LAMMPS (2 Jun 2022)
KOKKOS mode is enabled (src/KOKKOS/kokkos.cpp:105)
will use up to 1 GPU(s) per node
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 (31.235943 31.235943 31.235943)
1 by 1 by 1 MPI processor grid
reading atoms ...
1976 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 ...
2208 bonds
reading angles ...
3640 angles
reading dihedrals ...
5728 dihedrals
reading impropers ...
1200 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 = 0.034 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
1976 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 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 1.2.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) = 0.26630181
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0015512748
estimated relative force accuracy = 4.6716181e-06
using double precision KISS FFT
3d grid and FFT values/proc = 8000 3375
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 cg/kk style minimization ...
Unit style : real
Current step : 0
WARNING: Fixes cannot yet send exchange data in Kokkos communication, switching to classic exchange/border communication (src/KOKKOS/comm_kokkos.cpp:581)
Per MPI rank memory allocation (min/avg/max) = 13.72 | 13.72 | 13.72 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 23160.759 65172.74 452806.97 30476.414 1.0000099 -373177.26 -513177.9 -472065.76 83331.218 48051.603 -41267.239 89026.545 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 -1.6896706e-11 -1.679723e-11 4.2543746e-12
100 30.242906 159.30751 4289.2763 30476.414 1.0000099 -473.53408 -10209.838 -2184.4565 2555.1202 3805.5598 -3314.1006 14765.149 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 1.4632739e-12 3.2973624e-14 9.0594199e-13
200 33.983561 140.54638 -905.98242 30476.414 1.0000099 3169.1368 -1802.4409 1351.2514 1955.0791 1846.4691 -2191.3132 12789.834 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 -7.0399242e-12 -8.6216034e-12 -1.2868234e-11
300 20.406577 75.240826 -1505.7788 30476.414 1.0000099 2719.5916 -55.886807 1853.6315 847.75661 1078.2518 -668.86349 12162.75 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 -1.1233237e-11 -9.7208908e-12 -9.8699382e-12
400 7.506577 38.434527 -1269.761 30476.414 1.0000099 2043.6623 500.46461 1265.1561 452.77768 484.57946 -192.46335 11991.632 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 -1.1504048e-11 1.5029838e-11 1.1592699e-11
500 5.4345361 31.791224 -1560.8655 30476.414 1.0000099 2318.5758 728.81634 1635.2043 427.23376 356.58165 -280.0594 11930.01 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 1.1457724e-11 -3.6304293e-13 -4.8214766e-12
600 3.0053984 23.079396 -1728.4459 30476.414 1.0000099 2096.0971 1274.7955 1814.4453 356.28545 179.49336 -249.1075 11890.207 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 4.0742687e-12 6.1814442e-13 9.4589336e-12
700 1.8612759 21.350407 -1856.2108 30476.414 1.0000099 2238.9491 1483.6916 1845.9918 211.4643 218.7216 -237.13473 11860.377 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 -1.8205659e-11 -1.0680457e-11 2.6899316e-12
800 2.4931177 22.147436 -2104.2784 30476.414 1.0000099 2657.9357 1811.6868 1843.2127 65.297055 219.35861 -162.32457 11833.653 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 -5.2243765e-12 6.8594574e-12 -7.1424255e-12
900 1.9312631 17.487746 -2028.1965 30476.414 1.0000099 2494.734 1783.5723 1806.2831 -105.15686 61.718975 -91.087768 11810.245 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 7.6912365e-12 7.8402007e-12 1.046635e-12
1000 1.6714278 15.444574 -2004.2729 30476.414 1.0000099 2206.0515 1915.6966 1891.0707 -36.691829 128.74431 -187.05687 11792.851 31.235943 31.235943 31.235943 1.5707963 1.5707963 1.5707963 -2.1461305e-12 -9.6465058e-12 1.8254981e-11
Loop time of 6.59405 on 1 procs for 1000 steps with 1976 atoms
74.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
89026.5450160229 11793.0253598962 11792.8506435027
Force two-norm initial, final = 65172.74 15.444574
Force max component initial, final = 23160.759 1.6714278
Final line search alpha, max atom move = 0.0029030734 0.0048522776
Iterations, force evaluations = 1000 1810
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67884 | 0.67884 | 0.67884 | 0.0 | 10.29
Bond | 1.0756 | 1.0756 | 1.0756 | 0.0 | 16.31
Kspace | 4.007 | 4.007 | 4.007 | 0.0 | 60.77
Neigh | 0.33826 | 0.33826 | 0.33826 | 0.0 | 5.13
Comm | 0.080338 | 0.080338 | 0.080338 | 0.0 | 1.22
Output | 0.0077711 | 0.0077711 | 0.0077711 | 0.0 | 0.12
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.4062 | | | 6.16
Nlocal: 1976 ave 1976 max 1976 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8307 ave 8307 max 8307 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 818806 ave 818806 max 818806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 818806
Ave neighs/atom = 414.37551
Ave special neighs/atom = 5.9190283
Neighbor list builds = 31
Dangerous builds = 0
undump sci
log 1.3_Velocities.out
#-------------------------------------------------------------------------------
# Stage 1.3: Set the initial velocities for 30 °C
#-------------------------------------------------------------------------------
velocity movable create 303.15 72489 dist gaussian mom yes rot no
log 1.4_NPT.out
#-------------------------------------------------------------------------------
# Stage 1.4: NPT integration for 50 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 1000
fix 2 movable ave/time 1 4999 5000 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 5 1 5 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 50000 1.4.restart
dump sci all custom 5000 1.4.xyz id mol type q xs ys zs
timestep 1
run 50000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26630181
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0015512748
estimated relative force accuracy = 4.6716181e-06
using double precision KISS FFT
3d grid and FFT values/proc = 8000 3375
Generated 0 of 21 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) = 13.25 | 13.25 | 13.25 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-06 672.60127 30476.414 1.0000099 303.15 531.59516 1834.9227 9890.9284 69.04847 -456.55311 1076.8281 -130.19985 -1153.9191 11792.851 1784.6743