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simongravellesimongravelle
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add files for tutorial 6
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‎files/shared-pyplot‎

‎files/tutorial6/solution/H2O.mol‎

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../H2O.mol

‎files/tutorial6/solution/SiO.1990.vashishta‎

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../SiO.1990.vashishta

‎files/tutorial6/solution/SiO.data‎

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../SiO.data

‎files/tutorial6/solution/cracking.data‎

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‎files/tutorial6/solution/cracking.lmp‎

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units metal
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boundary p p p
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atom_style full
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pair_style vashishta
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neighbor 1.0 bin
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neigh_modify delay 1
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read_data generate.data
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pair_coeff * * SiO.1990.vashishta Si O
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dump mydmp all image 200 myimage-*.ppm type type &
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shiny 0.1 box no 0.01 view 180 90 zoom 1.2 size 1000 650
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dump_modify mydmp backcolor white &
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acolor Si yellow adiam Si 2.5 &
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acolor O red adiam O 2
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thermo 1000
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thermo_style custom step temp etotal vol lx ly lz
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fix nvt1 all nvt temp 300 300 0.1
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timestep 0.001
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thermo 1000
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#variable var loop 45
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#label loop
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fix mydef all deform 1 x erate 0.015
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#change_box all x scale 1.005 remap
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run 20000
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#next var
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#jump cracking.lmp
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write_data cracking.data

‎files/tutorial6/solution/cracking.log‎

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using 8 OpenMP thread(s) per MPI task
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using multi-threaded neighbor list subroutines
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Reading data file ...
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orthogonal box = (0.91061361 1.6226589 -1.2373349) to (24.821359 18.962919 21.822913)
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1 by 1 by 1 MPI processor grid
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reading atom labelmap ...
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reading atoms ...
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720 atoms
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reading velocities ...
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720 velocities
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.020 seconds
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Reading vashishta potential file SiO.1990.vashishta with DATE: 2015-10-14
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Last active /omp style is pair_style vashishta/omp
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Neighbor list info ...
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update: every = 1 steps, delay = 1 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11
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ghost atom cutoff = 11
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binsize = 5.5, bins = 5 4 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair vashishta/omp, perpetual
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attributes: full, newton on, omp
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pair build: full/bin/omp
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stencil: full/bin/3d
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bin: standard
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Setting up Verlet run ...
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Unit style : metal
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Current step : 0
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Time step : 0.001
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Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes
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Step Temp TotEng Volume Lx Ly Lz
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0 301.17448 -6427.659 9561.206 23.910745 17.34026 23.060247
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1000 279.44119 -6428.5784 9704.624 24.269406 17.34026 23.060247
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2000 295.50824 -6425.4113 9848.0421 24.628067 17.34026 23.060247
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3000 298.6945 -6419.5557 9991.4602 24.986728 17.34026 23.060247
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4000 282.51392 -6416.8589 10134.878 25.34539 17.34026 23.060247
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5000 304.60827 -6405.7082 10278.296 25.704051 17.34026 23.060247
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6000 298.10251 -6398.6524 10421.714 26.062712 17.34026 23.060247
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7000 295.81949 -6388.8453 10565.133 26.421373 17.34026 23.060247
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8000 319.62403 -6375.837 10708.551 26.780034 17.34026 23.060247
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9000 314.49787 -6368.534 10851.969 27.138695 17.34026 23.060247
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10000 296.82693 -6360.4751 10995.387 27.497357 17.34026 23.060247
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11000 287.74596 -6348.8833 11138.805 27.856018 17.34026 23.060247
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12000 289.74339 -6342.7617 11282.223 28.214679 17.34026 23.060247
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13000 301.77567 -6334.3267 11425.641 28.57334 17.34026 23.060247
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14000 294.91747 -6340.0743 11569.059 28.932001 17.34026 23.060247
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15000 294.22476 -6329.1306 11712.477 29.290663 17.34026 23.060247
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16000 311.42893 -6327.6932 11855.895 29.649324 17.34026 23.060247
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17000 303.34378 -6324.195 11999.313 30.007985 17.34026 23.060247
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18000 302.47749 -6319.3108 12142.732 30.366646 17.34026 23.060247
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19000 312.49613 -6310.5494 12286.15 30.725307 17.34026 23.060247
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20000 332.7128 -6323.9637 12429.568 31.083968 17.34026 23.060247
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Loop time of 38.4353 on 8 procs for 20000 steps with 720 atoms
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Performance: 44.959 ns/day, 0.534 hours/ns, 520.356 timesteps/s, 374.656 katom-step/s
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773.7% CPU use with 1 MPI tasks x 8 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 | 33.078 | 33.078 | 33.078 | 0.0 | 86.06
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Bond | 0.0013156 | 0.0013156 | 0.0013156 | 0.0 | 0.00
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Neigh | 0.50724 | 0.50724 | 0.50724 | 0.0 | 1.32
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Comm | 0.75904 | 0.75904 | 0.75904 | 0.0 | 1.97
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Output | 2.7063 | 2.7063 | 2.7063 | 0.0 | 7.04
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Modify | 1.3162 | 1.3162 | 1.3162 | 0.0 | 3.42
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Other | | 0.06739 | | | 0.18
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Nlocal: 720 ave 720 max 720 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5018 ave 5018 max 5018 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 241106 ave 241106 max 241106 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 241106
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Ave neighs/atom = 334.86944
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Ave special neighs/atom = 0
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Neighbor list builds = 385
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Dangerous builds = 0
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System init for write_data ...
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Last active /omp style is pair_style vashishta/omp

‎files/tutorial6/solution/cracking.png‎

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