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 1.1_Initialize.out
#-------------------------------------------------------------------------------
# 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
#-------------------------------------------------------------------------------
# Stage 1.2: NVT integration for 10 ps with a timestep of 1 fs
# Initial temperature 30 °C, final 300 °C
#-------------------------------------------------------------------------------
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
thermo ${Nthermo}
thermo 0
fix 1 movable nvt temp 303.15 573.15 100 drag 0.0
fix 2 movable ave/time 1 1000 1000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 1.2_averages.txt off 1
fix 3 movable ave/time 1 1 1 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 1.2_instantaneous.txt
restart 10000 1.2.restart
dump sci all custom 1000 1.2.xyz id mol type q xs ys zs
timestep 1
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.25435239
grid = 12 12 12
stencil order = 5
estimated absolute RMS force accuracy = 0.0025681422
estimated relative force accuracy = 7.7338839e-06
using double precision KISS FFT
3d grid and FFT values/proc = 2601 576
Generated 0 of 21 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 Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 7.837 | 7.971 | 8.124 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 121446.82 22847.269 1.0000099 0 3285.0122 1116.464 8013.7701 1.1735338 18817.68 744.41483 -97.568277 -782.13718 31196.378 0