Updating pair tracker example
This commit is contained in:
jtclemm
File diff suppressed because it is too large
Load Diff
@ -11,7 +11,7 @@ mass 1 1.0
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mass 2 1.0
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mass 2 1.0
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velocity all create 2.0 87287 loop geom
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velocity all create 2.0 87287 loop geom
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pair_style hybrid/overlay lj/cut 2.5 tracker
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pair_style hybrid/overlay lj/cut 2.5 tracker trackfix 1000 id1 id2 time/created time/broken time/total time/min 0.5
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pair_coeff * * lj/cut 1.0 1.0 2.5
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pair_coeff * * lj/cut 1.0 1.0 2.5
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pair_coeff * * tracker 2.5
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pair_coeff * * tracker 2.5
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@ -19,10 +19,9 @@ neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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fix 1 all nve
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fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5
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fix 2 all ave/histo 1000 1 1000 0 6 30 f_trackfix[5] mode vector kind local file lifetime_hist.dat
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fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat
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dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4]
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dump 1 all local 1000 contact_history.dat f_trackfix[1] f_trackfix[2] f_trackfix[3] f_trackfix[4]
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dump_modify 1 header no
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dump_modify 1 header no
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# compute 1 all property/local patom1 patom2
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# compute 1 all property/local patom1 patom2
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@ -1,4 +1,4 @@
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# Histogrammed data for fix 3
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# Histogrammed data for fix 2
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# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
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# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
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# Bin Coord Count Count/Total
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# Bin Coord Count Count/Total
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0 30 0 0 1e+20 -1e+20
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0 30 0 0 1e+20 -1e+20
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@ -32,34 +32,34 @@
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28 5.5 0 0
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28 5.5 0 0
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29 5.7 0 0
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29 5.7 0 0
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30 5.9 0 0
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30 5.9 0 0
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1000 30 8122 0 0.5 5
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1000 30 528 20285 1 1000
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1 0.1 0 0
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1 0.1 0 0
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2 0.3 0 0
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2 0.3 0 0
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3 0.5 910 0.112041
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3 0.5 0 0
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4 0.7 1253 0.154272
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4 0.7 0 0
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5 0.9 953 0.117336
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5 0.9 0 0
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6 1.1 747 0.0919724
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6 1.1 17 0.032197
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7 1.3 559 0.0688254
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7 1.3 0 0
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8 1.5 501 0.0616843
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8 1.5 0 0
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9 1.7 421 0.0518345
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9 1.7 0 0
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10 1.9 356 0.0438316
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10 1.9 0 0
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11 2.1 300 0.0369367
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11 2.1 51 0.0965909
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12 2.3 281 0.0345974
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12 2.3 0 0
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13 2.5 242 0.0297956
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13 2.5 0 0
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14 2.7 226 0.0278257
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14 2.7 0 0
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15 2.9 175 0.0215464
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15 2.9 0 0
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16 3.1 168 0.0206846
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16 3.1 80 0.151515
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17 3.3 162 0.0199458
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17 3.3 0 0
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18 3.5 129 0.0158828
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18 3.5 0 0
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19 3.7 151 0.0185915
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19 3.7 0 0
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20 3.9 137 0.0168678
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20 3.9 0 0
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21 4.1 98 0.012066
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21 4.1 91 0.172348
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22 4.3 104 0.0128047
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22 4.3 0 0
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23 4.5 83 0.0102192
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23 4.5 0 0
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24 4.7 77 0.00948042
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24 4.7 0 0
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25 4.9 86 0.0105885
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25 4.9 0 0
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26 5.1 3 0.000369367
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26 5.1 117 0.221591
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27 5.3 0 0
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27 5.3 0 0
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28 5.5 0 0
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28 5.5 0 0
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29 5.7 0 0
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29 5.7 0 0
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30 5.9 0 0
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30 5.9 172 0.325758
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108
examples/tracker/log.29Aug24.tracker.g++.1
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108
examples/tracker/log.29Aug24.tracker.g++.1
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@ -0,0 +1,108 @@
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-731-g5ce635757f)
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# 3d Lennard-Jones melt with tracking
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 4 0 4 0 4
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create_box 2 box
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Created orthogonal box = (0 0 0) to (6.7183848 6.7183848 6.7183848)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 256 atoms
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using lattice units in orthogonal box = (0 0 0) to (6.7183848 6.7183848 6.7183848)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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mass 2 1.0
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velocity all create 2.0 87287 loop geom
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pair_style hybrid/overlay lj/cut 2.5 tracker trackfix 1000 id1 id2 time/created time/broken time/total time/min 0.5
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pair_coeff * * lj/cut 1.0 1.0 2.5
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pair_coeff * * tracker 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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fix 2 all ave/histo 1000 1 1000 0 6 30 f_trackfix[5] mode vector kind local file lifetime_hist.dat
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dump 1 all local 1000 contact_history.dat f_trackfix[1] f_trackfix[2] f_trackfix[3] f_trackfix[4]
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dump_modify 1 header no
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# compute 1 all property/local patom1 patom2
