LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
log 1.1_Initialize.out
#-------------------------------------------------------------------------------
# Stage 1.1: Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units real
boundary p p p
atom_style full
pair_style lj/class2 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 (16.653635 16.653635 16.653635)
3 by 1 by 1 MPI processor grid
reading atoms ...
465 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
30 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
505 bonds
reading angles ...
830 angles
reading dihedrals ...
1250 dihedrals
reading impropers ...
300 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
14 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.010 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 1.417 470.84 -627.62 1327.6 # cp cp
bond_coeff 4 1.3912 447.04 -784.53 886.17 # cp nn
bond_coeff 5 1.3768 428.88 -738.24 1115 # cp o
bond_coeff 6 1.3768 428.88 -738.24 1115 # cp o
bond_coeff 7 1.501 321.9 -521.82 572.16 # c cp
bond_coeff 8 1.53 299.67 -501.77 679.81 # c c
bond_coeff 9 1.101 345 -691.89 844.6 # c h
bond_coeff 10 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 3 118.9 61.023 -34.993 0 # cp cp cp
angle_coeff 4 117.94 35.156 -12.468 0 # cp cp h
angle_coeff 5 118.9 61.023 -34.993 0 # cp cp cp
angle_coeff 6 123.42 73.678 -21.679 0 # cp cp o
angle_coeff 7 121.46 61.065 -21.617 0 # cp cp nn
angle_coeff 8 123.42 73.678 -21.679 0 # cp cp o
angle_coeff 9 120 65 0 0 # * cp_ *
angle_coeff 10 120 50 0 0 # * n_ *
angle_coeff 11 111.87 40.837 -15.667 0 # cp nn h*
angle_coeff 12 109.5 60 0 0 # * o_ *
angle_coeff 13 120.05 44.715 -22.735 0 # c cp cp
angle_coeff 14 111 44.323 -9.4454 0 # cp c cp
angle_coeff 15 108.4 43.959 -8.3924 -9.3379 # c c cp
angle_coeff 16 112.67 39.516 -7.443 -9.5583 # c c c
angle_coeff 17 110.77 41.453 -10.604 5.129 # c c h
angle_coeff 18 107.66 39.641 -12.921 -2.4318 # h c h
angle_coeff 19 118.9 61.023 -34.993 0 # cp cp cp
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 8.3667 0 1.1932 0 0 0 # cp cp cp cp
dihedral_coeff 4 0 0 5.3826 0 0 0 # cp cp cp nn
dihedral_coeff 5 0 0 4.8498 0 0 0 # cp cp cp o
dihedral_coeff 6 0 0 3.9661 0 0 0 # cp cp cp h
dihedral_coeff 7 0 0 1.8769 0 0 0 # h cp cp h
dihedral_coeff 8 8.3667 0 1.1932 0 0 0 # cp cp cp cp
dihedral_coeff 9 0 0 4.8498 0 0 0 # cp cp cp o
dihedral_coeff 10 0 0 3.9661 0 0 0 # h cp cp cp
dihedral_coeff 11 0 0 1.7234 0 0 0 # h cp cp o
dihedral_coeff 12 0 0 1.8 0 0 0 # * cp_ o_ *
dihedral_coeff 13 0 0 2.25 0 0 0 # * cp_ n_ *
dihedral_coeff 14 0 0 1.219 0 0 0 # cp cp nn h*
dihedral_coeff 15 0 0 2.25 0 0 0 # * cp_ n_ *
dihedral_coeff 16 0 0 2.25 0 0 0 # * cp_ n_ *
dihedral_coeff 17 0 0 1.559 0 0 0 # c cp cp h
dihedral_coeff 18 0 0 4.4072 0 0 0 # c cp cp cp
dihedral_coeff 19 -0.2802 0 -0.0678 0 -0.0122 0 # cp c cp cp
dihedral_coeff 20 -0.2802 0 -0.0678 0 -0.0122 0 # c c cp cp
dihedral_coeff 21 -0.0228 0 0.028 0 -0.1863 0 # cp c c h
dihedral_coeff 22 0 0 0.0316 0 -0.1681 0 # c c c h
dihedral_coeff 23 0 0 1.3331 0 0 0 # h cp cp nn
dihedral_coeff 24 0 0 5.3826 0 0 0 # cp cp cp nn
dihedral_coeff 25 0 0 4.8498 0 0 0 # cp cp cp o
dihedral_coeff 26 8.3667 0 1.1932 0 0 0 # cp cp cp cp
improper_coeff 1 7.1794 0 # cp cp cp cp
improper_coeff 2 4.8912 0 # cp cp cp h
