forked from lijiext/lammps
make example input / output conform with LAMMPS conventions (no dump files, no log command) and update reference outputs
This commit is contained in:
Axel Kohlmeyer
parent
23925b3a57
commit
7193fffe0d
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@ -1,4 +1,3 @@
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log log_substrate
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units lj
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atom_style ellipsoid
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boundary p p f
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@ -26,6 +25,6 @@ compute qj all property/atom quatj
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compute qk all property/atom quatk
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#------------------------------------#
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thermo 500
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dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
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#dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
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run 40000
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@ -1,4 +1,3 @@
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log log_region
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units lj
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atom_style ellipsoid
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boundary p p p
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@ -25,6 +24,6 @@ compute qj all property/atom quatj
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compute qk all property/atom quatk
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#------------------------------------#
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thermo 500
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dump 1 all custom 1000 dump_region id type x y z c_qw c_qi c_qj c_qk
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#dump 1 all custom 1000 dump_region id type x y z c_qw c_qi c_qj c_qk
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run 50000
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@ -0,0 +1,162 @@
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LAMMPS (23 Jun 2017)
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using 1 OpenMP thread(s) per MPI task
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units lj
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atom_style ellipsoid
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boundary p p f
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read_data Data_wall
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orthogonal box = (0 0 0) to (60 60 60)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1 atoms
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1 ellipsoids
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reading velocities ...
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1 velocities
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#------------------------------------#
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pair_style resquared 1
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pair_coeff 1 1 10.0 1.0 0.5 0.5 4 0.5 0.5 4 1
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#------------------------------------#
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timestep 0.0002
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#------------------------------------#
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compute temp all temp/asphere
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thermo_modify temp temp
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fix EES_substrate all wall/ees zhi EDGE 10 1 10 zlo EDGE 10 1 10
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#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
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thermo_style custom step temp press etotal f_EES_substrate f_EES_substrate[1]
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)
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fix NVE all nve/asphere
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#------------------------------------#
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compute qw all property/atom quatw
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compute qi all property/atom quati
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compute qj all property/atom quatj
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compute qk all property/atom quatk
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#------------------------------------#
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thermo 500
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#dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
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run 40000
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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 = 1.3
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ghost atom cutoff = 1.3
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binsize = 0.65, bins = 93 93 93
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair resquared, 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.95 | 7.95 | 7.95 Mbytes
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Step Temp Press TotEng f_EES_substrate f_EES_substrate[1]
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0 0 0.00054301475 0 0 0
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500 0 0.00054301501 0 -0.002011167 -0.00089853601
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1000 0 0.0005430153 0 -0.0021039425 -0.00095953758
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1500 0 0.00054301561 0 -0.0022030914 -0.0010262478
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2000 0 0.00054301593 0 -0.002309218 -0.0010993652
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2500 0 0.00054301628 0 -0.0024230015 -0.0011796956
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3000 0 0.00054301666 0 -0.0025452078 -0.0012681725
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3500 0 0.00054301707 0 -0.0026767034 -0.0013658817
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4000 0 0.00054301751 0 -0.0028184722 -0.0014740918
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4500 0 0.00054301798 0 -0.0029716352 -0.0015942917
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5000 0 0.00054301849 0 -0.0031374752 -0.0017282378
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5500 0 0.00054301905 0 -0.0033174662 -0.0018780129
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6000 0 0.00054301965 0 -0.0035133093 -0.0020461007
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6500 0 0.00054302031 0 -0.0037269778 -0.0022354811
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7000 0 0.00054302103 0 -0.0039607721 -0.0024497521
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7500 0 0.00054302182 0 -0.0042173892 -0.0026932881
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8000 0 0.0005430227 0 -0.0045000102 -0.0029714471
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8500 0 0.00054302366 0 -0.0048124114 -0.003290844
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9000 0 0.00054302473 0 -0.0051591071 -0.0036597154
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9500 0 0.00054302592 0 -0.0055455349 -0.0040884113
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10000 0 0.00054302726 0 -0.0059782985 -0.0045900652
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10500 0 0.00054302876 0 -0.0064654891 -0.0051815166
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11000 0 0.00054303046 0 -0.0070171161 -0.0058845936
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11500 0 0.0005430324 0 -0.0076456899 -0.0067279075
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12000 0 0.00054303463 0 -0.0083670175 -0.0077493697
