From fd3eade6d27920a2f0080e213f0da6dcfb316794 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 May 2019 20:42:36 -0400 Subject: [PATCH] update reference date and examples for changes in REBO --- doc/src/pair_airebo.txt | 2 +- .../USER/misc/kolmogorov_crespi_z/CH.airebo | 1 - .../USER/misc/kolmogorov_crespi_z/CH.rebo | 1 + .../kolmogorov_crespi_z/in.bilayer-graphene | 2 +- .../log.16Mar18.bilayer-graphene.g++.1 | 208 ----------------- .../log.16Mar18.bilayer-graphene.g++.4 | 208 ----------------- .../log.30Apr19.bilayer-graphene.g++.1 | 210 ++++++++++++++++++ .../log.30Apr19.bilayer-graphene.g++.4 | 210 ++++++++++++++++++ examples/airebo/CH.rebo | 1 + examples/airebo/in.airebo-0-0 | 2 +- examples/airebo/in.rebo2 | 4 +- ...0.g++.1 => log.30Apr2019.airebo-0-0.g++.1} | 30 +-- ...0.g++.4 => log.30Apr2019.airebo-0-0.g++.4} | 30 +-- ...o-m.g++.1 => log.30Apr2019.airebo-m.g++.1} | 26 ++- ...o-m.g++.4 => log.30Apr2019.airebo-m.g++.4} | 26 ++- ...irebo.g++.1 => log.30Apr2019.airebo.g++.1} | 26 ++- ...irebo.g++.4 => log.30Apr2019.airebo.g++.4} | 26 ++- ....rebo2.g++.1 => log.30Apr2019.rebo2.g++.1} | 32 +-- ....rebo2.g++.4 => log.30Apr2019.rebo2.g++.4} | 32 +-- 19 files changed, 549 insertions(+), 528 deletions(-) delete mode 120000 examples/USER/misc/kolmogorov_crespi_z/CH.airebo create mode 120000 examples/USER/misc/kolmogorov_crespi_z/CH.rebo delete mode 100644 examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1 delete mode 100644 examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4 create mode 100644 examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 create mode 100644 examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 create mode 120000 examples/airebo/CH.rebo rename examples/airebo/{log.12Dec18.airebo-0-0.g++.1 => log.30Apr2019.airebo-0-0.g++.1} (74%) rename examples/airebo/{log.12Dec18.airebo-0-0.g++.4 => log.30Apr2019.airebo-0-0.g++.4} (74%) rename examples/airebo/{log.12Dec18.airebo-m.g++.1 => log.30Apr2019.airebo-m.g++.1} (78%) rename examples/airebo/{log.12Dec18.airebo-m.g++.4 => log.30Apr2019.airebo-m.g++.4} (78%) rename examples/airebo/{log.12Dec18.airebo.g++.1 => log.30Apr2019.airebo.g++.1} (78%) rename examples/airebo/{log.12Dec18.airebo.g++.4 => log.30Apr2019.airebo.g++.4} (78%) rename examples/airebo/{log.12Dec18.rebo2.g++.1 => log.30Apr2019.rebo2.g++.1} (73%) rename examples/airebo/{log.12Dec18.rebo2.g++.4 => log.30Apr2019.rebo2.g++.4} (73%) diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index e9d47a721c..4956ba7575 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -116,7 +116,7 @@ various dihedral angle preferences in hydrocarbon configurations. Only a single pair_coeff command is used with the {airebo}, {airebo} or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential file with parameters for C and H. Note that as of LAMMPS version -15 November 2018 the {rebo} style in LAMMPS uses its own potential +15 May 2019 the {rebo} style in LAMMPS uses its own potential file (CH.rebo). These are mapped to LAMMPS atom types by specifying N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: diff --git a/examples/USER/misc/kolmogorov_crespi_z/CH.airebo b/examples/USER/misc/kolmogorov_crespi_z/CH.airebo deleted file mode 120000 index e43e44c133..0000000000 --- a/examples/USER/misc/kolmogorov_crespi_z/CH.airebo +++ /dev/null @@ -1 +0,0 @@ -../../../../potentials/CH.airebo \ No newline at end of file diff --git a/examples/USER/misc/kolmogorov_crespi_z/CH.rebo b/examples/USER/misc/kolmogorov_crespi_z/CH.rebo new file mode 120000 index 0000000000..c5a6a40100 --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_z/CH.rebo @@ -0,0 +1 @@ +../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene index 3d63fc09ed..b019b3e5bb 100644 --- a/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene +++ b/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene @@ -22,7 +22,7 @@ group adsorbant type 2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 #################################################################### -pair_coeff * * rebo CH.airebo C C # chemical +pair_coeff * * rebo CH.rebo C C # chemical pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range #################################################################### diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1 b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1 deleted file mode 100644 index 3ba8bfd5df..0000000000 --- a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1 +++ /dev/null @@ -1,208 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style atomic -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data data.bilayer-graphene # read lammps data file - orthogonal box = (0 0 -20) to (17.04 19.6761 40) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 256 atoms -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes -# Separate atom groups -group membrane type 1 -128 atoms in group membrane -group adsorbant type 2 -128 atoms in group adsorbant - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 -#################################################################### -pair_coeff * * rebo CH.airebo C C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range -#################################################################### - -#### Simulation settings #### -timestep 0.0001 -velocity all create 300.0 12345 -fix thermostat all nve -compute COM1 membrane com -compute COM2 adsorbant com -############################ - -# Output -#dump 1 all xyz 100 trajec.xyz -#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" -thermo 10 -thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu -thermo_modify line one format float %14.8f - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 3 3 8 - 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair rebo, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (2) pair kolmogorov/crespi/z, perpetual, skip from (3) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) neighbor class addition, 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) = 4.998 | 4.998 | 4.998 Mbytes -Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] - 0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000 - 10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126 - 20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357 - 30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673 - 40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055 - 50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486 - 60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952 - 70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441 - 80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946 - 90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458 - 100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973 - 110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489 - 120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004 - 130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519 - 140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038 - 150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562 - 160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099 - 170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654 - 180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235 - 190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851 - 200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512 - 210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230 - 220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016 - 230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883 - 240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845 - 250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913 - 260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097 - 270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408 - 280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849 - 290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424 - 300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129 - 310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957 - 320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898 - 330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935 - 340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046 - 350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207 - 360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390 - 370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561 - 380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688 - 390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734 - 400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664 - 410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442 - 420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033 - 430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405 - 440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527 - 450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373 - 460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918 - 470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143 - 480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030 - 490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565 - 500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740 - 510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547 - 520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981 - 530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040 - 540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724 - 550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032 - 560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963 - 570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517 - 580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691 - 590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478 - 600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871 - 610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856 - 620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416 - 630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531 - 640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176 - 650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323 - 660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937 - 670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986 - 680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430 - 690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229 - 700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343 - 710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729 - 720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344 - 730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148 - 740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098 - 750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156 - 760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282 - 770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441 - 780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599 - 790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726 - 800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792 - 