improper_coeff 3 4.8912 0 # cp cp cp h
improper_coeff 4 13.042 0 # cp cp cp o
improper_coeff 5 10 0 # * cp_ * *
improper_coeff 6 0.1 0 # * n_ * *
improper_coeff 7 7.8153 0 # c cp cp cp
improper_coeff 8 0.0 0.0 # c3 c0 cp cp
improper_coeff 9 0.0 0.0 # c3 c0 c3 cp
improper_coeff 10 0.0 0.0 # c0 c3 hc hc
improper_coeff 11 0.0 0.0 # hc c3 hc hc
improper_coeff 12 0.1 0 # * n_ * *
improper_coeff 13 10.786 0 # cp cp cp nn
improper_coeff 14 4.8912 0 # cp cp cp h
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 68.286 1.417 1.417 # cp cp cp
angle_coeff 4 bb 1.0795 1.417 1.0982 # cp cp h
angle_coeff 5 bb 68.286 1.417 1.417 # cp cp cp
angle_coeff 6 bb 48.475 1.417 1.3768 # cp cp o
angle_coeff 7 bb 46.951 1.417 1.3912 # cp cp nn
angle_coeff 8 bb 48.475 1.417 1.3768 # cp cp o
angle_coeff 9 bb 0.0 1.3912 1.3768 # * cp_ *
angle_coeff 10 bb 0.0 1.3912 1.3912 # * n_ *
angle_coeff 11 bb 4.5393 1.3912 1.0012 # cp nn h*
angle_coeff 12 bb 0.0 1.3768 1.3768 # * o_ *
angle_coeff 13 bb 12.068 1.501 1.417 # c cp cp
angle_coeff 14 bb 0.0 1.501 1.501 # cp c cp
angle_coeff 15 bb 0 1.53 1.501 # c c cp
angle_coeff 16 bb 0 1.53 1.53 # c c c
angle_coeff 17 bb 3.3872 1.53 1.101 # c c h
angle_coeff 18 bb 5.3316 1.101 1.101 # h c h
angle_coeff 19 bb 68.286 1.417 1.417 # cp cp cp
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 28.871 28.871 1.417 1.417 # cp cp cp
angle_coeff 4 ba 20.003 24.218 1.417 1.0982 # cp cp h
angle_coeff 5 ba 28.871 28.871 1.417 1.417 # cp cp cp
angle_coeff 6 ba 58.479 107.68 1.417 1.3768 # cp cp o
angle_coeff 7 ba 39.404 73.655 1.417 1.3912 # cp cp nn
angle_coeff 8 ba 58.479 107.68 1.417 1.3768 # cp cp o
angle_coeff 9 ba 0.0 0.0 1.3912 1.3768 # * cp_ *
angle_coeff 10 ba 0.0 0.0 1.3912 1.3912 # * n_ *
angle_coeff 11 ba 38.57 16.552 1.3912 1.0012 # cp nn h*
angle_coeff 12 ba 0.0 0.0 1.3768 1.3768 # * o_ *
angle_coeff 13 ba 47.058 31.077 1.501 1.417 # c cp cp
angle_coeff 14 ba 0.0 0.0 1.501 1.501 # cp c cp
angle_coeff 15 ba 0 0 1.53 1.501 # c c cp
angle_coeff 16 ba 8.016 8.016 1.53 1.53 # c c c
angle_coeff 17 ba 20.754 11.421 1.53 1.101 # c c h
angle_coeff 18 ba 18.103 18.103 1.101 1.101 # h c h
angle_coeff 19 ba 28.871 28.871 1.417 1.417 # cp cp cp
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 27.599 -2.312 0 1.417 # cp cp cp cp
dihedral_coeff 4 mbt 0 -0.5693 0 1.417 # cp cp cp nn
dihedral_coeff 5 mbt 0 4.8255 0 1.417 # cp cp cp o
dihedral_coeff 6 mbt 0 -1.1521 0 1.417 # cp cp cp h
dihedral_coeff 7 mbt 0 4.8228 0 1.417 # h cp cp h
dihedral_coeff 8 mbt 27.599 -2.312 0 1.417 # cp cp cp cp
dihedral_coeff 9 mbt 0 4.8255 0 1.417 # cp cp cp o
dihedral_coeff 10 mbt 0 -1.1521 0 1.417 # h cp cp cp
dihedral_coeff 11 mbt 0 5.5432 0 1.417 # h cp cp o
dihedral_coeff 12 mbt 0.0 0.0 0.0 1.3768 # * cp_ o_ *
dihedral_coeff 13 mbt 0.0 0.0 0.0 1.3912 # * cp_ n_ *
dihedral_coeff 14 mbt 0 3.2085 0 1.3912 # cp cp nn h*
dihedral_coeff 15 mbt 0.0 0.0 0.0 1.3912 # * cp_ n_ *
dihedral_coeff 16 mbt 0.0 0.0 0.0 1.3912 # * cp_ n_ *
dihedral_coeff 17 mbt 0 3.9421 0 1.417 # c cp cp h
dihedral_coeff 18 mbt 0 9.1792 0 1.417 # c cp cp cp
dihedral_coeff 19 mbt 0.0 0.0 0.0 1.501 # cp c cp cp
dihedral_coeff 20 mbt 0 0 0 1.501 # c c cp cp
dihedral_coeff 21 mbt 0 0 0 1.53 # cp c c h
dihedral_coeff 22 mbt -14.879 -3.6581 -0.3138 1.53 # c c c h