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12500 0 0.00054303721 0 -0.0092012967 -0.0089996821
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13000 0 0.00054304021 0 -0.010174616 -0.010546991
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13500 0 0.00054304375 0 -0.011320967 -0.012482357
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14000 0 0.00054304796 0 -0.012684757 -0.01492338
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14500 0 0.00054305301 0 -0.014323176 -0.01800425
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15000 0 0.00054305913 0 -0.016305242 -0.021804766
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15500 0 0.0005430665 0 -0.018693849 -0.026019991
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16000 0 0.00054307501 0 -0.021450982 -0.028460977
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16500 0 0.0005430828 0 -0.023974925 -0.017549988
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17000 0 0.00054307849 0 -0.022577692 0.07296284
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17500 0 0.00054298744 0 0.0069237358 0.72962844
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18000 0 0.00054212125 0 0.28756839 7.5171061
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18500 0 0.00052809177 0 4.8331004 159.56814
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19000 0 0.00019717774 0 112.04947 5692.3379
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19500 0 0.00051978321 0 7.5250598 262.38764
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20000 0 0.00054179603 0 0.39293697 10.289153
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20500 0 0.00054296932 0 0.01279406 0.89377639
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21000 0 0.00054308425 0 -0.02444466 0.081890707
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21500 0 0.0005430907 0 -0.026532401 -0.021386086
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22000 0 0.00054308271 0 -0.023944983 -0.032642459
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22500 0 0.00054307381 0 -0.02106205 -0.029524272
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23000 0 0.00054306612 0 -0.018569361 -0.024753431
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23500 0 0.00054305976 0 -0.01650866 -0.020566675
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24000 0 0.00054305452 0 -0.014811253 -0.017216347
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24500 0 0.00054305017 0 -0.013402896 -0.014581066
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25000 0 0.00054304653 0 -0.012222687 -0.01250069
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25500 0 0.00054304345 0 -0.011223677 -0.0108418
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26000 0 0.00054304081 0 -0.010370111 -0.0095034766
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26500 0 0.00054303854 0 -0.0096346546 -0.0084112161
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27000 0 0.00054303657 0 -0.0089962072 -0.0075100751
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27500 0 0.00054303485 0 -0.0084382935 -0.0067592209
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28000 0 0.00054303334 0 -0.0079478992 -0.0061279726
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28500 0 0.000543032 0 -0.0075146283 -0.0055930001
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29000 0 0.00054303081 0 -0.0071300893 -0.0051363504
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29500 0 0.00054302976 0 -0.0067874426 -0.00474405
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30000 0 0.00054302881 0 -0.0064810641 -0.0044051051
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30500 0 0.00054302796 0 -0.0062062911 -0.0041107799
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31000 0 0.0005430272 0 -0.0059592289 -0.0038540677
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31500 0 0.00054302651 0 -0.0057366023 -0.0036293011
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32000 0 0.00054302589 0 -0.0055356393 -0.0034318592
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32500 0 0.00054302533 0 -0.0053539804 -0.0032579475
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33000 0 0.00054302482 0 -0.0051896066 -0.0031044289
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33500 0 0.00054302436 0 -0.0050407818 -0.0029686945
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34000 0 0.00054302395 0 -0.0049060063 -0.002848562
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34500 0 0.00054302357 0 -0.0047839795 -0.002742197
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35000 0 0.00054302323 0 -0.0046735688 -0.0026480503
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35500 0 0.00054302292 0 -0.0045737849 -0.0025648085
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36000 0 0.00054302264 0 -0.0044837605 -0.0024913535
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36500 0 0.00054302239 0 -0.0044027327 -0.0024267309
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37000 0 0.00054302217 0 -0.0043300292 -0.0023701236
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37500 0 0.00054302197 0 -0.0042650554 -0.0023208304
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38000 0 0.00054302179 0 -0.0042072838 -0.0022782486
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38500 0 0.00054302163 0 -0.0041562461 -0.0022418592
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39000 0 0.0005430215 0 -0.0041115244 -0.0022112152
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39500 0 0.00054302138 0 -0.0040727453 -0.0021859312
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40000 0 0.00054302127 0 -0.0040395743 -0.0021656748
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Loop time of 0.111517 on 1 procs for 40000 steps with 1 atoms
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Performance: 6198147.516 tau/day, 358689.092 timesteps/s
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98.6% 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 | 0.0082421 | 0.0082421 | 0.0082421 | 0.0 | 7.39
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Neigh | 0.021163 | 0.021163 | 0.021163 | 0.0 | 18.98
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Comm | 0.045411 | 0.045411 | 0.045411 | 0.0 | 40.72
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Output | 0.0012326 | 0.0012326 | 0.0012326 | 0.0 | 1.11
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Modify | 0.022813 | 0.022813 | 0.022813 | 0.0 | 20.46
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Other | | 0.01265 | | | 11.35
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Nlocal: 1 ave 1 max 1 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 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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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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Total # of neighbors = 0
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Ave neighs/atom = 0
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Neighbor list builds = 33
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Dangerous builds = 0
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Total wall time: 0:00:00
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@ -0,0 +1,162 @@
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LAMMPS (23 Jun 2017)
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using 1 OpenMP thread(s) per MPI task
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units lj
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atom_style ellipsoid
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boundary p p f
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read_data Data_wall
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orthogonal box = (0 0 0) to (60 60 60)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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1 atoms
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1 ellipsoids
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reading velocities ...
