LAMMPS (2 Jun 2022)
KOKKOS mode is enabled (src/KOKKOS/kokkos.cpp:105)
will use up to 1 GPU(s) per node
WARNING: Detected MPICH. Disabling GPU-aware MPI (src/KOKKOS/kokkos.cpp:317)
using 1 OpenMP thread(s) per MPI task
log 2.1_Initialize.out
#-------------------------------------------------------------------------------
# Stage 2.1: 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 (24.929034 24.929034 24.929034)
1 by 1 by 3 MPI processor grid
reading atoms ...
1100 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
16 = max angles/atom
scanning dihedrals ...
38 = max dihedrals/atom
scanning impropers ...
12 = max impropers/atom
reading bonds ...
1204 bonds
reading angles ...
1992 angles
reading dihedrals ...
3032 dihedrals
reading impropers ...
720 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 = 0.063 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 11 109.5 60 0 0 # * o_ *
angle_coeff 12 120.05 44.715 -22.735 0 # c cp cp
angle_coeff 13 111 44.323 -9.4454 0 # cp c cp
angle_coeff 14 108.4 43.959 -8.3924 -9.3379 # c c cp
angle_coeff 15 112.67 39.516 -7.443 -9.5583 # c c c
angle_coeff 16 110.77 41.453 -10.604 5.129 # c c h
angle_coeff 17 107.66 39.641 -12.921 -2.4318 # h c h
angle_coeff 18 118.9 61.023 -34.993 0 # cp cp cp
angle_coeff 19 111.87 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 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 2.25 0 0 0 # * cp_ n_ *
dihedral_coeff 15 0 0 1.559 0 0 0 # c cp cp h
dihedral_coeff 16 0 0 4.4072 0 0 0 # c cp cp cp
dihedral_coeff 17 -0.2802 0 -0.0678 0 -0.0122 0 # cp c cp cp
dihedral_coeff 18 -0.2802 0 -0.0678 0 -0.0122 0 # c c cp cp
dihedral_coeff 19 -0.0228 0 0.028 0 -0.1863 0 # cp c c h
dihedral_coeff 20 0 0 0.0316 0 -0.1681 0 # c c c h
dihedral_coeff 21 0 0 1.3331 0 0 0 # h cp cp nn
dihedral_coeff 22 0 0 5.3826 0 0 0 # cp cp cp nn
dihedral_coeff 23 0 0 4.8498 0 0 0 # cp cp cp o
dihedral_coeff 24 8.3667 0 1.1932 0 0 0 # cp cp cp cp
dihedral_coeff 25 0 0 1.219 0 0 0 # cp cp nn h*
dihedral_coeff 26 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 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 10.786 0 # cp cp cp nn
improper_coeff 13 4.8912 0 # cp cp cp h
improper_coeff 14 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 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 0.0 1.3768 1.3768 # * o_ *
angle_coeff 12 bb 12.068 1.501 1.417 # c cp cp
angle_coeff 13 bb 0.0 1.501 1.501 # cp c cp
angle_coeff 14 bb 0 1.53 1.501 # c c cp
angle_coeff 15 bb 0 1.53 1.53 # c c c
angle_coeff 16 bb 3.3872 1.53 1.101 # c c h
angle_coeff 17 bb 5.3316 1.101 1.101 # h c h
angle_coeff 18 bb 68.286 1.417 1.417 # cp cp cp
angle_coeff 19 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 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 0.0 0.0 1.3768 1.3768 # * o_ *
angle_coeff 12 ba 47.058 31.077 1.501 1.417 # c cp cp
angle_coeff 13 ba 0.0 0.0 1.501 1.501 # cp c cp
angle_coeff 14 ba 0 0 1.53 1.501 # c c cp
angle_coeff 15 ba 8.016 8.016 1.53 1.53 # c c c
angle_coeff 16 ba 20.754 11.421 1.53 1.101 # c c h
angle_coeff 17 ba 18.103 18.103 1.101 1.101 # h c h
angle_coeff 18 ba 28.871 28.871 1.417 1.417 # cp cp cp
angle_coeff 19 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 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 0.0 0.0 0.0 1.3912 # * cp_ n_ *
dihedral_coeff 15 mbt 0 3.9421 0 1.417 # c cp cp h
dihedral_coeff 16 mbt 0 9.1792 0 1.417 # c cp cp cp