dihedral_coeff 23 mbt 0 2.2883 0 1.417 # h cp cp nn
dihedral_coeff 24 mbt 0 -0.5693 0 1.417 # cp cp cp nn
dihedral_coeff 25 mbt 0 4.8255 0 1.417 # cp cp cp o
dihedral_coeff 26 mbt 27.599 -2.312 0 1.417 # cp cp cp cp
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 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 # cp cp cp cp
dihedral_coeff 4 ebt 0 -6.5404 0 0 -7.3477 0 1.417 1.3912 # cp cp cp nn
dihedral_coeff 5 ebt 0 0.2655 0 0 4.8905 0 1.417 1.3768 # cp cp cp o
dihedral_coeff 6 ebt 0 -6.8958 0 0 -0.4669 0 1.417 1.0982 # cp cp cp h
dihedral_coeff 7 ebt 0 -0.689 0 0 -0.689 0 1.0982 1.0982 # h cp cp h
dihedral_coeff 8 ebt -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 # cp cp cp cp
dihedral_coeff 9 ebt 0 0.2655 0 0 4.8905 0 1.417 1.3768 # cp cp cp o
dihedral_coeff 10 ebt 0 -0.4669 0 0 -6.8958 0 1.0982 1.417 # h cp cp cp
dihedral_coeff 11 ebt 0 -1.5867 0 0 4.2641 0 1.0982 1.3768 # h cp cp o
dihedral_coeff 12 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.417 1.3768 # * cp_ o_ *
dihedral_coeff 13 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.417 1.3912 # * cp_ n_ *
dihedral_coeff 14 ebt 0 -3.7281 0 0 0.2849 0 1.417 1.0012 # cp cp nn h*
dihedral_coeff 15 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3912 # * cp_ n_ *
dihedral_coeff 16 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0012 # * cp_ n_ *
dihedral_coeff 17 ebt 0 -1.797 0 0 -0.4879 0 1.501 1.0982 # c cp cp h
dihedral_coeff 18 ebt 0 0.2421 0 0 -0.6918 0 1.501 1.417 # c cp cp cp
dihedral_coeff 19 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.501 1.417 # cp c cp cp
dihedral_coeff 20 ebt 0 0 0 0 0 0 1.53 1.417 # c c cp cp
dihedral_coeff 21 ebt 0 0 0 0 0 0 1.501 1.101 # cp c c h
dihedral_coeff 22 ebt 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 # c c c h
dihedral_coeff 23 ebt 0 -2.6482 0 0 -1.6402 0 1.0982 1.3912 # h cp cp nn
dihedral_coeff 24 ebt 0 -6.5404 0 0 -7.3477 0 1.417 1.3912 # cp cp cp nn
dihedral_coeff 25 ebt 0 0.2655 0 0 4.8905 0 1.417 1.3768 # cp cp cp o
dihedral_coeff 26 ebt -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 # cp cp cp cp
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 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 4 at 0 9.0901 0 0 -6.0882 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 5 at 0 10.015 0 0 1.7404 0 118.9 123.42 # cp cp cp o
dihedral_coeff 6 at 0 2.5014 0 0 2.7147 0 118.9 117.94 # cp cp cp h
dihedral_coeff 7 at 0 2.4501 0 0 2.4501 0 117.94 117.94 # h cp cp h
dihedral_coeff 8 at 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 9 at 0 10.015 0 0 1.7404 0 118.9 123.42 # cp cp cp o
dihedral_coeff 10 at 0 2.7147 0 0 2.5014 0 117.94 118.9 # h cp cp cp
dihedral_coeff 11 at 0 1.8729 0 0 2.5706 0 117.94 123.42 # h cp cp o
dihedral_coeff 12 at 0.0 0.0 0.0 0.0 0.0 0.0 123.42 109.5 # * cp_ o_ *
dihedral_coeff 13 at 0.0 0.0 0.0 0.0 0.0 0.0 121.46 120 # * cp_ n_ *
dihedral_coeff 14 at 0 1.2616 0 0 0.7744 0 121.46 111.87 # cp cp nn h*
dihedral_coeff 15 at 0.0 0.0 0.0 0.0 0.0 0.0 120 120 # * cp_ n_ *
dihedral_coeff 16 at 0.0 0.0 0.0 0.0 0.0 0.0 120 111.87 # * cp_ n_ *
dihedral_coeff 17 at 0 -0.1242 0 0 3.4601 0 120.05 117.94 # c cp cp h
dihedral_coeff 18 at 0 -4.4683 0 0 3.8987 0 120.05 118.9 # c cp cp cp
