198 lines
8.4 KiB
Groff
198 lines
8.4 KiB
Groff
LAMMPS (19 Sep 2019)
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# Ar in metal units
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# simulation params in reduced units
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# settable from command line
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# epsilon, sigma, mass set below
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variable x index 5
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variable y index 5
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variable z index 5
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variable rhostar index 0.8842
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variable dt index 0.005
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variable cutoff index 2.5
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variable skin index 0.3
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variable tinitial index 1.0
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variable nthermo index 10
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variable nsteps index 100
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# physical constants from update.cpp
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variable kb index 8.617343e-5 # kB in eV/K
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variable avogadro index 6.02214129e23 # Avogadro's number
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# Ar properties in metal units
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variable epskb index 117.7 # LJ epsilon/kB in degrees K
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variable sigma index 3.504 # LJ sigma in Angstroms
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variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV
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variable epsilon equal 117.7*${kb}
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variable epsilon equal 117.7*8.617343e-5
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variable mass index 39.95 # mass in g/mole
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# scale factors
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# sigma = scale factor on distance, converts reduced distance to Angs
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# epsilon = scale factor on energy, converts reduced energy to eV
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# tmpscale = scale factor on temperature, converts reduced temp to degrees K
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# tscale = scale factor on time, converts reduced time to ps
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# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
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# use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds
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# pscale = scale factor on pressure, converts reduced pressure to bars
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# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
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# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars
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variable eVtoJoule index 1.602e-19 # convert eV to Joules
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variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars
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variable tmpscale equal ${epskb}
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variable tmpscale equal 117.7
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variable epsilonJ equal ${epsilon}*${eVtoJoule}
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variable epsilonJ equal 0.010142612711*${eVtoJoule}
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variable epsilonJ equal 0.010142612711*1.602e-19
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variable massKgAtom equal ${mass}/1000.0/${avogadro}
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variable massKgAtom equal 39.95/1000.0/${avogadro}
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variable massKgAtom equal 39.95/1000.0/6.02214129e23
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variable sigmaM equal ${sigma}/1.0e10
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variable sigmaM equal 3.504/1.0e10
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variable sigmaMsq equal ${sigmaM}*${sigmaM}
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variable sigmaMsq equal 3.504e-10*${sigmaM}
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variable sigmaMsq equal 3.504e-10*3.504e-10
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variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
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variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq})
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variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq})
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variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19)
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variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
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variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
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variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
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variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
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variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
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variable pscale equal 1e-05/(${sigmaM3}/(${epsilonJ}))
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variable pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ}))
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variable pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21))
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# variables
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# alat = lattice constant in Angs (at reduced density rhostar)
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# temp = reduced temperature for output
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# epair,emol,etotal = reduced epair,emol,etotal energies for output
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# press = reduced pressure for output
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variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
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variable temp equal temp/${tmpscale}
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variable temp equal temp/117.7
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variable epair equal epair/${epsilon}
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variable epair equal epair/0.010142612711
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variable emol equal emol/${epsilon}
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variable emol equal emol/0.010142612711
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variable etotal equal etotal/${epsilon}
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variable etotal equal etotal/0.010142612711
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variable press equal press/${pscale}
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variable press equal press/377.676586146256
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# same script as in.ar.lj
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units metal
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atom_style atomic
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lattice fcc ${alat}
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lattice fcc 5.79518437579763
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Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
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region box block 0 $x 0 $y 0 $z
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region box block 0 5 0 $y 0 $z
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region box block 0 5 0 5 0 $z
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region box block 0 5 0 5 0 5
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create_box 1 box
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Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 500 atoms
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create_atoms CPU = 0.000674009 secs
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mass 1 ${mass}
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mass 1 39.95
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velocity all create $(v_tinitial*v_epskb) 12345
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velocity all create 117.70000000000000284 12345
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pair_style lj/cut $(v_cutoff*v_sigma)
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pair_style lj/cut 8.7599999999999997868
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pair_coeff 1 1 ${epsilon} ${sigma}
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pair_coeff 1 1 0.010142612711 ${sigma}
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pair_coeff 1 1 0.010142612711 3.504
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neighbor $(v_skin*v_sigma) bin
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neighbor 1.0511999999999999122 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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timestep $(v_dt*v_tscale)
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timestep 0.011194658410003900315
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# columns 2,3,4 = temp,pe,press in metal units
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# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
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# need to include metal unit output to enable use of reduced variables
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thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
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thermo_modify norm yes
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thermo ${nthermo}
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thermo 10
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run ${nsteps}
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run 100
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 9.8112
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ghost atom cutoff = 9.8112
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binsize = 4.9056, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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) = 2.609 | 2.609 | 2.609 Mbytes
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Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press
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0 117.7 -0.07203931 -1934.8523 1 -7.1026383 0 -5.6056383 -5.12304
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10 86.648851 -0.06811179 -1166.7855 0.73618395 -6.7154088 0 -5.6133414 -3.0893774
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20 42.107954 -0.062497536 -143.06615 0.35775662 -6.1618774 0 -5.6263157 -0.37880598
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30 55.484504 -0.064263032 -416.20245 0.47140615 -6.3359445 0 -5.6302495 -1.1020075
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40 54.538222 -0.064148334 -414.88071 0.46336637 -6.3246361 0 -5.6309766 -1.0985079
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50 57.367693 -0.064511259 -463.67683 0.48740606 -6.3604182 0 -5.6307714 -1.2277087
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60 59.828794 -0.064824938 -519.05997 0.50831601 -6.3913451 0 -5.630396 -1.3743504
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70 60.014616 -0.064848979 -533.07604 0.50989478 -6.3937154 0 -5.6304029 -1.4114617
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80 63.47861 -0.065285885 -622.71073 0.53932549 -6.4367917 0 -5.6294215 -1.6487936
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90 65.060881 -0.065484011 -664.99883 0.55276874 -6.4563257 0 -5.6288309 -1.7607627
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100 64.637033 -0.065427467 -653.00765 0.54916765 -6.4507508 0 -5.6286468 -1.7290128
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Loop time of 0.0258265 on 4 procs for 100 steps with 500 atoms
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Performance: 3745.060 ns/day, 0.006 hours/ns, 3871.990 timesteps/s
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99.6% CPU use with 4 MPI tasks x no 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 | 0.0090213 | 0.012419 | 0.015494 | 2.1 | 48.09
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Neigh | 0.0013709 | 0.0018765 | 0.0022483 | 0.7 | 7.27
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Comm | 0.0071132 | 0.010597 | 0.014538 | 2.6 | 41.03
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Output | 0.00039983 | 0.00042897 | 0.00049567 | 0.0 | 1.66
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Modify | 0.00024104 | 0.00028801 | 0.00031543 | 0.0 | 1.12
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Other | | 0.0002173 | | | 0.84
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Nlocal: 125 ave 133 max 117 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 1099 ave 1107 max 1091 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 4908.75 ave 5492 max 4644 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 19635
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Ave neighs/atom = 39.27
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Neighbor list builds = 5
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Dangerous builds not checked
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Total wall time: 0:00:00
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