dihedral_coeff 17 mbt 0.0 0.0 0.0 1.501 # cp c cp cp
dihedral_coeff 18 mbt 0 0 0 1.501 # c c cp cp
dihedral_coeff 19 mbt 0 0 0 1.53 # cp c c h
dihedral_coeff 20 mbt -14.879 -3.6581 -0.3138 1.53 # c c c h
dihedral_coeff 21 mbt 0 2.2883 0 1.417 # h cp cp nn
dihedral_coeff 22 mbt 0 -0.5693 0 1.417 # cp cp cp nn
dihedral_coeff 23 mbt 0 4.8255 0 1.417 # cp cp cp o
dihedral_coeff 24 mbt 27.599 -2.312 0 1.417 # cp cp cp cp
dihedral_coeff 25 mbt 0 3.2085 0 1.3912 # cp cp nn h*
dihedral_coeff 26 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 -0.1185 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 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3912 # * cp_ n_ *
dihedral_coeff 15 ebt 0 -1.797 0 0 -0.4879 0 1.501 1.0982 # c cp cp h
dihedral_coeff 16 ebt 0 0.2421 0 0 -0.6918 0 1.501 1.417 # c cp cp cp
dihedral_coeff 17 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.501 1.417 # cp c cp cp
dihedral_coeff 18 ebt 0 0 0 0 0 0 1.53 1.417 # c c cp cp
dihedral_coeff 19 ebt 0 0 0 0 0 0 1.501 1.101 # cp c c h
dihedral_coeff 20 ebt 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 # c c c h
dihedral_coeff 21 ebt 0 -2.6482 0 0 -1.6402 0 1.0982 1.3912 # h cp cp nn
dihedral_coeff 22 ebt 0 -6.5404 0 0 -7.3477 0 1.417 1.3912 # cp cp cp nn
dihedral_coeff 23 ebt 0 0.2655 0 0 4.8905 0 1.417 1.3768 # cp cp cp o
dihedral_coeff 24 ebt -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 # cp cp cp cp
dihedral_coeff 25 ebt 0 -3.7281 0 0 0.2849 0 1.417 1.0012 # cp cp nn h*
dihedral_coeff 26 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 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 0.0 0.0 0.0 0.0 0.0 0.0 120 120 # * cp_ n_ *
dihedral_coeff 15 at 0 -0.1242 0 0 3.4601 0 120.05 117.94 # c cp cp h
dihedral_coeff 16 at 0 -4.4683 0 0 3.8987 0 120.05 118.9 # c cp cp cp
dihedral_coeff 17 at 0.0 0.0 0.0 0.0 0.0 0.0 111 120.05 # cp c cp cp
dihedral_coeff 18 at 0 0 0 0 0 0 108.4 120.05 # c c cp cp
dihedral_coeff 19 at 0 0 0 0 0 0 108.4 110.77 # cp c c h
dihedral_coeff 20 at -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77 # c c c h
dihedral_coeff 21 at 0 2.9813 0 0 0.2787 0 117.94 121.46 # h cp cp nn
dihedral_coeff 22 at 0 9.0901 0 0 -6.0882 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 23 at 0 10.015 0 0 1.7404 0 118.9 123.42 # cp cp cp o
dihedral_coeff 24 at 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 25 at 0 1.2616 0 0 0.7744 0 121.46 111.87 # cp cp nn h*
dihedral_coeff 26 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 0 118.9 118.9 # 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 0.0 120 120 # * cp_ n_ *
dihedral_coeff 15 aat 4.4444 120.05 117.94 # c cp cp h
dihedral_coeff 16 aat -14.41 120.05 118.9 # c cp cp cp
dihedral_coeff 17 aat 0.0 111 120.05 # cp c cp cp
dihedral_coeff 18 aat 0 108.4 120.05 # c c cp cp
dihedral_coeff 19 aat 0 108.4 110.77 # cp c c h
dihedral_coeff 20 aat -16.164 112.67 110.77 # c c c h
dihedral_coeff 21 aat 0 117.94 121.46 # h cp cp nn
dihedral_coeff 22 aat 0 118.9 121.46 # cp cp cp nn
dihedral_coeff 23 aat -21.025 118.9 123.42 # cp cp cp o
dihedral_coeff 24 aat 0 118.9 118.9 # cp cp cp cp
dihedral_coeff 25 aat -7.1755 121.46 111.87 # cp cp nn h*
dihedral_coeff 26 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 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 0.0 1.3768 1.3912 # * cp_ n_ *
dihedral_coeff 15 bb13 0.8743 1.501 1.0982 # c cp cp h
dihedral_coeff 16 bb13 2.5085 1.501 1.417 # c cp cp cp
