h
dihedral_coeff 6 aat 0.0 121.46 120 # * cp_ n_ *
dihedral_coeff 7 aat 0.0 120 120 # * cp_ n_ *
dihedral_coeff 8 aat 0 117.94 121.46 # h cp cp nn
dihedral_coeff 9 aat -4.8141 118.9 117.94 # cp cp cp h
dihedral_coeff 10 aat 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 11 aat -4.8141 117.94 118.9 # h cp cp cp
dihedral_coeff 12 aat 4.2296 117.94 123.42 # h cp cp o
dihedral_coeff 13 aat 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 14 aat -21.025 118.9 123.42 # cp cp cp o
dihedral_coeff 15 aat 0.0 123.42 109.5 # * cp_ o_ *
dihedral_coeff 16 aat -7.1755 121.46 111.87 # cp cp nn h*
dihedral_coeff 17 aat 0.0 120 111.87 # * cp_ n_ *
dihedral_coeff 1 bb13 53 1.417 1.417 # cp cp cp cp
dihedral_coeff 2 bb13 -6.2741 1.417 1.0982 # cp cp cp h
dihedral_coeff 3 bb13 -9.7999 1.417 1.3912 # cp cp cp nn
dihedral_coeff 4 bb13 -2.2436 1.417 1.3768 # cp cp cp o
dihedral_coeff 5 bb13 -1.7077 1.0982 1.0982 # h cp cp h
dihedral_coeff 6 bb13 0.0 1.417 1.3912 # * cp_ n_ *
dihedral_coeff 7 bb13 0.0 1.3768 1.3912 # * cp_ n_ *
dihedral_coeff 8 bb13 -1.0746 1.0982 1.3912 # h cp cp nn
dihedral_coeff 9 bb13 -6.2741 1.417 1.0982 # cp cp cp h
dihedral_coeff 10 bb13 53 1.417 1.417 # cp cp cp cp
dihedral_coeff 11 bb13 -6.2741 1.0982 1.417 # h cp cp cp
dihedral_coeff 12 bb13 2.0517 1.0982 1.3768 # h cp cp o
dihedral_coeff 13 bb13 53 1.417 1.417 # cp cp cp cp
dihedral_coeff 14 bb13 -2.2436 1.417 1.3768 # cp cp cp o
dihedral_coeff 15 bb13 0.0 1.417 1.3768 # * cp_ o_ *
dihedral_coeff 16 bb13 4.2366 1.417 1.0012 # cp cp nn h*
dihedral_coeff 17 bb13 0.0 1.3768 1.0012 # * cp_ n_ *
improper_coeff 1 aa 0 0 0 118.9 118.9 118.9 # cp cp cp cp
improper_coeff 2 aa 0 0 0 118.9 117.94 117.94 # cp cp cp h
improper_coeff 3 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * cp_ * *
improper_coeff 4 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * n_ * *
improper_coeff 5 aa 0 0 0 118.9 121.46 121.46 # cp cp cp nn
improper_coeff 6 aa 0 0 0 118.9 117.94 117.94 # cp cp cp h
improper_coeff 7 aa 0 0 0 118.9 123.42 123.42 # cp cp cp o
improper_coeff 8 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * n_ * *
pair_coeff 1 1 0.0668 3.9147 # cp -
pair_coeff 2 2 0.0568 3.9147 # cpc -
pair_coeff 3 3 0.023 2.878 # h -
pair_coeff 4 4 0.008 1.087 # h* -
pair_coeff 5 5 0.092 3.89 # nn -
pair_coeff 6 6 0.096 3.58 # o -
pair_coeff 7 7 0.12 3.3 # oc -
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
kspace_style pppm 0.00001
variable R equal 0.00198722
variable sysvol equal vol
variable sysmass equal mass(all)/6.0221367e+23
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
1476 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 1.2_NVT.out