a04f267b54
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10655 f3b2605a-c512-4ea7-a41b-209d697bcdaa
276 lines
14 KiB
Plaintext
276 lines
14 KiB
Plaintext
LAMMPS (24 Aug 2013)
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# create domain
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#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
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# NOTE following 3 lines added for restart
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boundary f p p
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pair_style lj/cut 13.5
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read_data temp.init
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Reading data file ...
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orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215)
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2 by 1 by 2 MPI processor grid
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1440 atoms
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1440 velocities
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lattice fcc 5.405 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 5.405 5.405 5.405
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region simRegion block -12 12 -3 3 -3 3
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# create atoms, NOTE commented out for restart
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#region mdRegion block -5 5 -3 3 -3 3
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#boundary f p p
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#create_box 1 mdRegion
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#create_atoms 1 region mdRegion
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#mass 1 39.95
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# specify interal/ghost atoms
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region mdInternal block -4 4 -3 3 -3 3
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group internal region mdInternal
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1152 atoms in group internal
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group ghost subtract all internal
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288 atoms in group ghost
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# velocities have Vcm = 0, NOTE next four lines commented out for restart
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#velocity internal create 40. 87287 mom yes loop geom
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#pair_style lj/cut 13.5
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##pair_coeff 1 1 0.010323166 3.405 13.5
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#pair_coeff 1 1 .238 3.405 13.5
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc thermal Ar_thermal.mat
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ATC: constructing thermal coupling with parameter file Ar_thermal.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: 3 materials defined from Ar_thermal.mat
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fix_modify AtC boundary ghost
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create 12 1 1 simRegion f p p
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ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
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fix_modify AtC internal_quadrature off
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# fix a temperature
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fix_modify AtC fix temperature all 20.
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# turn on thermostat
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fix_modify AtC control thermal rescale 10
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# equilibrate MD field
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#dump D1 all atom 100 dump.bar1d
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#fix_modify AtC output bar1dfe 100
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timestep 5
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variable xdof equal 3*count(ghost)
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compute_modify thermo_temp extra ${xdof}
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compute_modify thermo_temp extra 864
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thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
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thermo_modify format 1 %6i format 2 %7.2g
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thermo 100
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run 400
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Setting up run ...
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ATC: WARNING: material: [vacuum] cannot find heat_flux
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ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
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Memory usage per processor = 51.6077 Mbytes
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Step CPU TotEng PotEng AtC[1] Temp AtC[2]
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0 0 -2573.6428 -2710.8793 412.06718 39.965279 20
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100 0.7 -2537.6764 -2606.3542 412.06718 20 20
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200 1.4 -2584.8754 -2653.5532 412.06718 20 20
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300 2.1 -2575.3126 -2643.9904 412.06718 20 20
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400 2.8 -2573.4199 -2642.0977 412.06718 20 20
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Loop time of 2.78741 on 4 procs for 400 steps with 1440 atoms
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Pair time (%) = 1.39204 (49.9404)
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Neigh time (%) = 0.56545 (20.2859)
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Comm time (%) = 0.175334 (6.29021)
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Outpt time (%) = 0.00167495 (0.0600899)
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Other time (%) = 0.652907 (23.4234)
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Nlocal: 360 ave 360 max 360 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 4060 ave 4060 max 4060 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 104865 ave 104966 max 104653 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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FullNghs: 209730 ave 209902 max 209521 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Total # of neighbors = 838918
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Ave neighs/atom = 582.582
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Neighbor list builds = 40
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Dangerous builds = 0
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# change thermostat to hoover
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fix_modify AtC unfix temperature all
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fix_modify AtC control thermal hoover
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#fix_modify AtC localized_lambda on
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fix_modify AtC filter type exponential
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fix_modify AtC filter scale 10000.0
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fix_modify AtC filter on
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# add nodesets
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# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
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fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
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ATC: created nodeset lbc with 1 nodes
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fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
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ATC: created nodeset rbc with 1 nodes
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fix_modify AtC fix temperature lbc 40.
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fix_modify AtC fix temperature rbc 20.
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# initialize filter
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#thermo 1
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run 100
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Setting up run ...
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ATC: WARNING: material: [vacuum] cannot find heat_flux
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ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
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Memory usage per processor = 58.8926 Mbytes
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Step CPU TotEng PotEng AtC[1] Temp AtC[2]
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400 0 -2573.4199 -2642.0977 412.06718 20 20
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500 0.77 -2573.7738 -2643.7447 433.14294 20.376549 21.713472
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Loop time of 0.774979 on 4 procs for 100 steps with 1440 atoms
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Pair time (%) = 0.348038 (44.9093)
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Neigh time (%) = 0.142239 (18.3539)
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Comm time (%) = 0.0426333 (5.50122)
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Outpt time (%) = 0.000411689 (0.0531226)
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Other time (%) = 0.241658 (31.1825)
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Nlocal: 360 ave 360 max 360 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 4060 ave 4060 max 4060 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 104765 ave 105086 max 104556 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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FullNghs: 209530 ave 209833 max 209326 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Total # of neighbors = 838118
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Ave neighs/atom = 582.026
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Neighbor list builds = 10
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Dangerous builds = 0
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# set up output, should be before a "run"
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fix_modify AtC output bar1dFE 100 text binary
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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# ouput command
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#dump D1 all atom 1000 dump.bar1d
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# run with FE
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reset_timestep 0
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thermo 100
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run 10000
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Setting up run ...