dihedral_coeff 17 bb13 0.0 1.501 1.417 # cp c cp cp
dihedral_coeff 18 bb13 0.0 1.53 1.417 # c c cp cp
dihedral_coeff 19 bb13 0.0 1.501 1.101 # cp c c h
dihedral_coeff 20 bb13 0.0 1.53 1.101 # c c c h
dihedral_coeff 21 bb13 -1.0746 1.0982 1.3912 # h cp cp nn
dihedral_coeff 22 bb13 -9.7999 1.417 1.3912 # cp cp cp nn
dihedral_coeff 23 bb13 -2.2436 1.417 1.3768 # cp cp cp o
dihedral_coeff 24 bb13 53 1.417 1.417 # cp cp cp cp
dihedral_coeff 25 bb13 4.2366 1.417 1.0012 # cp cp nn h*
dihedral_coeff 26 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 0 118.9 117.94 117.94 # 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 0 118.9 121.46 121.46 # cp cp cp nn
improper_coeff 13 aa 0 0 0 118.9 117.94 117.94 # cp cp cp h
improper_coeff 14 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * n_ * *
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
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
1100 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
#-------------------------------------------------------------------------------
# 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
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
dump sci all custom 1000 2.2.xyz id mol type q xs ys zs
thermo 100
minimize 0.0 1.0 1000 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26652381
grid = 12 12 12
stencil order = 5
estimated absolute RMS force accuracy = 0.0016375551
estimated relative force accuracy = 4.9314486e-06
using double precision KISS FFT
3d grid and FFT values/proc = 2601 576
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 = 11.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2/coul/long/kk, perpetual
attributes: full, newton off, kokkos_device
pair build: full/bin/kk/device
stencil: full/bin/3d
bin: kk/device
Setting up cg/kk style minimization ...
Unit style : real
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 10.61 | 10.92 | 11.12 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 8747.1009 24633.062 295472.31 15492.316 1.0000106 -292000.83 -294919.78 -299496.31 21833.304 12656.642 -6099.2082 28766.189 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 -8.3559826e-12 1.0857093e-11 9.094947e-12
100 43.25502 144.70039 6707.5556 15492.316 1.0000106 -6124.2054 -8236.0385 -5762.4228 -198.5057 -1398.0432 -1039.4342 3073.508 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 6.7110761e-12 1.5418777e-12 -7.1054274e-13
200 15.122845 63.916102 402.50422 15492.316 1.0000106 -276.01999 -1101.2257 169.73302 -102.3735 -413.76433 -895.70366 2529.936 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 8.5478291e-12 1.4937385e-11 6.5050187e-12
300 6.8514831 36.521187 102.51045 15492.316 1.0000106 -372.33653 -319.91588 384.72107 -343.81952 -481.10416 -683.55598 2416.043 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 6.4606098e-12 1.3402612e-12 1.5965007e-11
400 4.2407347 32.359349 12.144899 15492.316 1.0000106 -791.26774 193.84289 560.99016 19.547782 -149.62287 -327.15357 2354.651 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 -6.0618177e-12 -4.2081894e-12 6.6631145e-12
500 3.1192114 25.959472 33.351555 15492.316 1.0000106 -40.286554 558.76215 -618.53026 -856.51633 130.77951 71.924699 2303.9439 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 5.7154281e-12 -3.6822906e-12 -1.6490143e-12