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1 velocities
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#------------------------------------#
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pair_style resquared 1
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pair_coeff 1 1 10.0 1.0 0.5 0.5 4 0.5 0.5 4 1
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#------------------------------------#
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timestep 0.0002
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#------------------------------------#
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compute temp all temp/asphere
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thermo_modify temp temp
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fix EES_substrate all wall/ees zhi EDGE 10 1 10 zlo EDGE 10 1 10
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#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
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thermo_style custom step temp press etotal f_EES_substrate f_EES_substrate[1]
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)
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fix NVE all nve/asphere
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#------------------------------------#
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compute qw all property/atom quatw
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compute qi all property/atom quati
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compute qj all property/atom quatj
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compute qk all property/atom quatk
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#------------------------------------#
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thermo 500
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#dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
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run 40000
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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 = 1.3
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ghost atom cutoff = 1.3
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binsize = 0.65, bins = 93 93 93
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair resquared, 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.128 | 5.41 | 5.753 Mbytes
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Step Temp Press TotEng f_EES_substrate f_EES_substrate[1]
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0 0 0.00054301475 0 0 0
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500 0 0.00054301501 0 -0.002011167 -0.00089853601
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1000 0 0.0005430153 0 -0.0021039425 -0.00095953758
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1500 0 0.00054301561 0 -0.0022030914 -0.0010262478
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2000 0 0.00054301593 0 -0.002309218 -0.0010993652
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2500 0 0.00054301628 0 -0.0024230015 -0.0011796956
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3000 0 0.00054301666 0 -0.0025452078 -0.0012681725
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3500 0 0.00054301707 0 -0.0026767034 -0.0013658817
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4000 0 0.00054301751 0 -0.0028184722 -0.0014740918
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4500 0 0.00054301798 0 -0.0029716352 -0.0015942917
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5000 0 0.00054301849 0 -0.0031374752 -0.0017282378
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5500 0 0.00054301905 0 -0.0033174662 -0.0018780129
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6000 0 0.00054301965 0 -0.0035133093 -0.0020461007
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6500 0 0.00054302031 0 -0.0037269778 -0.0022354811
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7000 0 0.00054302103 0 -0.0039607721 -0.0024497521
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7500 0 0.00054302182 0 -0.0042173892 -0.0026932881
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8000 0 0.0005430227 0 -0.0045000102 -0.0029714471
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8500 0 0.00054302366 0 -0.0048124114 -0.003290844
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9000 0 0.00054302473 0 -0.0051591071 -0.0036597154
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9500 0 0.00054302592 0 -0.0055455349 -0.0040884113
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10000 0 0.00054302726 0 -0.0059782985 -0.0045900652
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10500 0 0.00054302876 0 -0.0064654891 -0.0051815166
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11000 0 0.00054303046 0 -0.0070171161 -0.0058845936
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11500 0 0.0005430324 0 -0.0076456899 -0.0067279075
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12000 0 0.00054303463 0 -0.0083670175 -0.0077493697