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ATC: WARNING: material: [vacuum] cannot find heat_flux
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ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
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Memory usage per processor = 58.8926 Mbytes
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Step CPU TotEng PotEng AtC[1] Temp AtC[2]
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0 0 -2573.7738 -2643.7447 433.14294 20.376549 21.713472
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100 0.79 -2573.654 -2645.0562 436.6146 20.793359 21.86901
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200 1.6 -2574.0035 -2642.057 439.70235 19.818183 22.007349
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300 2.3 -2573.5186 -2646.5507 442.73301 21.268004 22.143129
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400 3.1 -2573.2662 -2641.032 445.39809 19.734394 22.262531
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500 3.9 -2573.5673 -2644.7553 447.93109 20.730998 22.376015
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600 4.7 -2572.9368 -2641.5818 450.33706 19.990452 22.483808
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700 5.5 -2573.2457 -2642.9406 452.61859 20.296182 22.586025
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800 6.3 -2573.215 -2642.7311 454.75264 20.244128 22.681635
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900 7 -2572.7227 -2643.5215 456.77865 20.617654 22.772405
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1000 7.8 -2572.411 -2644.5969 458.68289 21.021605 22.857719
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1100 9.4 -2571.4099 -2642.08 460.52888 20.580181 22.940424
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1200 10 -2570.5495 -2641.7296 462.26173 20.728698 23.01806
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1300 11 -2570.2491 -2640.8115 463.9083 20.548784 23.09183
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1400 13 -2570.159 -2641.2853 465.40156 20.713007 23.158731
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1500 13 -2569.5061 -2642.2055 467.00405 21.171116 23.230527
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1600 14 -2568.7522 -2639.5247 468.45299 20.609988 23.295442
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1700 15 -2569.1809 -2642.0975 469.79048 21.23439 23.355365
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1800 16 -2568.7484 -2643.2103 471.10946 21.684386 23.414458
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1900 17 -2568.2581 -2641.5017 472.49875 21.329637 23.476701
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2000 18 -2568.192 -2641.4647 473.7794 21.338078 23.534077
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2100 19 -2568.0746 -2639.9335 474.99711 20.926347 23.588633
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2200 20 -2567.2717 -2642.2868 476.13779 21.845489 23.639738
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2300 21 -2566.7209 -2639.9022 477.31159 21.311461 23.692327
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2400 21 -2566.6054 -2638.8118 478.44655 21.027558 23.743176
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2500 22 -2565.7629 -2639.6423 479.55196 21.514764 23.792701
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2600 23 -2565.9248 -2642.5794 480.54223 22.322945 23.837067
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2700 24 -2564.9995 -2640.0503 481.61938 21.855895 23.885326
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2800 25 -2565.2468 -2638.033 482.61597 21.196395 23.929975
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2900 26 -2565.0496 -2639.4905 483.63717 21.678286 23.975727
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3000 26 -2565.1382 -2637.5132 484.58683 21.076652 24.018275
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3100 27 -2564.4793 -2636.7861 485.5364 21.056785 24.060817
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3200 29 -2564.1799 -2637.5024 486.53294 21.352561 24.105465
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3300 30 -2564.4531 -2641.3463 487.42873 22.392434 24.145598
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3400 32 -2564.2323 -2641.0072 488.30292 22.357973 24.184764
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3500 33 -2563.378 -2635.3819 489.17087 20.968574 24.22365
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3600 34 -2563.5014 -2637.8324 490.1027 21.646291 24.265398
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3700 35 -2563.4092 -2638.0479 490.92648 21.735889 24.302305
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3800 36 -2563.0307 -2637.5397 491.76937 21.698123 24.340068
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3900 37 -2562.1415 -2637.2704 492.65132 21.878653 24.379582
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4000 38 -2561.9969 -2637.3928 493.4009 21.956415 24.413165
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4100 38 -2560.7688 -2636.0902 494.20978 21.934699 24.449405
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4200 39 -2561.3033 -2638.2324 494.92948 22.402886 24.481649
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4300 40 -2560.9897 -2637.0909 495.72929 22.161791 24.517482
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4400 41 -2561.1677 -2638.5004 496.4863 22.520422 24.551398
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4500 42 -2560.4797 -2637.3716 497.21153 22.392069 24.58389
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4600 42 -2560.5787 -2637.0577 497.94655 22.271795 24.61682
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4700 43 -2560.9645 -2639.5115 498.65048 22.874032 24.648358
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4800 44 -2560.4451 -2637.6681 499.40401 22.488483 24.682118
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4900 45 -2559.5243 -2635.9383 500.10679 22.252874 24.713604
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5000 46 -2559.4948 -2637.7238 500.83953 22.781444 24.746432
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5100 47 -2559.6822 -2636.169 501.53339 22.274071 24.777518
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5200 47 -2559.6398 -2637.3169 502.26381 22.620718 24.810243
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5300 48 -2558.6285 -2634.5293 502.8444 22.103424 24.836255
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5400 49 -2558.6394 -2637.9487 503.59005 23.096025 24.869662