600 2.2416425 19.235867 -42.067651 15492.316 1.0000106 -559.74369 583.15225 102.79439 -833.2665 -77.882173 -222.78851 2271.1704 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 1.4033219e-11 -2.0493829e-11 -6.4748207e-12
700 1.5879381 14.510315 -730.75818 15492.316 1.0000106 187.97862 1151.5426 852.75332 -639.12426 -22.712245 -130.25781 2253.4566 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 1.029532e-11 -7.2883921e-12 -2.0445867e-12
800 1.4768549 12.885319 -723.37407 15492.316 1.0000106 98.524272 967.81435 1103.7836 -239.98092 164.67466 -82.064145 2241.995 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 8.8786756e-12 -1.4697132e-12 -4.7823967e-12
900 1.4722253 13.083768 -941.60784 15492.316 1.0000106 345.61538 1175.1933 1304.0148 -187.20566 -235.95442 -250.8072 2231.7663 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 2.3119284e-12 -5.7704952e-12 7.9145579e-12
1000 1.681409 10.396776 -155.04756 15492.316 1.0000106 -360.84541 51.983729 774.00436 201.79692 171.87141 -199.01403 2222.3491 24.929034 24.929034 24.929034 1.5707963 1.5707963 1.5707963 5.3297367e-12 -7.1853634e-12 -8.2431839e-12
Loop time of 59.8459 on 3 procs for 1000 steps with 1100 atoms
66.9% CPU use with 3 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
28766.1894110631 2222.41750259416 2222.34905071368
Force two-norm initial, final = 24633.062 10.396776
Force max component initial, final = 8747.1009 1.681409
Final line search alpha, max atom move = 0.0040585583 0.0068240965
Iterations, force evaluations = 1000 1891
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3576 | 1.7158 | 1.9916 | 20.3 | 2.87
Bond | 4.6231 | 4.8053 | 5.0369 | 7.9 | 8.03
Kspace | 50.002 | 50.098 | 50.228 | 1.3 | 83.71
Neigh | 0.53821 | 0.55341 | 0.56216 | 1.5 | 0.92
Comm | 0.37314 | 0.38374 | 0.40168 | 2.1 | 0.64
Output | 0.010357 | 0.010555 | 0.010936 | 0.3 | 0.02
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.279 | | | 3.81
Nlocal: 366.667 ave 455 max 320 min
Histogram: 2 0 0 0 0 0 0 0 0 1
Nghost: 4867.33 ave 5052 max 4574 min
Histogram: 1 0 0 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
FullNghs: 171707 ave 223911 max 145420 min
Histogram: 2 0 0 0 0 0 0 0 0 1
Total # of neighbors = 515122
Ave neighs/atom = 468.29273
Ave special neighs/atom = 5.8109091
Neighbor list builds = 28
Dangerous builds = 0
undump sci
log 2.3_Velocities.out
#-------------------------------------------------------------------------------
# Stage 2.3: Set the initial velocities for 25 °C
#-------------------------------------------------------------------------------
velocity movable create 298.15 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
# Initial temperature 30 °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 303.15 573.15 100 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 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
restart 100000 2.4.restart
dump sci all custom 10000 2.4.xyz id mol type q xs ys zs
timestep 1
run 100000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26652381
grid = 12 12 12
stencil order = 5
estimated absolute RMS force accuracy = 0.0016375551
estimated relative force accuracy = 4.9314486e-06
using double precision KISS FFT
3d grid and FFT values/proc = 2601 576
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) = 10.46 | 10.8 | 11.06 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 2726.8817 15492.316 1.0000106 298.15 210.37467 699.75492 1755.796 24.360781 -190.46875 381.6772 -66.477164 -659.14579 2222.3491 976.71264