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12500 0 0.00054303721 0 -0.0092012967 -0.0089996821
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13000 0 0.00054304021 0 -0.010174616 -0.010546991
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13500 0 0.00054304375 0 -0.011320967 -0.012482357
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14000 0 0.00054304796 0 -0.012684757 -0.01492338
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14500 0 0.00054305301 0 -0.014323176 -0.01800425
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15000 0 0.00054305913 0 -0.016305242 -0.021804766
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15500 0 0.0005430665 0 -0.018693849 -0.026019991
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16000 0 0.00054307501 0 -0.021450982 -0.028460977
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16500 0 0.0005430828 0 -0.023974925 -0.017549988
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17000 0 0.00054307849 0 -0.022577692 0.07296284
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17500 0 0.00054298744 0 0.0069237358 0.72962844
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18000 0 0.00054212125 0 0.28756839 7.5171061
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18500 0 0.00052809177 0 4.8331004 159.56814
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19000 0 0.00019717774 0 112.04947 5692.3379
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19500 0 0.00051978321 0 7.5250598 262.38764
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20000 0 0.00054179603 0 0.39293697 10.289153
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20500 0 0.00054296932 0 0.01279406 0.89377639
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21000 0 0.00054308425 0 -0.02444466 0.081890707
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21500 0 0.0005430907 0 -0.026532401 -0.021386086
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||||
22000 0 0.00054308271 0 -0.023944983 -0.032642459
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||||
22500 0 0.00054307381 0 -0.02106205 -0.029524272
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||||
23000 0 0.00054306612 0 -0.018569361 -0.024753431
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||||
23500 0 0.00054305976 0 -0.01650866 -0.020566675
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||||
24000 0 0.00054305452 0 -0.014811253 -0.017216347
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||||
24500 0 0.00054305017 0 -0.013402896 -0.014581066
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||||
25000 0 0.00054304653 0 -0.012222687 -0.01250069
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25500 0 0.00054304345 0 -0.011223677 -0.0108418
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26000 0 0.00054304081 0 -0.010370111 -0.0095034766
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26500 0 0.00054303854 0 -0.0096346546 -0.0084112161
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27000 0 0.00054303657 0 -0.0089962072 -0.0075100751
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27500 0 0.00054303485 0 -0.0084382935 -0.0067592209
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28000 0 0.00054303334 0 -0.0079478992 -0.0061279726
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28500 0 0.000543032 0 -0.0075146283 -0.0055930001
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29000 0 0.00054303081 0 -0.0071300893 -0.0051363504
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29500 0 0.00054302976 0 -0.0067874426 -0.00474405
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30000 0 0.00054302881 0 -0.0064810641 -0.0044051051
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30500 0 0.00054302796 0 -0.0062062911 -0.0041107799
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31000 0 0.0005430272 0 -0.0059592289 -0.0038540677
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31500 0 0.00054302651 0 -0.0057366023 -0.0036293011
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32000 0 0.00054302589 0 -0.0055356393 -0.0034318592
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32500 0 0.00054302533 0 -0.0053539804 -0.0032579475
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33000 0 0.00054302482 0 -0.0051896066 -0.0031044289
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33500 0 0.00054302436 0 -0.0050407818 -0.0029686945
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34000 0 0.00054302395 0 -0.0049060063 -0.002848562
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34500 0 0.00054302357 0 -0.0047839795 -0.002742197
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35000 0 0.00054302323 0 -0.0046735688 -0.0026480503
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35500 0 0.00054302292 0 -0.0045737849 -0.0025648085
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36000 0 0.00054302264 0 -0.0044837605 -0.0024913535
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36500 0 0.00054302239 0 -0.0044027327 -0.0024267309
|
||||
37000 0 0.00054302217 0 -0.0043300292 -0.0023701236