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5500 50 -2558.1403 -2636.176 504.21716 22.725144 24.897757
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5600 51 -2558.0703 -2635.1367 504.9347 22.442865 24.929905
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5700 53 -2558.0656 -2636.7197 505.52087 22.905225 24.956167
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5800 54 -2557.3777 -2634.8266 506.20982 22.554253 24.987033
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5900 55 -2557.2526 -2635.9743 506.86422 22.924918 25.016352
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6000 57 -2557.3833 -2637.2291 507.48018 23.25228 25.043948
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6100 58 -2556.0263 -2633.5407 508.11625 22.573338 25.072446
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6200 59 -2555.7442 -2634.4379 508.74696 22.916758 25.100703
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6300 59 -2555.855 -2635.6232 509.35007 23.229653 25.127723
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6400 60 -2555.9332 -2634.2034 509.90097 22.793416 25.152405
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6500 61 -2555.6529 -2635.6085 510.47402 23.284242 25.178079
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6600 62 -2554.8702 -2633.8042 511.0317 22.986719 25.203064
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6700 63 -2555.4594 -2637.4199 511.60862 23.868095 25.228911
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6800 64 -2555.1345 -2633.0307 512.18015 22.684507 25.254517
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6900 64 -2555.2031 -2635.8935 512.79344 23.498217 25.281994
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7000 65 -2554.4149 -2634.996 513.32816 23.466386 25.305951
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7100 66 -2555.5655 -2636.9961 513.95657 23.713805 25.334105
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7200 67 -2554.6219 -2632.7377 514.567 22.748451 25.361454
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7300 68 -2553.7348 -2633.5176 515.135 23.233924 25.386901
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7400 68 -2553.6835 -2632.7483 515.7035 23.024829 25.412371
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7500 69 -2554.1585 -2634.2224 516.25704 23.315779 25.437171
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7600 70 -2553.7146 -2636.4167 516.79495 24.084074 25.461271
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7700 71 -2553.0976 -2633.1654 517.39991 23.316903 25.488375
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7800 73 -2553.7234 -2633.6408 517.98568 23.273102 25.514618
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7900 74 -2553.1575 -2635.2362 518.49062 23.902519 25.537241
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8000 75 -2553.0069 -2632.9282 519.06292 23.274267 25.562881
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8100 76 -2552.2172 -2632.9349 519.57824 23.506176 25.585969
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8200 77 -2552.6329 -2633.705 520.13682 23.609392 25.610994
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8300 77 -2553.0514 -2636.5364 520.66438 24.312051 25.63463
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8400 78 -2551.9158 -2634.5593 521.15401 24.066989 25.656566
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8500 79 -2551.162 -2632.582 521.69313 23.710703 25.68072
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8600 80 -2551.323 -2631.8792 522.25824 23.459141 25.706039
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8700 81 -2551.3995 -2634.1924 522.75555 24.110486 25.728319
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8800 81 -2551.5524 -2635.9593 523.28139 24.580545 25.751878
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8900 83 -2550.9859 -2634.5116 523.74996 24.3239 25.772871
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9000 83 -2550.3986 -2630.9451 524.29066 23.456323 25.797095
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9100 84 -2550.2258 -2632.4852 524.79409 23.955138 25.81965
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9200 85 -2549.7276 -2633.251 525.32924 24.323252 25.843626
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9300 86 -2549.2309 -2632.0111 525.82326 24.1068 25.86576
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9400 87 -2549.1793 -2631.7908 526.23399 24.057681 25.884161
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9500 88 -2549.3234 -2632.8586 526.74802 24.326659 25.907191
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9600 89 -2548.7761 -2630.2005 527.18774 23.711964 25.926891
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9700 90 -2548.5531 -2631.9225 527.62451 24.27839 25.946459
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9800 92 -2548.3632 -2632.4871 528.04194 24.49812 25.965161
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9900 92 -2548.2216 -2631.2195 528.52701 24.170186 25.986893
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10000 93 -2547.7787 -2631.2232 528.97935 24.300246 26.007159
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Loop time of 93.2645 on 4 procs for 10000 steps with 1440 atoms
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Pair time (%) = 36.4073 (39.0367)
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Neigh time (%) = 15.1901 (16.2872)
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Comm time (%) = 11.3509 (12.1706)
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Outpt time (%) = 0.102398 (0.109793)
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Other time (%) = 30.2137 (32.3958)
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Nlocal: 360 ave 360 max 360 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 4060 ave 4060 max 4060 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 104823 ave 104983 max 104416 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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FullNghs: 209646 ave 209959 max 209315 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Total # of neighbors = 838584
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Ave neighs/atom = 582.35
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Neighbor list builds = 1000
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Dangerous builds = 0
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