dihedral_coeff 19 at 0.0 0.0 0.0 0.0 0.0 0.0 111 120.05 # cp c cp cp
dihedral_coeff 20 at 0 0 0 0 0 0 108.4 120.05 # c c cp cp
dihedral_coeff 21 at 0 0 0 0 0 0 108.4 110.77 # cp c c h
dihedral_coeff 22 at -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77 # c c c h
dihedral_coeff 23 at 0 2.9813 0 0 0.2787 0 117.94 121.46 # h cp cp nn
dihedral_coeff 24 at 0 9.0901 0 0 -6.0882 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 25 at 0 10.015 0 0 1.7404 0 118.9 123.42 # cp cp cp o
dihedral_coeff 26 at 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 # cp cp cp cp
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 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 4 aat 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 5 aat -21.025 118.9 123.42 # cp cp cp o
dihedral_coeff 6 aat -4.8141 118.9 117.94 # cp cp cp h
dihedral_coeff 7 aat 0.3598 117.94 117.94 # h cp cp h
dihedral_coeff 8 aat 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 9 aat -21.025 118.9 123.42 # cp cp cp o
dihedral_coeff 10 aat -4.8141 117.94 118.9 # h cp cp cp
dihedral_coeff 11 aat 4.2296 117.94 123.42 # h cp cp o
dihedral_coeff 12 aat 0.0 123.42 109.5 # * cp_ o_ *
dihedral_coeff 13 aat 0.0 121.46 120 # * cp_ n_ *
dihedral_coeff 14 aat -7.1755 121.46 111.87 # cp cp nn h*
dihedral_coeff 15 aat 0.0 120 120 # * cp_ n_ *
dihedral_coeff 16 aat 0.0 120 111.87 # * cp_ n_ *
dihedral_coeff 17 aat 4.4444 120.05 117.94 # c cp cp h
dihedral_coeff 18 aat -14.41 120.05 118.9 # c cp cp cp
dihedral_coeff 19 aat 0.0 111 120.05 # cp c cp cp
dihedral_coeff 20 aat 0 108.4 120.05 # c c cp cp
dihedral_coeff 21 aat 0 108.4 110.77 # cp c c h
dihedral_coeff 22 aat -16.164 112.67 110.77 # c c c h
dihedral_coeff 23 aat 0 117.94 121.46 # h cp cp nn
dihedral_coeff 24 aat 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 25 aat -21.025 118.9 123.42 # cp cp cp o
dihedral_coeff 26 aat 0 118.9 118.9 # cp cp cp cp
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 53 1.417 1.417 # cp cp cp cp
dihedral_coeff 4 bb13 -9.7999 1.417 1.3912 # cp cp cp nn
dihedral_coeff 5 bb13 -2.2436 1.417 1.3768 # cp cp cp o
dihedral_coeff 6 bb13 -6.2741 1.417 1.0982 # cp cp cp h
dihedral_coeff 7 bb13 -1.7077 1.0982 1.0982 # h cp cp h
dihedral_coeff 8 bb13 53 1.417 1.417 # cp cp cp cp
dihedral_coeff 9 bb13 -2.2436 1.417 1.3768 # cp cp cp o
dihedral_coeff 10 bb13 -6.2741 1.0982 1.417 # h cp cp cp
dihedral_coeff 11 bb13 2.0517 1.0982 1.3768 # h cp cp o
dihedral_coeff 12 bb13 0.0 1.417 1.3768 # * cp_ o_ *
dihedral_coeff 13 bb13 0.0 1.417 1.3912 # * cp_ n_ *
dihedral_coeff 14 bb13 4.2366 1.417 1.0012 # cp cp nn h*
dihedral_coeff 15 bb13 0.0 1.3768 1.3912 # * cp_ n_ *
dihedral_coeff 16 bb13 0.0 1.3768 1.0012 # * cp_ n_ *
dihedral_coeff 17 bb13 0.8743 1.501 1.0982 # c cp cp h
dihedral_coeff 18 bb13 2.5085 1.501 1.417 # c cp cp cp
dihedral_coeff 19 bb13 0.0 1.501 1.417 # cp c cp cp
dihedral_coeff 20 bb13 0.0 1.53 1.417 # c c cp cp
dihedral_coeff 21 bb13 0.0 1.501 1.101 # cp c c h
dihedral_coeff 22 bb13 0.0 1.53 1.101 # c c c h
dihedral_coeff 23 bb13 -1.0746 1.0982 1.3912 # h cp cp nn
dihedral_coeff 24 bb13 -9.7999 1.417 1.3912 # cp cp cp nn
dihedral_coeff 25 bb13 -2.2436 1.417 1.3768 # cp cp cp o
dihedral_coeff 26 bb13 53 1.417 1.417 # cp cp cp cp