|
||||
37500 0 0.00054302197 0 -0.0042650554 -0.0023208304
|
||||
38000 0 0.00054302179 0 -0.0042072838 -0.0022782486
|
||||
38500 0 0.00054302163 0 -0.0041562461 -0.0022418592
|
||||
39000 0 0.0005430215 0 -0.0041115244 -0.0022112152
|
||||
39500 0 0.00054302138 0 -0.0040727453 -0.0021859312
|
||||
40000 0 0.00054302127 0 -0.0040395743 -0.0021656748
|
||||
Loop time of 0.216115 on 4 procs for 40000 steps with 1 atoms
|
||||
|
||||
Performance: 3198303.409 tau/day, 185087.003 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0020442 | 0.0047204 | 0.012008 | 6.1 | 2.18
|
||||
Neigh | 0.0069654 | 0.0072649 | 0.0074701 | 0.2 | 3.36
|
||||
Comm | 0.024762 | 0.039833 | 0.056166 | 7.4 | 18.43
|
||||
Output | 0.0020285 | 0.0023268 | 0.0026891 | 0.5 | 1.08
|
||||
Modify | 0.0081856 | 0.013537 | 0.029052 | 7.7 | 6.26
|
||||
Other | | 0.1484 | | | 68.68
|
||||
|
||||
Nlocal: 0.25 ave 1 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0.25 ave 1 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,180 @@
|
|||
LAMMPS (23 Jun 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
boundary p p p
|
||||
read_data Data_region
|
||||
orthogonal box = (0 0 0) to (60 60 60)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
3 ellipsoids
|
||||
reading velocities ...
|
||||
3 velocities
|
||||
#------------------------------------#
|
||||
region the_wall block 20. 40. 20. 40. 20. 40. side out
|
||||
#------------------------------------#
|
||||
pair_style resquared 1
|
||||
pair_coeff 1 1 10.0 1.0 0.5 0.5 4 0.5 0.5 4 1
|
||||
#------------------------------------#
|
||||
timestep 0.0005
|
||||
#------------------------------------#
|
||||
|
||||
fix EES_block all wall/region/ees the_wall 10. 1. 20
|
||||
#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
|
||||
|
||||
thermo_style custom step temp press etotal f_EES_block[1] f_EES_block[3]
|
||||
|
||||
fix NVE all nve/asphere
|
||||
#------------------------------------#
|
||||
compute qw all property/atom quatw
|
||||
compute qi all property/atom quati
|
||||
compute qj all property/atom quatj
|
||||
compute qk all property/atom quatk
|
||||
#------------------------------------#
|
||||
thermo 500
|
||||
#dump 1 all custom 1000 dump_region id type x y z c_qw c_qi c_qj c_qk
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 93 93 93
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair resquared, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.958 | 7.958 | 7.958 Mbytes
|
||||
Step Temp Press TotEng f_EES_block[1] f_EES_block[3]
|
||||
0 161.26842 0.0014932261 161.26842 -0.00042715909 -0.00015747012
|
||||
500 161.26864 0.0014932281 161.26864 -0.00055836679 -0.00017557792
|
||||
1000 161.26891 0.0014932306 161.26891 -0.00075239934 -0.00019646897
|
||||
1500 161.26926 0.0014932339 161.26926 -0.0010543331 -0.0002206925
|
||||
2000 161.26975 0.0014932385 161.26975 -0.0015566164 -0.00024893301
|
||||
2500 161.27047 0.0014932451 161.27047 -0.0024700842 -0.00028205104
|
||||
3000 161.27163 0.0014932558 161.27163 -0.0043191186 -0.00032113859
|
||||
3500 161.27364 0.0014932745 161.27364 -0.0073109231 -0.00036759584
|
||||
4000 161.26391 0.0014931843 161.26391 0.2453813 -0.00042323837
|
||||
4500 77.783029 0.00072021324 77.783029 4908.2333 -0.00049044991
|
||||
5000 160.23852 0.00148369 160.23852 0.13220034 -0.00057240356
|
||||
5500 160.2431 0.0014837324 160.2431 -0.0072005112 -0.00067338844
|
||||
6000 160.24148 0.0014837174 160.24148 -0.0040896209 -0.0007993028
|
||||
6500 160.24071 0.0014837103 160.24071 -0.0023574992 -0.00095841662
|
||||
7000 160.24038 0.0014837072 160.24038 -0.001495267 -0.001162584
|
||||
7500 160.24031 0.0014837066 160.24031 -0.0010172907 -0.0014292316
|
||||
8000 160.24043 0.0014837077 160.24043 -0.00072823316 -0.0017847384
|
||||
8500 160.24073 0.0014837105 160.24073 -0.00054165121 -0.0022704187
|
||||
9000 160.24121 0.0014837149 160.24121 -0.00041506183 -0.0029536182
|
||||
9500 160.24192 0.0014837215 160.24192 -0.00032574317 -0.0039493769
|
||||
10000 160.24293 0.0014837308 160.24293 -0.00026069929 -0.0054649542
|
||||
10500 160.2444 0.0014837444 160.2444 -0.00021208476 -0.0078936604
|
||||
11000 160.2466 0.0014837648 160.2466 -0.00017494913 -0.011981095
|
||||
11500 160.25001 0.0014837964 160.25001 -0.00014605132 -0.018414768
|
||||
12000 160.25411 0.0014838343 160.25411 -0.00012320207 -0.0069059119
|
||||
12500 160.18929 0.0014832342 160.18929 -0.00010488251 1.4672359
|
||||
13000 127.86814 0.0011839642 127.86814 -9.0014128e-05 1420.4476
|
||||
13500 154.09961 0.0014268483 154.09961 -7.7815401e-05 5.4703004
|
||||
14000 154.31359 0.0014288295 154.31359 -6.7709777e-05 0.025351973
|
||||
14500 154.3112 0.0014288074 154.3112 -5.9265083e-05 -0.020243217
|
||||
15000 154.30773 0.0014287753 154.30773 -5.2152714e-05 -0.013791198
|
||||
15500 154.30551 0.0014287547 154.30551 -4.6119584e-05 -0.0090829354
|
||||
16000 154.30409 0.0014287415 154.30409 -4.0968492e-05 -0.0062748728
|
||||
16500 154.30315 0.0014287329 154.30315 -3.6544144e-05 -0.004532774
|
||||
17000 154.30254 0.0014287272 154.30254 -3.2723062e-05 -0.003394041
|
||||