810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773 - 820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647 - 830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393 - 840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995 - 850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439 - 860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713 - 870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805 - 880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706 - 890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408 - 900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904 - 910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186 - 920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247 - 930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078 - 940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670 - 950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015 - 960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101 - 970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915 - 980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444 - 990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672 - 1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581 -Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms - -Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.8786 | 3.8786 | 3.8786 | 0.0 | 99.41 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.010816 | 0.010816 | 0.010816 | 0.0 | 0.28 -Output | 0.002461 | 0.002461 | 0.002461 | 0.0 | 0.06 -Modify | 0.0051703 | 0.0051703 | 0.0051703 | 0.0 | 0.13 -Other | | 0.004447 | | | 0.11 - -Nlocal: 256 ave 256 max 256 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1721 ave 1721 max 1721 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37312 ave 37312 max 37312 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 94592 ave 94592 max 94592 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 94592 -Ave neighs/atom = 369.5 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4 b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4 deleted file mode 100644 index b2dd551654..0000000000 --- a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4 +++ /dev/null @@ -1,208 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style atomic -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data data.bilayer-graphene # read lammps data file - orthogonal box = (0 0 -20) to (17.04 19.6761 40) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 256 atoms -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes -# Separate atom groups -group membrane type 1 -128 atoms in group membrane -group adsorbant type 2 -128 atoms in group adsorbant - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 -#################################################################### -pair_coeff * * rebo CH.airebo C C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range -#################################################################### - -#### Simulation settings #### -timestep 0.0001 -velocity all create 300.0 12345 -fix thermostat all nve -compute COM1 membrane com -compute COM2 adsorbant com -############################ - -# Output -#dump 1 all xyz 100 trajec.xyz -#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" -thermo 10 -thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu -thermo_modify line one format float %14.8f - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 3 3 8 - 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair rebo, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (2) pair kolmogorov/crespi/z, perpetual, skip from (3) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) neighbor class addition, 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) = 4.572 | 4.572 | 4.572 Mbytes -Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] - 0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000 - 10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126 - 20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357 - 30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673 - 40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055 - 50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486 - 60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952 - 70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441 - 80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946 - 90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458 - 100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973 - 110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489 - 120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004 - 130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519 - 140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038 - 150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562 - 160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099 - 170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654 - 180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235 - 190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851 - 200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512 - 210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230 - 220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016 - 230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883 - 240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845 - 250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913 - 260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097 - 270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408 - 280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849 - 290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424 - 300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129 - 310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957 - 320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898 - 330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935 - 340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046 - 350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207 - 360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390 - 370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561 - 380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688 - 390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734 - 400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664 - 410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442 - 420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033 - 430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405 - 440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527 - 450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373 - 460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918 - 470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143 - 480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030 - 490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565 - 500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740 - 510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547 - 520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981 - 530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040 - 540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724 - 550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032 - 560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963 - 570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517 - 580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691 - 590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478 - 600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871 - 610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856 - 620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416 - 630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531 - 640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176 - 650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323 - 660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937 - 670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986 - 680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430 - 690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229 - 700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343 - 710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729 - 720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344 - 730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148 - 740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098 - 750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156 - 760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282 - 770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441 - 780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599 - 790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726 - 800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792 - 810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773 - 820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647 - 830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393 - 840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995 - 850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439 - 860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713 - 870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805 - 880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706 - 890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408 - 900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904 - 910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186 - 920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247 - 930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078 - 940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670 - 950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015 - 960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101 - 970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915 - 980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444 - 990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672 - 1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581 -Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms - -Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s -98.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1157 | 1.172 | 1.2369 | 4.0 | 88.66 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.071678 | 0.13667 | 0.19304 | 11.8 | 10.34 -Output | 0.0029244 | 0.0031272 | 0.0035112 | 0.4 | 0.24 -Modify | 0.0016961 | 0.0017477 | 0.0017846 | 0.1 | 0.13 -Other | | 0.008334 | | | 0.63 - -Nlocal: 64 ave 64 max 64 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 1265 ave 1265 max 1265 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 9328 ave 9328 max 9328 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 23648 ave 23648 max 23648 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 94592 -Ave neighs/atom = 369.5 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 new file mode 100644 index 0000000000..5c8616749e --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 @@ -0,0 +1,210 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.bilayer-graphene # read lammps data file + orthogonal box = (0 0 -20) to (17.04 19.6761 40) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 256 atoms + read_data CPU = 0.000291348 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +128 atoms in group membrane +group adsorbant type 2 +128 atoms in group adsorbant + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +velocity all create 300.0 12345 +fix thermostat all nve +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 10 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 3 3 8 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair kolmogorov/crespi/z, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, 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) = 4.998 | 4.998 | 4.998 Mbytes +Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] + 0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000 + 10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126 + 20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357 + 30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673 + 40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055 + 50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486 + 60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952 + 70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441 + 80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946 + 90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458 + 100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973 + 110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489 + 120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004 + 130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519 + 140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038 + 150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562 + 160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099 + 170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654 + 180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235 + 190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851 + 200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512 + 210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230 + 220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016 + 230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883 + 240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845 + 250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913 + 260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097 + 270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408 + 280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 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3.31621664 + 410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442 + 420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033 + 430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405 + 440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527 + 450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373 + 460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918 + 470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143 + 480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030 + 490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565 + 500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740 + 510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547 + 520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 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3.36125581 +Loop time of 2.60456 on 1 procs for 1000 steps with 256 atoms + +Performance: 3.317 ns/day, 7.235 hours/ns, 383.942 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5864 | 2.5864 | 2.5864 | 0.0 | 99.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0079134 | 0.0079134 | 0.0079134 | 0.0 | 0.30 +Output | 0.0027175 | 0.0027175 | 0.0027175 | 0.0 | 0.10 +Modify | 0.00419 | 0.00419 | 0.00419 | 0.0 | 0.16 +Other | | 0.00331 | | | 0.13 + +Nlocal: 256 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1721 ave 1721 max 1721 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37312 ave 37312 max 37312 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 94592 ave 94592 max 94592 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 94592 +Ave neighs/atom = 369.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 new file mode 100644 index 0000000000..13d402b512 --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 @@ -0,0 +1,210 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.bilayer-graphene # read lammps data file + orthogonal box = (0 0 -20) to (17.04 19.6761 40) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 256 atoms + read_data CPU = 0.0488505 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +128 atoms in group membrane +group adsorbant type 2 +128 atoms in group adsorbant + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +velocity all create 300.0 12345 +fix thermostat all nve +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 10 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 3 3 8 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair kolmogorov/crespi/z, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, 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) = 4.572 | 4.572 | 4.572 Mbytes +Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] + 0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000 + 10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126 + 20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357 + 30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673 + 40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 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3.34240282 + 770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441 + 780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599 + 790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726 + 800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792 + 810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773 + 820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647 + 830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393 + 840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995 + 850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439 + 860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713 + 870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805 + 880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706 + 890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408 + 900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904 + 910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186 + 920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247 + 930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078 + 940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670 + 950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015 + 960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101 + 970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915 + 980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444 + 990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672 + 1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581 +Loop time of 1.55992 on 4 procs for 1000 steps with 256 atoms + +Performance: 5.539 ns/day, 4.333 hours/ns, 641.059 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3161 | 1.3724 | 1.4128 | 3.0 | 87.98 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11734 | 0.16017 | 0.21617 | 8.9 | 10.27 +Output | 0.0032182 | 0.0051764 | 0.010916 | 4.6 | 0.33 +Modify | 0.0020187 | 0.0022321 | 0.0026002 | 0.5 | 0.14 +Other | | 0.0199 | | | 1.28 + +Nlocal: 64 ave 64 max 64 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1265 ave 1265 max 1265 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 9328 ave 9328 max 9328 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 23648 ave 23648 max 23648 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 94592 +Ave neighs/atom = 369.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/airebo/CH.rebo b/examples/airebo/CH.rebo new file mode 120000 index 0000000000..9272e57972 --- /dev/null +++ b/examples/airebo/CH.rebo @@ -0,0 +1 @@ +../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/airebo/in.airebo-0-0 b/examples/airebo/in.airebo-0-0 index edcb1561fb..077da68912 100644 --- a/examples/airebo/in.airebo-0-0 +++ b/examples/airebo/in.airebo-0-0 @@ -11,7 +11,7 @@ neighbor 0.5 bin neigh_modify delay 5 every 1 pair_style airebo 3.0 0 0 -pair_coeff * * ../../potentials/CH.airebo C H +pair_coeff * * CH.airebo C H velocity all create 300.0 761341 diff --git a/examples/airebo/in.rebo2 b/examples/airebo/in.rebo2 index 6834528ffb..e06cf462ca 100644 --- a/examples/airebo/in.rebo2 +++ b/examples/airebo/in.rebo2 @@ -1,4 +1,4 @@ -# AIREBO polyethelene benchmark +# REBO polyethelene benchmark units metal atom_style atomic @@ -11,7 +11,7 @@ neighbor 0.5 bin neigh_modify delay 5 every 1 pair_style rebo -pair_coeff * * ../../potentials/CH.rebo C H +pair_coeff * * CH.rebo C H velocity all create 300.0 761341 diff --git a/examples/airebo/log.12Dec18.airebo-0-0.g++.1 b/examples/airebo/log.30Apr2019.airebo-0-0.g++.1 similarity index 74% rename from examples/airebo/log.12Dec18.airebo-0-0.g++.1 rename to examples/airebo/log.30Apr2019.airebo-0-0.g++.1 index 7efacc2dd7..47f5f04a83 100644 --- a/examples/airebo/log.12Dec18.airebo-0-0.g++.1 +++ b/examples/airebo/log.30Apr2019.airebo-0-0.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -10,19 +11,20 @@ read_data data.airebo 1 by 1 by 1 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000232458 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms - Time spent = 0.00132823 secs + replicate CPU = 0.00206327 secs neighbor 0.5 bin neigh_modify delay 5 every 1 pair_style airebo 3.0 0 0 -pair_coeff * * ../../potentials/CH.airebo C H -Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25 +pair_coeff * * CH.airebo C H +Reading potential file CH.airebo with DATE: 2011-10-25 velocity all create 300.0 761341 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 202.34667 -138029.28 0 -137175.59 -7623.6634 90 194.92367 -137997.12 0 -137174.75 -32277.173 100 185.2078 -137954.64 0 -137173.26 -6888.5104 -Loop time of 4.96876 on 1 procs for 100 steps with 32640 atoms +Loop time of 9.70367 on 1 procs for 100 steps with 32640 atoms -Performance: 0.869 ns/day, 27.604 hours/ns, 20.126 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.445 ns/day, 53.909 hours/ns, 10.305 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.4535 | 3.4535 | 3.4535 | 0.0 | 69.50 -Neigh | 1.4688 | 1.4688 | 1.4688 | 0.0 | 29.56 -Comm | 0.015106 | 0.015106 | 0.015106 | 0.0 | 0.30 -Output | 0.00098944 | 0.00098944 | 0.00098944 | 0.0 | 0.02 -Modify | 0.021631 | 0.021631 | 0.021631 | 0.0 | 0.44 -Other | | 0.008734 | | | 0.18 +Pair | 7.2508 | 7.2508 | 7.2508 | 0.0 | 74.72 +Neigh | 2.3573 | 2.3573 | 2.3573 | 0.0 | 24.29 +Comm | 0.03116 | 0.03116 | 0.03116 | 0.0 | 0.32 +Output | 0.0014739 | 0.0014739 | 0.0014739 | 0.0 | 0.02 +Modify | 0.0447 | 0.0447 | 0.0447 | 0.0 | 0.46 +Other | | 0.01819 | | | 0.19 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -84,4 +86,4 @@ Total # of neighbors = 4902134 Ave neighs/atom = 150.188 Neighbor list builds = 9 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:10 diff --git a/examples/airebo/log.12Dec18.airebo-0-0.g++.4 b/examples/airebo/log.30Apr2019.airebo-0-0.g++.4 similarity index 74% rename from examples/airebo/log.12Dec18.airebo-0-0.g++.4 rename to examples/airebo/log.30Apr2019.airebo-0-0.g++.4 index e2afb10452..a777e17885 100644 --- a/examples/airebo/log.12Dec18.airebo-0-0.g++.4 +++ b/examples/airebo/log.30Apr2019.airebo-0-0.