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 0 118.9 117.94 117.94 # cp cp cp h
improper_coeff 4 aa 0 0 0 118.9 123.42 123.42 # cp cp cp o
improper_coeff 5 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * cp_ * *
improper_coeff 6 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * n_ * *
improper_coeff 7 aa 0 0 0 120.05 120.05 118.9 # c cp cp cp
improper_coeff 8 aa 0.0 0.0 0.0 120.0 120.0 120.0 # c3 c0 cp cp
improper_coeff 9 aa 0.0 0.0 0.0 120.0 120.0 120.0 # c3 c0 c3 cp
improper_coeff 10 aa 0.2738 -0.4825 0.2738 110.77 110.77 107.66 # c c h h
improper_coeff 11 aa -0.3157 -0.3157 -0.3157 107.66 107.66 107.66 # h c h h
improper_coeff 12 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * n_ * *
improper_coeff 13 aa 0 0 0 118.9 121.46 121.46 # cp cp cp nn
improper_coeff 14 aa 0 0 0 118.9 117.94 117.94 # cp cp cp h
pair_coeff 1 1 0.007 3.75 # c0 -
pair_coeff 2 2 0.071 3.884 # c3 -
pair_coeff 3 3 0.0668 3.9147 # cp -
pair_coeff 4 4 0.0568 3.9147 # cpc -
pair_coeff 5 5 0.023 2.878 # h -
pair_coeff 6 6 0.008 1.087 # h* -
pair_coeff 7 7 0.092 3.89 # nn -
pair_coeff 8 8 0.096 3.58 # o -
pair_coeff 9 9 0.12 3.3 # oc -
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
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
465 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_Minimization.out
#-------------------------------------------------------------------------------
# Stage 1.2: Minimization
#-------------------------------------------------------------------------------
min_style cg
min_modify dmax 0.05 line fast
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
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
dump sci all custom 1000 1.2.xyz id mol type q xs ys zs
thermo 100
minimize 0.0 1.0 1000 10000
Generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5
ghost atom cutoff = 11.5
binsize = 5.75, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : real
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 22.15 | 22.16 | 22.17 Mbytes
Step Fmax Fnorm Press Volume v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy PotEng v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz
0 3247.952 12745.868 711620.03 4618.7784 1.4000149 -798754.76 -816783.34 -519321.98 -16239.608 38245.659 130437.53 17946.548 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -1.8189894e-11 5.0022209e-12 -1.2505552e-11
100 23.197626 79.056159 23988.716 4618.7784 1.4000149 -27022.428 -33631.611 -11312.111 -3622.4055 4483.4878 -1073.4569 1402.2142 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -1.2789769e-13 1.7763568e-14 0
200 5.4320027 40.076991 16000.716 4618.7784 1.4000149 -18294.679 -19853.794 -9853.6756 -864.74629 3012.6148 -512.77421 1228.9216 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -4.0856207e-14 6.3948846e-14 5.5511151e-14
300 2.4775201 21.566397 16109.76 4618.7784 1.4000149 -18325.075 -18574.441 -11429.765 822.69135 2368.2337 666.01393 1162.1466 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -4.8294702e-14 -4.2854609e-14 -1.7408297e-13
400 3.2032951 25.255155 12315.803 4618.7784 1.4000149 -13236.94 -16393.473 -7316.9958 -527.40356 3713.9997 1718.9275 1139.2081 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -9.7144515e-14 3.7081449e-14 -3.2862602e-14