17500 154.30216 0.0014287237 154.30216 -2.9406189e-05 -0.0026153428
|
||||
18000 154.30195 0.0014287218 154.30195 -2.6513408e-05 -0.0020627306
|
||||
18500 154.30188 0.0014287211 154.30188 -2.397943e-05 -0.0016584214
|
||||
19000 154.30194 0.0014287216 154.30194 -2.1750674e-05 -0.0013550174
|
||||
19500 154.3021 0.0014287232 154.3021 -1.9782885e-05 -0.0011224153
|
||||
20000 154.30239 0.0014287258 154.30239 -1.8039282e-05 -0.00094080826
|
||||
20500 154.30279 0.0014287295 154.30279 -1.6489128e-05 -0.00079676335
|
||||
21000 154.30332 0.0014287345 154.30332 -1.5106598e-05 -0.00068092925
|
||||
21500 154.30401 0.0014287409 154.30401 -1.3869884e-05 -0.000586646
|
||||
22000 154.30489 0.001428749 154.30489 -1.2760487e-05 -0.00050907464
|
||||
22500 154.30601 0.0014287593 154.30601 -1.1762643e-05 -0.00044463657
|
||||
23000 154.30743 0.0014287725 154.30743 -1.0862863e-05 -0.00039064328
|
||||
23500 154.30924 0.0014287893 154.30924 -1.004956e-05 -0.00034504622
|
||||
24000 154.31159 0.001428811 154.31159 -9.3127419e-06 -0.0003062645
|
||||
24500 154.31464 0.0014288393 154.31464 8.7817413e-06 -0.00027306395
|
||||
25000 154.31848 0.0014288748 154.31848 9.4348998e-06 -0.00024447093
|
||||
25500 154.32222 0.0014289094 154.32222 1.0150613e-05 -0.00021970994
|
||||
26000 154.31667 0.0014288581 154.31667 1.0936298e-05 -0.0001981578
|
||||
26500 154.19679 0.0014277481 154.19679 1.1800434e-05 -0.00017930967
|
||||
27000 151.70582 0.0014046835 151.70582 1.2752738e-05 -0.00016275349
|
||||
27500 144.06864 0.0013339689 144.06864 1.3804382e-05 -0.00014815061
|
||||
28000 153.30039 0.0014194481 153.30039 1.4968247e-05 -0.00013522085
|
||||
28500 153.70626 0.0014232061 153.70626 1.6259237e-05 -0.00012373107
|
||||
29000 153.73143 0.0014234392 153.73143 1.7694652e-05 -0.00011348611
|
||||
29500 153.72942 0.0014234205 153.72942 1.9294649e-05 -0.0001043218
|
||||
30000 153.72536 0.001423383 153.72536 2.1082798e-05 -9.6099303e-05
|
||||
30500 153.72189 0.0014233508 153.72189 2.3086777e-05 -8.8700684e-05
|
||||
31000 153.71915 0.0014233255 153.71915 2.533922e-05 -8.2025314e-05
|
||||
31500 153.71701 0.0014233056 153.71701 2.7878775e-05 -7.5986974e-05
|
||||
32000 153.7153 0.0014232898 153.7153 3.0751438e-05 -7.05115e-05
|
||||
32500 153.71392 0.0014232771 153.71392 3.4012214e-05 -6.5534861e-05
|
||||
33000 153.7128 0.0014232667 153.7128 3.7727241e-05 -6.1001578e-05
|
||||
33500 153.71187 0.001423258 153.71187 4.1976497e-05 -5.686342e-05
|
||||
34000 153.71109 0.0014232508 153.71109 4.6857282e-05 -5.3078322e-05
|
||||
34500 153.71043 0.0014232447 153.71043 5.2488748e-05 -4.9609488e-05
|
||||
35000 153.70987 0.0014232395 153.70987 5.9017833e-05 -4.6424634e-05
|
||||
35500 153.70939 0.0014232351 153.70939 6.6627108e-05 -4.3495356e-05
|
||||
36000 153.70898 0.0014232313 153.70898 7.5545279e-05 -4.0796599e-05
|
||||
36500 153.70863 0.001423228 153.70863 8.6061387e-05 -3.8306204e-05
|
||||
37000 153.70832 0.0014232252 153.70832 9.8544264e-05 -3.6004526e-05
|
||||
37500 153.70806 0.0014232227 153.70806 0.00011346953 -3.3874109e-05
|
||||
38000 153.70783 0.0014232207 153.70783 0.00013145761 -3.1899404e-05
|
||||
38500 153.70764 0.0014232189 153.70764 0.00015332826 -3.0066532e-05
|
||||
39000 153.70748 0.0014232174 153.70748 0.00018017988 -2.836308e-05
|
||||
39500 153.70736 0.0014232163 153.70736 0.00021350768 -2.6777922e-05
|
||||
40000 153.70726 0.0014232154 153.70726 0.00025538329 -2.5301066e-05
|
||||
40500 153.70719 0.0014232147 153.70719 0.00030873482 -2.3923522e-05
|
||||
41000 153.70716 0.0014232145 153.70716 0.00037779644 -2.2637186e-05
|
||||
41500 153.70717 0.0014232145 153.70717 0.00046885357 -2.1434741e-05
|
||||
42000 153.70722 0.001423215 153.70722 0.00059152584 -2.0309568e-05
|
||||
42500 153.70733 0.001423216 153.70733 0.00076107465 -1.9255668e-05
|
||||
43000 153.70751 0.0014232177 153.70751 0.0010027741 -1.82676e-05
|
||||
43500 153.7078 0.0014232203 153.7078 0.0013607156 -1.7340414e-05
|
||||
44000 153.70823 0.0014232244 153.70823 0.0019168919 -1.6469607e-05
|
||||
44500 153.70891 0.0014232306 153.70891 0.0028362183 -1.5651071e-05
|
||||
45000 153.70999 0.0014232407 153.70999 0.0044814624 -1.4881056e-05
|
||||
45500 153.71183 0.0014232577 153.71183 0.0076783372 -1.4156133e-05
|
||||
46000 153.71504 0.0014232874 153.71504 0.012021529 -1.347316e-05
|
||||
46500 153.70337 0.0014231794 153.70337 -0.27386631 -1.2829258e-05
|
||||
47000 109.96863 0.0010182281 109.96863 -1552.3264 -1.2221783e-05
|
||||
47500 56.442204 0.000522613 56.442204 -0.62595366 -1.1648303e-05
|
||||
48000 56.439532 0.00052258826 56.439532 0.015282177 -1.1106581e-05
|
||||
48500 56.439907 0.00052259173 56.439907 0.01178542 -1.0594552e-05
|
||||
49000 56.44015 0.00052259399 56.44015 0.0080268131 -1.0110314e-05
|
||||
49500 56.440316 0.00052259552 56.440316 0.0061338692 -9.6521057e-06
|
||||
50000 56.440444 0.0005225967 56.440444 0.005195231 -9.2183009e-06
|
||||
Loop time of 0.344104 on 1 procs for 50000 steps with 3 atoms
|
||||
|
||||
Performance: 6277171.077 tau/day, 145304.886 timesteps/s
|
||||
98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.023412 | 0.023412 | 0.023412 | 0.0 | 6.80
