400 lines
18 KiB
Groff
400 lines
18 KiB
Groff
LAMMPS (24 Dec 2020)
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using 1 OpenMP thread(s) per MPI task
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# This script reproduces stress trajectories from Fig. 1 in
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# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
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#
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# Three thermostatting scenarios are visited: undamped (nodrag),
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# damped (drag) and Nose-Hoover chain (nhchains).
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#
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# The axial and shear stress trajectories are printed to the
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# file "stress_vs_t.dat". For the damped case, the original figure
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# seems to be a plot of 2*tau, rather than tau.
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#
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# The script also demonstrates how to
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# orient a crystal along <110>,
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# and how to use the lj/cubic pair style.
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units lj
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boundary p p p
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atom_style atomic
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# Set up FCC lattice with z axis along <110>
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lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
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Lattice spacing in x,y,z = 1.4142135 2.0000000 2.0000000
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region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
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create_box 1 mycell
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.0710677 9.9999999 9.9999999)
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1 by 1 by 1 MPI processor grid
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mass * 1.0
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create_atoms 1 box
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Created 1000 atoms
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create_atoms CPU = 0.001 seconds
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# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
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pair_style lj/cubic
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pair_coeff * * 1.0 0.8908987
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# Relax box dimensions
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fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
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thermo 100
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thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
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min_modify line quadratic
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minimize 0.0 1.0e-6 10000 100000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188)
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.8475372
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ghost atom cutoff = 1.8475372
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binsize = 0.92376862, bins = 8 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.247 | 4.247 | 4.247 Mbytes
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Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
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0 0 -6.2937536 -6.2937536 -2.7722424 -2.7722424 -2.7722424 7.0710677 9.9999999 9.9999999
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100 0 -6.3319014 -6.3319014 -0.75971257 -0.75971257 -0.75971257 7.0003571 9.8999999 9.8999999
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134 0 -6.3344253 -6.3344253 -4.3330648e-13 -4.7530261e-13 -4.7130069e-13 6.9780267 9.8684199 9.8684199
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Loop time of 0.200013 on 1 procs for 134 steps with 1000 atoms
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = force tolerance
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Energy initial, next-to-last, final =
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-6.29375358358557 -6.33442531515503 -6.33442531515503
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Force two-norm initial, final = 3395.2895 5.5740327e-10
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Force max component initial, final = 1960.2713 3.2730334e-10
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Final line search alpha, max atom move = 1.0000000 3.2730334e-10
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Iterations, force evaluations = 134 137
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.14357 | 0.14357 | 0.14357 | 0.0 | 71.78
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Neigh | 0.0017562 | 0.0017562 | 0.0017562 | 0.0 | 0.88
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Comm | 0.0049057 | 0.0049057 | 0.0049057 | 0.0 | 2.45
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Output | 5.126e-05 | 5.126e-05 | 5.126e-05 | 0.0 | 0.03
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.04973 | | | 24.86
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Nlocal: 1000.00 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1724.00 ave 1724 max 1724 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 21000.0 ave 21000 max 21000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 21000
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Ave neighs/atom = 21.000000
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Neighbor list builds = 1
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Dangerous builds = 0
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# Define initial velocity
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velocity all create 0.01 87287 mom yes rot yes dist gaussian
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write_restart restart.equil
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System init for write_restart ...