500 3.0742158 20.998617 11800.921 4618.7784 1.4000149 -12980.895 -15416.485 -7005.3812 -1394.9936 3932.8103 2100.2303 1095.9433 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 1.2767565e-14 -5.5067062e-14 -8.7041485e-14
600 2.6832889 19.100799 10432.966 4618.7784 1.4000149 -12711.57 -11009.741 -7577.587 -531.33819 4258.4918 1705.3723 1065.39 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 1.318945e-13 -7.1054274e-14 1.1168844e-13
700 0.90811493 7.7199905 10281.941 4618.7784 1.4000149 -12071.235 -11753.844 -7020.7424 -459.45831 4852.6819 1988.2724 1058.567 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -9.4813046e-14 2.1294078e-13 1.2867485e-13
800 0.47128731 3.8515289 10011.604 4618.7784 1.4000149 -11784.597 -12180.75 -6069.4644 -415.71284 4574.4633 1793.7085 1054.7854 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -1.3766766e-14 7.8381746e-14 4.7517545e-14
900 0.54861584 2.7866755 9929.4431 4618.7784 1.4000149 -11510.073 -12209.973 -6068.283 -338.39731 4686.4999 1830.6827 1054.2095 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 -3.8857806e-15 -4.7073456e-14 1.0758061e-13
1000 0.18057517 1.6275732 9820.6204 4618.7784 1.4000149 -11297.896 -12179.009 -5984.9561 -405.18624 4722.2299 1837.3293 1053.8958 16.653635 16.653635 16.653635 1.5707963 1.5707963 1.5707963 9.1482377e-14 -2.9753977e-14 2.7117197e-14
Loop time of 1.9054 on 3 procs for 1000 steps with 465 atoms
99.8% CPU use with 3 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
17946.5479823205 1053.89904555742 1053.89582709551
Force two-norm initial, final = 12745.868 1.6275732
Force max component initial, final = 3247.952 0.18057517
Final line search alpha, max atom move = 0.0011901514 0.0002149118
Iterations, force evaluations = 1000 1435
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0502 | 1.1238 | 1.197 | 5.7 | 58.98
Bond | 0.51688 | 0.52782 | 0.54791 | 2.0 | 27.70
Neigh | 0.045286 | 0.04536 | 0.045496 | 0.0 | 2.38
Comm | 0.092985 | 0.18645 | 0.27132 | 16.9 | 9.79
Output | 0.0014901 | 0.0015119 | 0.0015545 | 0.1 | 0.08
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02047 | | | 1.07
Nlocal: 155 ave 164 max 142 min
Histogram: 1 0 0 0 0 0 0 1 0 1
Nghost: 4366.67 ave 4453 max 4303 min
Histogram: 1 0 1 0 0 0 0 0 0 1
Neighs: 49150.3 ave 52338 max 45579 min
Histogram: 1 0 0 0 0 1 0 0 0 1
Total # of neighbors = 147451
Ave neighs/atom = 317.09892
Ave special neighs/atom = 5.7419355
Neighbor list builds = 22
Dangerous builds = 0
undump sci
log 1.3_Velocities.out
#-------------------------------------------------------------------------------
# Stage 1.3: Set the initial velocities for 50 °C
#-------------------------------------------------------------------------------
velocity movable create 323.15 8050 dist gaussian mom yes rot no
log 1.4_NPT.out
#-------------------------------------------------------------------------------
# Stage 1.4: NPT integration for 100 ps with a timestep of 1 fs
# Initial temperature 50 °C, final 300 °C
# Pressure 1 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}
thermo 0
fix 1 movable npt temp 323.15 573.15 100 iso 1 1 100 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 1.4_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 1.4_instantaneous.txt
restart 100000 1.4.restart