|
||||
Neigh | 0.13182 | 0.13182 | 0.13182 | 0.0 | 38.31
|
||||
Comm | 0.084006 | 0.084006 | 0.084006 | 0.0 | 24.41
|
||||
Output | 0.0023429 | 0.0023429 | 0.0023429 | 0.0 | 0.68
|
||||
Modify | 0.083383 | 0.083383 | 0.083383 | 0.0 | 24.23
|
||||
Other | | 0.01914 | | | 5.56
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1 ave 1 max 1 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 210
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,180 @@
|
|||
LAMMPS (23 Jun 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
boundary p p p
|
||||
read_data Data_region
|
||||
orthogonal box = (0 0 0) to (60 60 60)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
3 ellipsoids
|
||||
reading velocities ...
|
||||
3 velocities
|
||||
#------------------------------------#
|
||||
region the_wall block 20. 40. 20. 40. 20. 40. side out
|
||||
#------------------------------------#
|
||||
pair_style resquared 1
|
||||
pair_coeff 1 1 10.0 1.0 0.5 0.5 4 0.5 0.5 4 1
|
||||
#------------------------------------#
|
||||
timestep 0.0005
|
||||
#------------------------------------#
|
||||
|
||||
fix EES_block all wall/region/ees the_wall 10. 1. 20
|
||||
#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
|
||||
|
||||
thermo_style custom step temp press etotal f_EES_block[1] f_EES_block[3]
|
||||
|
||||
fix NVE all nve/asphere
|
||||
#------------------------------------#
|
||||
compute qw all property/atom quatw
|
||||
compute qi all property/atom quati
|
||||
compute qj all property/atom quatj
|
||||
compute qk all property/atom quatk
|
||||
#------------------------------------#
|
||||
thermo 500
|
||||
#dump 1 all custom 1000 dump_region id type x y z c_qw c_qi c_qj c_qk
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 93 93 93
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair resquared, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.722 | 5.754 Mbytes
|
||||
Step Temp Press TotEng f_EES_block[1] f_EES_block[3]
|
||||
0 161.26842 0.0014932261 161.26842 -0.00042715909 -0.00015747012
|
||||
500 161.26864 0.0014932281 161.26864 -0.00055836679 -0.00017557792
|
||||
1000 161.26891 0.0014932306 161.26891 -0.00075239934 -0.00019646897
|
||||
1500 161.26926 0.0014932339 161.26926 -0.0010543331 -0.0002206925
|
||||
2000 161.26975 0.0014932385 161.26975 -0.0015566164 -0.00024893301
|
||||
2500 161.27047 0.0014932451 161.27047 -0.0024700842 -0.00028205104
|
||||
3000 161.27163 0.0014932558 161.27163 -0.0043191186 -0.00032113859
|
||||
3500 161.27364 0.0014932745 161.27364 -0.0073109231 -0.00036759584
|
||||
4000 161.26391 0.0014931843 161.26391 0.2453813 -0.00042323837
|
||||
4500 77.783029 0.00072021324 77.783029 4908.2333 -0.00049044991
|
||||
5000 160.23852 0.00148369 160.23852 0.13220034 -0.00057240356
|
||||
5500 160.2431 0.0014837324 160.2431 -0.0072005112 -0.00067338844
|
||||
6000 160.24148 0.0014837174 160.24148 -0.0040896209 -0.0007993028
|
||||
6500 160.24071 0.0014837103 160.24071 -0.0023574992 -0.00095841662
|
||||
7000 160.24038 0.0014837072 160.24038 -0.001495267 -0.001162584
|
||||
7500 160.24031 0.0014837066 160.24031 -0.0010172907 -0.0014292316
|
||||
8000 160.24043 0.0014837077 160.24043 -0.00072823316 -0.0017847384
|
||||
8500 160.24073 0.0014837105 160.24073 -0.00054165121 -0.0022704187
|
||||
9000 160.24121 0.0014837149 160.24121 -0.00041506183 -0.0029536182
|
||||
9500 160.24192 0.0014837215 160.24192 -0.00032574317 -0.0039493769
|
||||
10000 160.24293 0.0014837308 160.24293 -0.00026069929 -0.0054649542
|
||||
10500 160.2444 0.0014837444 160.2444 -0.00021208476 -0.0078936604
|
||||
11000 160.2466 0.0014837648 160.2466 -0.00017494913 -0.011981095
|
||||
11500 160.25001 0.0014837964 160.25001 -0.00014605132 -0.018414768
|
||||
12000 160.25411 0.0014838343 160.25411 -0.00012320207 -0.0069059119
|
||||
12500 160.18929 0.0014832342 160.18929 -0.00010488251 1.4672359
|
||||
13000 127.86814 0.0011839642 127.86814 -9.0014128e-05 1420.4476
|
||||
13500 154.09961 0.0014268483 154.09961 -7.7815401e-05 5.4703004
|
||||
14000 154.31359 0.0014288295 154.31359 -6.7709777e-05 0.025351973
|
||||
14500 154.3112 0.0014288074 154.3112 -5.9265083e-05 -0.020243217
|
||||
15000 154.30773 0.0014287753 154.30773 -5.2152714e-05 -0.013791198
|
||||
15500 154.30551 0.0014287547 154.30551 -4.6119584e-05 -0.0090829354
|
||||
16000 154.30409 0.0014287415 154.30409 -4.0968492e-05 -0.0062748728
|
||||
16500 154.30315 0.0014287329 154.30315 -3.6544144e-05 -0.004532774
|
||||
17000 154.30254 0.0014287272 154.30254 -3.2723062e-05 -0.003394041
|
||||
17500 154.30216 0.0014287237 154.30216 -2.9406189e-05 -0.0026153428
|
||||
18000 154.30195 0.0014287218 154.30195 -2.6513408e-05 -0.0020627306
|
||||
18500 154.30188 0.0014287211 154.30188 -2.397943e-05 -0.0016584214
|
||||
19000 154.30194 0.0014287216 154.30194 -2.1750674e-05 -0.0013550174
|
||||
19500 154.3021 0.0014287232 154.3021 -1.9782885e-05 -0.0011224153
|
||||
20000 154.30239 0.0014287258 154.30239 -1.8039282e-05 -0.00094080826
|
||||
20500 154.30279 0.0014287295 154.30279 -1.6489128e-05 -0.00079676335
|
||||