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# Start Run #1
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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1 by 1 by 1 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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read_restart CPU = 0.001 seconds
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term off
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fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
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#dump id all atom 500 dump.hugoniostat
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#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
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1000 0.0093381492 0.013993217 -2.1704431 -4183.8284 129.15284 58.544409 8.3142517 -4.1816719 0.93744212 23.519052 3.7381985
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2000 0.24794859 0.37155095 -5.8915826 -528.38691 8.3849811 1.3744297 9.5938806 -0.52286688 -0.24350394 13.910493 0.41033425
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3000 0.3892042 0.5832225 -3.7686896 -3442.3257 72.742382 28.486576 8.6238082 -3.4391402 0.0038227739 19.697354 2.5139569
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4000 0.67010303 1.0041494 -4.2080956 -2935.8105 35.596234 3.9346859 8.7508489 -2.9326065 -0.58038927 14.529876 1.6677093
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5000 0.41845028 0.62704774 -4.8392822 -1894.6664 30.624319 4.6370699 8.7827304 -1.8904542 -0.31998377 13.670423 1.5249748
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6000 0.22409652 0.33580864 -3.7653422 -2666.4156 50.804071 7.220865 8.25496 -2.6629861 -0.017448126 14.48017 2.3883779
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7000 0.094832866 0.14210705 -4.5432169 -2337.0271 35.853414 3.4750842 8.4475655 -2.332626 -0.052659776 12.95347 1.8841809
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8000 0.043338745 0.06494311 -4.6249403 -1687.4892 39.679004 6.7256868 8.4321684 -1.6829292 0.070571417 13.554654 1.9927395
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9000 0.018233343 0.027322664 -4.425909 -1916.4941 41.680023 5.9079935 8.3470382 -1.9120955 0.090887676 13.502397 2.1013348
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10000 0.0082616415 0.01238007 -4.6221264 -1723.6542 39.842157 6.5678795 8.41093 -1.7190444 0.099616538 13.484322 2.0113699
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Loop time of 15.2001 on 1 procs for 10000 steps with 1000 atoms
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Performance: 56841.813 tau/day, 657.891 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 11.69 | 11.69 | 11.69 | 0.0 | 76.91
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Neigh | 0.34087 | 0.34087 | 0.34087 | 0.0 | 2.24
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Comm | 0.41211 | 0.41211 | 0.41211 | 0.0 | 2.71
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Output | 0.001153 | 0.001153 | 0.001153 | 0.0 | 0.01
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Modify | 2.6404 | 2.6404 | 2.6404 | 0.0 | 17.37
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Other | | 0.1158 | | | 0.76
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Nlocal: 1000.00 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1886.00 ave 1886 max 1886 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 20874.0 ave 20874 max 20874 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 20874
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Ave neighs/atom = 20.874000
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Neighbor list builds = 188
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Dangerous builds = 0
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# Start Run #2
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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1 by 1 by 1 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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read_restart CPU = 0.001 seconds
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term on
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fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
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1000 0.0062572988 0.0093765623 -5.989087 -1670.9191 18.918118 7.5844401 9.2338165 -1.6649394 0.023419337 13.976997 0.92138738
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2000 0.0068451081 0.010257394 -5.456581 -2537.81 37.064253 15.537266 8.9496405 -2.5323637 0.10230605 16.325406 1.5455016
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3000 0.0073276099 0.010980423 -5.3663421 -2643.8751 39.907292 16.807489 8.9154852 -2.6385198 0.11818116 16.63905 1.6326832
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4000 0.0069296906 0.010384141 -5.36234 -2655.7228 40.010742 16.851482 8.9144328 -2.6503709 0.11868137 16.651571 1.6356847
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5000 0.0076142461 0.011409948 -5.3631443 -2664.4499 39.997648 16.846756 8.9145416 -2.6590982 0.1184114 16.649779 1.6353254
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6000 0.0077053831 0.011546517 -5.3628538 -2673.2444 39.991598 16.840314 8.9145803 -2.667893 0.11818361 16.648852 1.6351691
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7000 0.0077405663 0.011599239 -5.3623531 -2682.1589 40.000448 16.844009 8.9145774 -2.6768081 0.11809899 16.650669 1.6353525
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8000 0.0080673569 0.012088934 -5.3623755 -2691.0104 39.995327 16.840134 8.9146099 -2.6856601 0.11787103 16.649882 1.6352204
