forked from lijiext/lammps
193 lines
7.9 KiB
Groff
193 lines
7.9 KiB
Groff
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# GayBerne ellipsoids in LJ background fluid
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units lj
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atom_style ellipsoid
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dimension 2
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lattice sq 0.02
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Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
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region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 400 atoms
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Time spent = 0.000507116 secs
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set group all type/fraction 2 0.1 95392
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45 settings made for type/fraction
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set type 1 mass 1.0
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355 settings made for mass
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set type 2 mass 1.5
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45 settings made for mass
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set type 1 shape 1 1 1
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355 settings made for shape
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set type 2 shape 3 1 1
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45 settings made for shape
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set group all quat/random 18238
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400 settings made for quat/random
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compute rot all temp/asphere
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group spheroid type 1
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355 atoms in group spheroid
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variable dof equal count(spheroid)+2
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compute_modify rot extra/dof ${dof}
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compute_modify rot extra/dof 357
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velocity all create 2.4 87287 loop geom
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pair_style gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
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pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
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pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
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neighbor 0.8 bin
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thermo_style custom step c_rot epair etotal press vol
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thermo 100
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timestep 0.002
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compute q all property/atom quatw quati quatj quatk
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#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
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#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
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#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
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#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
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#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
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fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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compute_modify 1_temp extra/dof ${dof}
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compute_modify 1_temp extra/dof 357
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# equilibrate to shrink box around dilute system
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run 2000
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 4.8
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ghost atom cutoff = 4.8
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binsize = 2.4, bins = 59 59 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair gayberne, 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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes
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Step c_rot E_pair TotEng Press Volume
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0 2.2718861 0 2.394 0.04788 20000
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100 1.7443419 0 1.8381003 0.035765442 20557.278
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200 2.2768798 0 2.3992621 0.046544845 20618.928
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300 1.8573086 0 1.9571389 0.04239709 18464.842
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400 2.1707875 -0.00045989278 2.2870073 0.066725499 13701.839
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500 1.9710982 -0.014545321 2.0486111 0.12205188 8490.5214
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600 2.0818888 -0.21572832 1.8356955 0.22333255 4697.3035
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700 2.1551458 -0.68175426 1.4003368 0.60385996 2541.157
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800 1.8879651 -1.6357045 0.21794544 1.0826917 1444.4484
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900 2.1993533 -3.0664068 -0.91036919 3.2142529 925.96691
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1000 1.4285977 -4.3962037 -2.9651113 3.1830461 744.91324
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1100 1.933074 -4.9398703 -3.0147256 1.4694937 715.30906
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1200 2.0872875 -4.5711608 -2.4689861 1.4091154 757.68606
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1300 1.8950043 -4.1568789 -2.2487345 0.19138859 846.69407
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1400 2.1773467 -3.7905723 -1.6164698 0.55639059 930.77026
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1500 1.934954 -3.5505876 -1.6187812 0.2572587 1020.2803
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1600 2.083004 -3.2707357 -1.1794873 0.68661802 1088.5587
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1700 1.9434093 -3.2434441 -1.3043926 0.72465776 1136.9866
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1800 1.9731416 -3.2692426 -1.3364608 0.52887378 1162.1022
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1900 2.0618126 -3.2264372 -1.162807 0.93455596 1155.8306
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2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713
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Loop time of 0.950695 on 1 procs for 2000 steps with 400 atoms
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Performance: 363523.513 tau/day, 2103.724 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 | 0.72638 | 0.72638 | 0.72638 | 0.0 | 76.40
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Neigh | 0.015026 | 0.015026 | 0.015026 | 0.0 | 1.58
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Comm | 0.015169 | 0.015169 | 0.015169 | 0.0 | 1.60
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Output | 0.0004487 | 0.0004487 | 0.0004487 | 0.0 | 0.05
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Modify | 0.18921 | 0.18921 | 0.18921 | 0.0 | 19.90
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Other | | 0.004463 | | | 0.47
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Nlocal: 400 ave 400 max 400 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 247 ave 247 max 247 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3021 ave 3021 max 3021 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3021
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Ave neighs/atom = 7.5525
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Neighbor list builds = 137
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Dangerous builds = 80
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# run dynamics on dense system
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unfix 1
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fix 1 all nve/asphere
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run 2000
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Per MPI rank memory allocation (min/avg/max) = 4.763 | 4.763 | 4.763 Mbytes
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Step c_rot E_pair TotEng Press Volume
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2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713
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2100 1.8880098 -3.3875135 -1.4857102 0.21017294 1125.7713
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2200 1.9098636 -3.4103342 -1.5286928 0.58806422 1125.7713
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2300 1.9069018 -3.4099451 -1.6100279 0.63472569 1125.7713
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2400 1.9773111 -3.4856999 -1.5268537 0.68904663 1125.7713
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2500 2.0027582 -3.5144592 -1.4900208 0.59925433 1125.7713
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2600 1.9616623 -3.4744355 -1.5230915 0.26873349 1125.7713
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2700 1.8601168 -3.3625754 -1.4872109 0.68399005 1125.7713
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2800 1.8194253 -3.319084 -1.5148077 0.62537226 1125.7713
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2900 1.8465082 -3.3451652 -1.5508026 0.60163613 1125.7713
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3000 1.8894551 -3.3918005 -1.5180435 0.61243969 1125.7713
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3100 1.866554 -3.3662479 -1.5275331 0.54334005 1125.7713
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3200 1.8233715 -3.3204693 -1.5180055 0.82717864 1125.7713
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3300 1.7945158 -3.2898507 -1.4976351 0.56745564 1125.7713
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3400 1.8242025 -3.3242538 -1.5070312 1.0550995 1125.7713
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3500 1.860405 -3.3595757 -1.5138968 0.56959347 1125.7713
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3600 1.76951 -3.2635375 -1.5302852 0.47091998 1125.7713
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3700 1.7874111 -3.2838743 -1.4858244 0.74507678 1125.7713
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3800 1.8084002 -3.3081089 -1.5294313 0.63717641 1125.7713
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3900 1.9201118 -3.4261733 -1.4874713 0.4111663 1125.7713
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4000 1.9130445 -3.4170846 -1.49357 0.35783848 1125.7713
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Loop time of 1.05944 on 1 procs for 2000 steps with 400 atoms
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Performance: 326208.857 tau/day, 1887.783 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 | 0.91753 | 0.91753 | 0.91753 | 0.0 | 86.60
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Neigh | 0.0072479 | 0.0072479 | 0.0072479 | 0.0 | 0.68
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Comm | 0.016155 | 0.016155 | 0.016155 | 0.0 | 1.52
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Output | 0.00042105 | 0.00042105 | 0.00042105 | 0.0 | 0.04
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Modify | 0.11222 | 0.11222 | 0.11222 | 0.0 | 10.59
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Other | | 0.005868 | | | 0.55
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Nlocal: 400 ave 400 max 400 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 243 ave 243 max 243 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3073 ave 3073 max 3073 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3073
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Ave neighs/atom = 7.6825
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Neighbor list builds = 46
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:02
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