21000 154.30332 0.0014287345 154.30332 -1.5106598e-05 -0.00068092925
|
||||
21500 154.30401 0.0014287409 154.30401 -1.3869884e-05 -0.000586646
|
||||
22000 154.30489 0.001428749 154.30489 -1.2760487e-05 -0.00050907464
|
||||
22500 154.30601 0.0014287593 154.30601 -1.1762643e-05 -0.00044463657
|
||||
23000 154.30743 0.0014287725 154.30743 -1.0862863e-05 -0.00039064328
|
||||
23500 154.30924 0.0014287893 154.30924 -1.004956e-05 -0.00034504622
|
||||
24000 154.31159 0.001428811 154.31159 -9.3127419e-06 -0.0003062645
|
||||
24500 154.31464 0.0014288393 154.31464 8.7817413e-06 -0.00027306395
|
||||
25000 154.31848 0.0014288748 154.31848 9.4348998e-06 -0.00024447093
|
||||
25500 154.32222 0.0014289094 154.32222 1.0150613e-05 -0.00021970994
|
||||
26000 154.31667 0.0014288581 154.31667 1.0936298e-05 -0.0001981578
|
||||
26500 154.19679 0.0014277481 154.19679 1.1800434e-05 -0.00017930967
|
||||
27000 151.70582 0.0014046835 151.70582 1.2752738e-05 -0.00016275349
|
||||
27500 144.06864 0.0013339689 144.06864 1.3804382e-05 -0.00014815061
|
||||
28000 153.30039 0.0014194481 153.30039 1.4968247e-05 -0.00013522085
|
||||
28500 153.70626 0.0014232061 153.70626 1.6259237e-05 -0.00012373107
|
||||
29000 153.73143 0.0014234392 153.73143 1.7694652e-05 -0.00011348611
|
||||
29500 153.72942 0.0014234205 153.72942 1.9294649e-05 -0.0001043218
|
||||
30000 153.72536 0.001423383 153.72536 2.1082798e-05 -9.6099303e-05
|
||||
30500 153.72189 0.0014233508 153.72189 2.3086777e-05 -8.8700684e-05
|
||||
31000 153.71915 0.0014233255 153.71915 2.533922e-05 -8.2025314e-05
|
||||
31500 153.71701 0.0014233056 153.71701 2.7878775e-05 -7.5986974e-05
|
||||
32000 153.7153 0.0014232898 153.7153 3.0751438e-05 -7.05115e-05
|
||||
32500 153.71392 0.0014232771 153.71392 3.4012214e-05 -6.5534861e-05
|
||||
33000 153.7128 0.0014232667 153.7128 3.7727241e-05 -6.1001578e-05
|
||||
33500 153.71187 0.001423258 153.71187 4.1976497e-05 -5.686342e-05
|
||||
34000 153.71109 0.0014232508 153.71109 4.6857282e-05 -5.3078322e-05
|
||||
34500 153.71043 0.0014232447 153.71043 5.2488748e-05 -4.9609488e-05
|
||||
35000 153.70987 0.0014232395 153.70987 5.9017833e-05 -4.6424634e-05
|
||||
35500 153.70939 0.0014232351 153.70939 6.6627108e-05 -4.3495356e-05
|
||||
36000 153.70898 0.0014232313 153.70898 7.5545279e-05 -4.0796599e-05
|
||||
36500 153.70863 0.001423228 153.70863 8.6061387e-05 -3.8306204e-05
|
||||
37000 153.70832 0.0014232252 153.70832 9.8544264e-05 -3.6004526e-05
|
||||
37500 153.70806 0.0014232227 153.70806 0.00011346953 -3.3874109e-05
|
||||
38000 153.70783 0.0014232207 153.70783 0.00013145761 -3.1899404e-05
|
||||
38500 153.70764 0.0014232189 153.70764 0.00015332826 -3.0066532e-05
|
||||
39000 153.70748 0.0014232174 153.70748 0.00018017988 -2.836308e-05
|
||||
39500 153.70736 0.0014232163 153.70736 0.00021350768 -2.6777922e-05
|
||||
40000 153.70726 0.0014232154 153.70726 0.00025538329 -2.5301066e-05
|
||||
40500 153.70719 0.0014232147 153.70719 0.00030873482 -2.3923522e-05
|
||||
41000 153.70716 0.0014232145 153.70716 0.00037779644 -2.2637186e-05
|
||||
41500 153.70717 0.0014232145 153.70717 0.00046885357 -2.1434741e-05
|
||||
42000 153.70722 0.001423215 153.70722 0.00059152584 -2.0309568e-05
|
||||
42500 153.70733 0.001423216 153.70733 0.00076107465 -1.9255668e-05
|
||||
43000 153.70751 0.0014232177 153.70751 0.0010027741 -1.82676e-05
|
||||
43500 153.7078 0.0014232203 153.7078 0.0013607156 -1.7340414e-05
|
||||
44000 153.70823 0.0014232244 153.70823 0.0019168919 -1.6469607e-05
|
||||
44500 153.70891 0.0014232306 153.70891 0.0028362183 -1.5651071e-05
|
||||
45000 153.70999 0.0014232407 153.70999 0.0044814624 -1.4881056e-05
|
||||
45500 153.71183 0.0014232577 153.71183 0.0076783372 -1.4156133e-05
|
||||
46000 153.71504 0.0014232874 153.71504 0.012021529 -1.347316e-05
|
||||
46500 153.70337 0.0014231794 153.70337 -0.27386631 -1.2829258e-05
|
||||
47000 109.96863 0.0010182281 109.96863 -1552.3264 -1.2221783e-05
|
||||
47500 56.442204 0.000522613 56.442204 -0.62595366 -1.1648303e-05
|
||||
48000 56.439532 0.00052258826 56.439532 0.015282177 -1.1106581e-05
|
||||
48500 56.439907 0.00052259173 56.439907 0.01178542 -1.0594552e-05
|
||||
49000 56.44015 0.00052259399 56.44015 0.0080268131 -1.0110314e-05
|
||||
49500 56.440316 0.00052259552 56.440316 0.0061338692 -9.6521057e-06
|
||||
50000 56.440444 0.0005225967 56.440444 0.005195231 -9.2183009e-06
|
||||
Loop time of 0.483531 on 4 procs for 50000 steps with 3 atoms
|
||||
|
||||
Performance: 4467138.628 tau/day, 103405.987 timesteps/s
|
||||
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0032809 | 0.010859 | 0.013737 | 4.2 | 2.25
|
||||
Neigh | 0.037744 | 0.039156 | 0.042488 | 1.0 | 8.10
|
||||
Comm | 0.19775 | 0.2088 | 0.21768 | 1.8 | 43.18
|
||||
Output | 0.0028036 | 0.0030343 | 0.0035536 | 0.6 | 0.63
|
||||
Modify | 0.011325 | 0.032141 | 0.039636 | 6.7 | 6.65
|
||||
Other | | 0.1895 | | | 39.20
|
||||
|
||||
Nlocal: 0.75 ave 1 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 1.75 ave 3 max 1 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 210
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
Loading…
Reference in New Issue