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9000 0.0083223083 0.012470979 -5.3622988 -2699.8929 40.00571 16.847764 8.9146503 -2.6945431 0.11781523 16.652389 1.6353987
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10000 0.0091249116 0.01367368 -5.3630138 -2708.966 39.987197 16.837314 8.9146848 -2.7036167 0.11743014 16.648832 1.6349911
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Loop time of 13.6753 on 1 procs for 10000 steps with 1000 atoms
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Performance: 63179.754 tau/day, 731.247 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 10.568 | 10.568 | 10.568 | 0.0 | 77.28
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Neigh | 0.019792 | 0.019792 | 0.019792 | 0.0 | 0.14
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Comm | 0.33708 | 0.33708 | 0.33708 | 0.0 | 2.46
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Output | 0.0011928 | 0.0011928 | 0.0011928 | 0.0 | 0.01
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Modify | 2.639 | 2.639 | 2.639 | 0.0 | 19.30
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Other | | 0.1101 | | | 0.81
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Nlocal: 1000.00 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1724.00 ave 1724 max 1724 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 21000.0 ave 21000 max 21000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 21000
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Ave neighs/atom = 21.000000
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Neighbor list builds = 11
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Dangerous builds = 0
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# Start Run #3
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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1 by 1 by 1 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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read_restart CPU = 0.001 seconds
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
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fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
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1000 0.0083300318 0.012482553 -5.5023183 -838.99233 35.610078 14.886668 8.9677982 -0.83350249 0.093761717 16.159482 1.500112
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2000 0.020386436 0.030549075 -5.294934 -1021.4347 41.760404 17.563313 8.8960328 -1.0161703 0.1178086 16.852842 1.6868239
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3000 0.049693082 0.074465084 -5.3469418 -982.1922 39.030412 16.123502 8.9325589 -0.97691972 0.073097533 16.601991 1.6003728
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4000 0.11859524 0.17771497 -5.207074 -1299.948 40.941639 16.507821 8.9213137 -1.2949186 0.018189971 16.904165 1.6487306
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5000 0.130146 0.19502378 -5.261025 -1208.3405 39.059595 15.609328 8.9431689 -1.2032745 -0.00023811036 16.701434 1.5920334
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6000 0.13812959 0.20698719 -5.1710048 -1334.1421 40.904888 16.242199 8.9222846 -1.329178 -0.0044756362 16.90509 1.6471606
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|
7000 0.12107441 0.18143001 -5.2602562 -1170.0585 39.060849 15.577606 8.9397535 -1.1649797 0.005587398 16.671517 1.5949415
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8000 0.14333426 0.21478639 -5.1717109 -1352.635 40.876285 16.205871 8.9218128 -1.3476781 -0.0069373292 16.895041 1.6469877
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9000 0.12159783 0.18221435 -5.2591928 -1186.8604 39.22852 15.6778 8.9376658 -1.1817834 0.0077335044 16.68885 1.6001243
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10000 0.15321647 0.22959488 -5.188176 -1391.2245 40.666599 16.146259 8.9228489 -1.3862659 -0.0091900905 16.860718 1.6418747
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Loop time of 13.963 on 1 procs for 10000 steps with 1000 atoms
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Performance: 61877.846 tau/day, 716.179 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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|
---------------------------------------------------------------
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Pair | 10.667 | 10.667 | 10.667 | 0.0 | 76.40
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Neigh | 0.16763 | 0.16763 | 0.16763 | 0.0 | 1.20
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Comm | 0.36182 | 0.36182 | 0.36182 | 0.0 | 2.59
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Output | 0.0011809 | 0.0011809 | 0.0011809 | 0.0 | 0.01
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Modify | 2.6516 | 2.6516 | 2.6516 | 0.0 | 18.99
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|
Other | | 0.1135 | | | 0.81
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Nlocal: 1000.00 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1724.00 ave 1724 max 1724 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 20654.0 ave 20654 max 20654 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 20654
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Ave neighs/atom = 20.654000
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Neighbor list builds = 94
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Dangerous builds = 0
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Total wall time: 0:00:43
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