dump sci all custom 10000 1.4.xyz id mol type q xs ys zs
timestep 1
run 100000
Generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 21.03 | 21.04 | 21.04 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 14244.081 4618.7784 1.4000149 323.15 84.037011 318.66987 747.33602 11.218305 -107.36538 0 -38.905475 0 1053.8958 446.94743
100000 100000 -5811.6078 6065.8652 1.0660241 584.15556 366.88019 522.97058 907.92077 43.106637 -72.729465 0 -29.624095 0 1768.1487 807.94314
Loop time of 127.485 on 3 procs for 100000 steps with 465 atoms
Performance: 67.773 ns/day, 0.354 hours/ns, 784.407 timesteps/s
99.7% CPU use with 3 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 60.303 | 62.048 | 62.966 | 15.7 | 48.67
Bond | 37.025 | 38.142 | 39.629 | 17.7 | 29.92
Neigh | 4.3942 | 4.4 | 4.4082 | 0.3 | 3.45
Comm | 6.3944 | 8.728 | 11.616 | 73.4 | 6.85
Output | 0.0023966 | 0.002437 | 0.0024697 | 0.1 | 0.00
Modify | 13.516 | 13.552 | 13.573 | 0.7 | 10.63
Other | | 0.6126 | | | 0.48
Nlocal: 155 ave 159 max 152 min
Histogram: 1 0 1 0 0 0 0 0 0 1
Nghost: 3743.33 ave 3773 max 3691 min
Histogram: 1 0 0 0 0 0 0 0 0 2
Neighs: 37355.3 ave 38456 max 36750 min
Histogram: 2 0 0 0 0 0 0 0 0 1
Total # of neighbors = 112066
Ave neighs/atom = 241.00215
Ave special neighs/atom = 5.7419355
Neighbor list builds = 3043
Dangerous builds = 0
undump sci
restart 0
dump sci all custom 100000 1.4.xyz id mol type q xs ys zs
run 0
Generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
Setting up Verlet run ...
Unit style : real
Current step : 100000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 21.02 | 21.03 | 21.04 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
100000 100000 -5811.6078 6065.8652 1.0660241 584.15556 366.88019 522.97058 907.92077 43.106637 -72.729465 0 -29.624095 0 1768.1487 807.94314
Loop time of 1.185e-06 on 3 procs for 0 steps with 465 atoms
140.6% CPU use with 3 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.185e-06 | | |100.00
Nlocal: 155 ave 159 max 152 min
Histogram: 1 0 1 0 0 0 0 0 0 1
Nghost: 3743.33 ave 3773 max 3691 min
Histogram: 1 0 0 0 0 0 0 0 0 2
Neighs: 37355.3 ave 38456 max 36750 min
Histogram: 2 0 0 0 0 0 0 0 0 1
Total # of neighbors = 112066
Ave neighs/atom = 241.00215
Ave special neighs/atom = 5.7419355
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
log 1.5_NPT.out
#-------------------------------------------------------------------------------
# Stage 1.5: NPT integration for 100 ps with a timestep of 1 fs
# Initial temperature 300 °C, final 30 °C
# Pressure 1 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}
thermo 0
fix 1 movable npt temp 573.15 303.15 100 iso 1 1 100 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 1.5_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 1.5_instantaneous.txt
restart 100000 1.5.restart
dump trj all custom 1000 1.5.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 1000 1 1000 v_etotal v_pe v_ke file 1.5.energies.txt
dump sci all custom 10000 1.5.xyz id mol type q xs ys zs
timestep 1
run 100000
Generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 22.28 | 22.29 | 22.29 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 -5811.6078 6065.8652 1.0660241 584.15556 366.88019 522.97058 907.92077 43.106637 -72.729465 0 -29.624095 0 1768.1487 807.94314