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# dump 2 all local 1 pairs.dat c_1[1] c_1[2]
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# dump 3 all atom 1 atoms.dat
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thermo 50
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run 1000 #0
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 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
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bin: standard
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(2) pair tracker, perpetual, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 8.679 | 8.679 | 8.679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2 -6.7733681 0 -3.7850868 -4.5535126
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50 1.0540428 -5.3670859 0 -3.7921977 2.3386375
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100 1.0402713 -5.3493439 0 -3.7950323 2.4553748
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150 1.0570745 -5.3738961 0 -3.7944781 2.3767396
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200 1.0431846 -5.3518647 0 -3.7932002 2.5010135
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250 1.070121 -5.3902744 0 -3.791363 2.4908658
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300 1.0667723 -5.3866302 0 -3.7927224 2.3589344
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350 1.000601 -5.2859643 0 -3.7909257 2.9065274
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400 0.99256113 -5.2738812 0 -3.7908553 2.8595867
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450 1.0482542 -5.357452 0 -3.7912128 2.4707397
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500 1.0196176 -5.3123538 0 -3.7889017 2.7230338
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550 0.98274535 -5.2586303 0 -3.7902706 2.9156947
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600 1.0683914 -5.3863229 0 -3.789996 2.3002719
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650 1.0130779 -5.303917 0 -3.7902362 2.8726423
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700 1.0583333 -5.3737358 0 -3.792437 2.5770307
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750 0.98274506 -5.2612464 0 -3.792887 2.9447027
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800 1.0294191 -5.332001 0 -3.7939042 2.5293193
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850 0.99240027 -5.2735754 0 -3.7907899 2.7672711
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900 1.0293488 -5.3306241 0 -3.7926323 2.6054041
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950 0.97137182 -5.2424403 0 -3.7910742 3.129989
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1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598
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Loop time of 0.286151 on 1 procs for 1000 steps with 256 atoms
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Performance: 1509690.552 tau/day, 3494.654 timesteps/s, 894.631 katom-step/s
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99.4% CPU use with 1 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 | 0.21578 | 0.21578 | 0.21578 | 0.0 | 75.41
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Neigh | 0.020262 | 0.020262 | 0.020262 | 0.0 | 7.08
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Comm | 0.0051679 | 0.0051679 | 0.0051679 | 0.0 | 1.81
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Output | 0.021204 | 0.021204 | 0.021204 | 0.0 | 7.41
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Modify | 0.02307 | 0.02307 | 0.02307 | 0.0 | 8.06
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Other | | 0.0006654 | | | 0.23
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Nlocal: 256 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1327 ave 1327 max 1327 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9612 ave 9612 max 9612 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9612
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Ave neighs/atom = 37.546875
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:00
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@ -1,107 +0,0 @@
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LAMMPS (8 Apr 2021)
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# 3d Lennard-Jones melt with tracking
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 4 0 4 0 4
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create_box 2 box
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 256 atoms
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create_atoms CPU = 0.001 seconds
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mass 1 1.0
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mass 2 1.0
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velocity all create 2.0 87287 loop geom
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pair_style hybrid/overlay lj/cut 2.5 tracker
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pair_coeff * * lj/cut 1.0 1.0 2.5
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pair_coeff * * tracker 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5
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fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat
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dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4]
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dump_modify 1 header no
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# compute 1 all property/local patom1 patom2
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# dump 2 all local 1 pairs.dat c_1[1] c_1[2]
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# dump 3 all atom 1 atoms.dat
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thermo 50
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run 1000 #0
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 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
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bin: standard
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(2) pair tracker, perpetual
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attributes: half, newton on, history
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2 -6.7733681 0 -3.7850868 -4.5535126
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50 1.0540428 -5.3670859 0 -3.7921977 2.3386375
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100 1.0402713 -5.3493439 0 -3.7950323 2.4553748
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150 1.0570745 -5.3738961 0 -3.7944781 2.3767396
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200 1.0431846 -5.3518647 0 -3.7932002 2.5010135
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250 1.070121 -5.3902744 0 -3.791363 2.4908658
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300 1.0667723 -5.3866302 0 -3.7927224 2.3589344
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350 1.000601 -5.2859643 0 -3.7909257 2.9065274
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400 0.99256113 -5.2738812 0 -3.7908553 2.8595867
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450 1.0482542 -5.357452 0 -3.7912128 2.4707397
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500 1.0196176 -5.3123538 0 -3.7889017 2.7230338
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550 0.98274535 -5.2586303 0 -3.7902706 2.9156947
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600 1.0683914 -5.3863229 0 -3.789996 2.3002719
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650 1.0130779 -5.303917 0 -3.7902362 2.8726423
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700 1.0583333 -5.3737358 0 -3.792437 2.5770307
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750 0.98274506 -5.2612464 0 -3.792887 2.9447027
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800 1.0294191 -5.332001 0 -3.7939042 2.5293193
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850 0.99240027 -5.2735754 0 -3.7907899 2.7672711
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900 1.0293488 -5.3306241 0 -3.7926323 2.6054041
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950 0.97137182 -5.2424403 0 -3.7910742 3.129989
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1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598
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Loop time of 0.310363 on 1 procs for 1000 steps with 256 atoms
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Performance: 1391918.252 tau/day, 3222.033 timesteps/s
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100.7% CPU use with 1 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 | 0.22132 | 0.22132 | 0.22132 | 0.0 | 71.31
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Neigh | 0.03458 | 0.03458 | 0.03458 | 0.0 | 11.14
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Comm | 0.0087938 | 0.0087938 | 0.0087938 | 0.0 | 2.83
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Output | 0.014075 | 0.014075 | 0.014075 | 0.0 | 4.54
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Modify | 0.02818 | 0.02818 | 0.02818 | 0.0 | 9.08
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Other | | 0.003411 | | | 1.10
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Nlocal: 256.000 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1327.00 ave 1327 max 1327 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9612.00 ave 9612 max 9612 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9612
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Ave neighs/atom = 37.546875
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:00
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Block a user