forked from lijiext/lammps
193 lines
7.9 KiB
Groff
193 lines
7.9 KiB
Groff
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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2 by 2 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 = 0.000466347 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) = 4.738 | 4.738 | 4.738 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 0.72465775 1136.9866
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1800 1.9731416 -3.2692426 -1.3364608 0.52887379 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 0.69021875 1125.7713
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Loop time of 0.349687 on 4 procs for 2000 steps with 400 atoms
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Performance: 988313.640 tau/day, 5719.408 timesteps/s
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95.9% CPU use with 4 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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Pair | 0.17051 | 0.19038 | 0.20513 | 3.1 | 54.44
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Neigh | 0.0039656 | 0.0043136 | 0.0049045 | 0.6 | 1.23
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Comm | 0.054327 | 0.071206 | 0.087044 | 4.9 | 20.36
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Output | 0.00043106 | 0.00062788 | 0.0012097 | 0.0 | 0.18
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Modify | 0.072846 | 0.077488 | 0.081302 | 1.2 | 22.16
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Other | | 0.005673 | | | 1.62
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Nlocal: 100 ave 112 max 84 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Nghost: 146.75 ave 156 max 137 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 755.25 ave 889 max 589 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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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) = 4.74 | 4.74 | 4.74 Mbytes
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Step c_rot E_pair TotEng Press Volume
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2000 1.894614 -3.3964158 -1.4932323 0.69021875 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 0.58806421 1125.7713
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2300 1.9069019 -3.4099452 -1.610028 0.63472573 1125.7713
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2400 1.9773106 -3.4856993 -1.5268537 0.68904883 1125.7713
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2500 2.0027578 -3.5144588 -1.4900205 0.59925475 1125.7713
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2600 1.9616631 -3.4744364 -1.5230915 0.26873516 1125.7713
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2700 1.8601136 -3.362572 -1.487211 0.68399725 1125.7713
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2800 1.8194391 -3.3190986 -1.5148092 0.62533318 1125.7713
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2900 1.846505 -3.3451617 -1.5508267 0.60156074 1125.7713
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3000 1.8894747 -3.3918215 -1.5180241 0.61210219 1125.7713
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3100 1.866832 -3.3665537 -1.5276291 0.54222093 1125.7713
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3200 1.8233362 -3.320323 -1.5177672 0.82891257 1125.7713
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3300 1.7946952 -3.2899252 -1.4974666 0.56782835 1125.7713
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3400 1.8283468 -3.3286169 -1.5065958 1.0370934 1125.7713
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3500 1.8538134 -3.3526037 -1.5116661 0.58945341 1125.7713
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3600 1.7851382 -3.2811082 -1.5306837 0.462114 1125.7713
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3700 1.7664573 -3.2622701 -1.4774432 0.86540402 1125.7713
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3800 1.8574677 -3.3592552 -1.5196884 0.45146881 1125.7713
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3900 1.9139087 -3.4196718 -1.5054647 0.79636137 1125.7713
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4000 1.9081675 -3.4146407 -1.5285325 0.69377107 1125.7713
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Loop time of 0.379139 on 4 procs for 2000 steps with 400 atoms
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Performance: 911539.742 tau/day, 5275.114 timesteps/s
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96.6% CPU use with 4 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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Pair | 0.20177 | 0.23758 | 0.28816 | 7.4 | 62.66
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Neigh | 0.0015984 | 0.001946 | 0.0022459 | 0.6 | 0.51
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Comm | 0.046169 | 0.093409 | 0.13456 | 11.9 | 24.64
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Output | 0.00048614 | 0.00087821 | 0.0016096 | 0.0 | 0.23
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Modify | 0.02563 | 0.029633 | 0.034698 | 2.0 | 7.82
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Other | | 0.01569 | | | 4.14
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Nlocal: 100 ave 117 max 87 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Nghost: 152.5 ave 169 max 131 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 771.25 ave 988 max 612 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Total # of neighbors = 3085
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Ave neighs/atom = 7.7125
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Neighbor list builds = 45
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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: 0:00:00
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