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -10,19 +11,20 @@ read_data data.airebo 1 by 1 by 4 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000363827 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms - Time spent = 0.000664234 secs + replicate CPU = 0.00244427 secs neighbor 0.5 bin neigh_modify delay 5 every 1 pair_style airebo 3.0 0 0 -pair_coeff * * ../../potentials/CH.airebo C H -Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25 +pair_coeff * * CH.airebo C H +Reading potential file CH.airebo with DATE: 2011-10-25 velocity all create 300.0 761341 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 202.34667 -138029.28 0 -137175.59 -7623.6634 90 194.92367 -137997.12 0 -137174.75 -32277.173 100 185.2078 -137954.64 0 -137173.26 -6888.5104 -Loop time of 1.44469 on 4 procs for 100 steps with 32640 atoms +Loop time of 6.71962 on 4 procs for 100 steps with 32640 atoms -Performance: 2.990 ns/day, 8.026 hours/ns, 69.219 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.643 ns/day, 37.331 hours/ns, 14.882 timesteps/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.92215 | 0.93812 | 0.95363 | 1.6 | 64.94 -Neigh | 0.45592 | 0.45842 | 0.46002 | 0.2 | 31.73 -Comm | 0.016539 | 0.03352 | 0.050276 | 8.6 | 2.32 -Output | 0.00043154 | 0.00059217 | 0.001025 | 0.0 | 0.04 -Modify | 0.0087888 | 0.0090455 | 0.0095809 | 0.3 | 0.63 -Other | | 0.004989 | | | 0.35 +Pair | 4.4598 | 4.6375 | 4.7708 | 5.5 | 69.01 +Neigh | 1.5903 | 1.6452 | 1.7207 | 3.8 | 24.48 +Comm | 0.16708 | 0.37041 | 0.56709 | 25.1 | 5.51 +Output | 0.001061 | 0.0059808 | 0.0090635 | 4.3 | 0.09 +Modify | 0.030086 | 0.03154 | 0.032522 | 0.5 | 0.47 +Other | | 0.02897 | | | 0.43 Nlocal: 8160 ave 8163 max 8157 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -84,4 +86,4 @@ Total # of neighbors = 4902134 Ave neighs/atom = 150.188 Neighbor list builds = 9 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:07 diff --git a/examples/airebo/log.12Dec18.airebo-m.g++.1 b/examples/airebo/log.30Apr2019.airebo-m.g++.1 similarity index 78% rename from examples/airebo/log.12Dec18.airebo-m.g++.1 rename to examples/airebo/log.30Apr2019.airebo-m.g++.1 index 8042130645..0115756737 100644 --- a/examples/airebo/log.12Dec18.airebo-m.g++.1 +++ b/examples/airebo/log.30Apr2019.airebo-m.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -10,12 +11,13 @@ read_data data.airebo 1 by 1 by 1 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000225067 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms - Time spent = 0.00136471 secs + replicate CPU = 0.00226521 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 164.28396 -138709.5 0 -138016.4 -1524.7353 90 180.26403 -138776.42 0 -138015.9 -27143.467 100 164.05694 -138706.58 0 -138014.44 5157.5517 -Loop time of 64.5779 on 1 procs for 100 steps with 32640 atoms +Loop time of 111.537 on 1 procs for 100 steps with 32640 atoms -Performance: 0.067 ns/day, 358.766 hours/ns, 1.549 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.039 ns/day, 619.650 hours/ns, 0.897 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 59.905 | 59.905 | 59.905 | 0.0 | 92.76 -Neigh | 4.615 | 4.615 | 4.615 | 0.0 | 7.15 -Comm | 0.024453 | 0.024453 | 0.024453 | 0.0 | 0.04 -Output | 0.00099945 | 0.00099945 | 0.00099945 | 0.0 | 0.00 -Modify | 0.021971 | 0.021971 | 0.021971 | 0.0 | 0.03 -Other | | 0.01029 | | | 0.02 +Pair | 103.58 | 103.58 | 103.58 | 0.0 | 92.87 +Neigh | 7.8371 | 7.8371 | 7.8371 | 0.0 | 7.03 +Comm | 0.046259 | 0.046259 | 0.046259 | 0.0 | 0.04 +Output | 0.001497 | 0.001497 | 0.001497 | 0.0 | 0.00 +Modify | 0.047151 | 0.047151 | 0.047151 | 0.0 | 0.04 +Other | | 0.02204 | | | 0.02 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -84,4 +86,4 @@ Total # of neighbors = 22210922 Ave neighs/atom = 680.482 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:01:05 +Total wall time: 0:01:53 diff --git a/examples/airebo/log.12Dec18.airebo-m.g++.4 b/examples/airebo/log.30Apr2019.airebo-m.g++.4 similarity index 78% rename from examples/airebo/log.12Dec18.airebo-m.g++.4 rename to examples/airebo/log.30Apr2019.airebo-m.g++.4 index 1aab3b3544..4139c58387 100644 --- a/examples/airebo/log.12Dec18.airebo-m.g++.4 +++ b/examples/airebo/log.30Apr2019.airebo-m.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -10,12 +11,13 @@ read_data data.airebo 1 by 1 by 4 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000880957 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms - Time spent = 0.000692129 secs + replicate CPU = 0.00271702 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 164.28396 -138709.5 0 -138016.4 -1524.7353 90 180.26403 -138776.42 0 -138015.9 -27143.467 100 164.05694 -138706.58 0 -138014.44 5157.5517 -Loop time of 17.8093 on 4 procs for 100 steps with 32640 atoms +Loop time of 68.9923 on 4 procs for 100 steps with 32640 atoms -Performance: 0.243 ns/day, 98.940 hours/ns, 5.615 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.063 ns/day, 383.290 hours/ns, 1.449 timesteps/s +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 15.932 | 16.012 | 16.082 | 1.5 | 89.91 -Neigh | 1.5933 | 1.6063 | 1.6173 | 0.7 | 9.02 -Comm | 0.098741 | 0.17402 | 0.2676 | 16.8 | 0.98 -Output | 0.00044513 | 0.00074279 | 0.0016048 | 0.0 | 0.00 -Modify | 0.0088906 | 0.0089375 | 0.008992 | 0.0 | 0.05 -Other | | 0.007106 | | | 0.04 +Pair | 60.09 | 60.276 | 60.515 | 2.1 | 87.37 +Neigh | 6.7521 | 6.8996 | 7.0678 | 4.3 | 10.00 +Comm | 1.5441 | 1.7514 | 2.0838 | 16.9 | 2.54 +Output | 0.0010803 | 0.001972 | 0.0043106 | 3.0 | 0.00 +Modify | 0.031365 | 0.032539 | 0.034404 | 0.7 | 0.05 +Other | | 0.03104 | | | 0.04 Nlocal: 8160 ave 8167 max 8153 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -84,4 +86,4 @@ Total # of neighbors = 22210922 Ave neighs/atom = 680.482 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:18 +Total wall time: 0:01:10 diff --git a/examples/airebo/log.12Dec18.airebo.g++.1 b/examples/airebo/log.30Apr2019.airebo.g++.1 similarity index 78% rename from examples/airebo/log.12Dec18.airebo.g++.1 rename to examples/airebo/log.30Apr2019.airebo.g++.1 index ccc156c15b..61792e9a7a 100644 --- a/examples/airebo/log.12Dec18.airebo.g++.1 +++ b/examples/airebo/log.30Apr2019.airebo.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -10,12 +11,13 @@ read_data data.airebo 1 by 1 by 1 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000217438 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms - Time spent = 0.0013268 secs + replicate CPU = 0.00204968 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 157.16184 -138695.77 0 -138032.72 19824.698 90 196.15907 -138860.65 0 -138033.07 -7950.8463 100 178.31875 -138784.89 0 -138032.57 30997.671 -Loop time of 57.482 on 1 procs for 100 steps with 32640 atoms +Loop time of 98.1502 on 1 procs for 100 steps with 32640 atoms -Performance: 0.075 ns/day, 319.344 hours/ns, 1.740 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.044 ns/day, 545.279 hours/ns, 1.019 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 52.796 | 52.796 | 52.796 | 0.0 | 91.85 -Neigh | 4.6286 | 4.6286 | 4.6286 | 0.0 | 8.05 -Comm | 0.024035 | 0.024035 | 0.024035 | 0.0 | 0.04 -Output | 0.00098443 | 0.00098443 | 0.00098443 | 0.0 | 0.00 -Modify | 0.021958 | 0.021958 | 0.021958 | 0.0 | 0.04 -Other | | 0.01014 | | | 0.02 +Pair | 90.237 | 90.237 | 90.237 | 0.0 | 91.94 +Neigh | 7.796 | 7.796 | 7.796 | 0.0 | 7.94 +Comm | 0.048884 | 0.048884 | 0.048884 | 0.0 | 0.05 +Output | 0.0016053 | 0.0016053 | 0.0016053 | 0.0 | 0.00 +Modify | 0.045511 | 0.045511 | 0.045511 | 0.0 | 0.05 +Other | | 0.0217 | | | 0.02 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -84,4 +86,4 @@ Total # of neighbors = 22217840 Ave neighs/atom = 680.694 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:58 +Total wall time: 0:01:39 diff --git a/examples/airebo/log.12Dec18.airebo.g++.4 b/examples/airebo/log.30Apr2019.airebo.g++.4 similarity index 78% rename from examples/airebo/log.12Dec18.airebo.g++.4 rename to examples/airebo/log.30Apr2019.airebo.g++.4 index fbdd9ed2e1..9857d9c741 100644 --- a/examples/airebo/log.12Dec18.airebo.g++.4 +++ b/examples/airebo/log.30Apr2019.airebo.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -10,12 +11,13 @@ read_data data.airebo 1 by 1 by 4 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000266314 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms - Time spent = 0.000614405 secs + replicate CPU = 0.00146151 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 157.16184 -138695.77 0 -138032.72 19824.698 90 196.15907 -138860.65 0 -138033.07 -7950.8463 100 178.31875 -138784.89 0 -138032.57 30997.671 -Loop time of 15.9743 on 4 procs for 100 steps with 32640 atoms +Loop time of 60.4943 on 4 procs for 100 steps with 32640 atoms -Performance: 0.270 ns/day, 88.746 hours/ns, 6.260 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.071 ns/day, 336.080 hours/ns, 1.653 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 14.13 | 14.185 | 14.258 | 1.3 | 88.80 -Neigh | 1.5945 | 1.6093 | 1.6237 | 0.9 | 10.07 -Comm | 0.075436 | 0.16329 | 0.23273 | 14.3 | 1.02 -Output | 0.00041533 | 0.00069332 | 0.0014405 | 0.0 | 0.00 -Modify | 0.0089853 | 0.0090484 | 0.0091338 | 0.1 | 0.06 -Other | | 0.007319 | | | 0.05 +Pair | 51.737 | 52.46 | 52.86 | 6.2 | 86.72 +Neigh | 6.5823 | 6.6605 | 6.726 | 2.0 | 11.01 +Comm | 0.92426 | 1.3125 | 2.0111 | 37.0 | 2.17 +Output | 0.0010669 | 0.0019811 | 0.0043974 | 3.1 | 0.00 +Modify | 0.030364 | 0.031523 | 0.032495 | 0.5 | 0.05 +Other | | 0.028 | | | 0.05 Nlocal: 8160 ave 8174 max 8146 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -84,4 +86,4 @@ Total # of neighbors = 22217840 Ave neighs/atom = 680.694 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:16 +Total wall time: 0:01:01 diff --git a/examples/airebo/log.12Dec18.rebo2.g++.1 b/examples/airebo/log.30Apr2019.rebo2.g++.1 similarity index 73% rename from examples/airebo/log.12Dec18.rebo2.g++.1 rename to examples/airebo/log.30Apr2019.rebo2.g++.1 index 83c3a8ebea..7cd3d65294 100644 --- a/examples/airebo/log.12Dec18.rebo2.g++.1 +++ b/examples/airebo/log.30Apr2019.rebo2.g++.1 @@ -1,6 +1,7 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task -# AIREBO polyethelene benchmark +# REBO polyethelene benchmark units metal atom_style atomic @@ -10,19 +11,20 @@ read_data data.airebo 1 by 1 by 1 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000190735 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms - Time spent = 0.0013907 secs + replicate CPU = 0.00197148 secs neighbor 0.5 bin neigh_modify delay 5 every 1 pair_style rebo -pair_coeff * * ../../potentials/CH.rebo C H -Reading potential file ../../potentials/CH.rebo with DATE: 2018-7-3 +pair_coeff * * CH.rebo C H +Reading potential file CH.rebo with DATE: 2018-7-3 velocity all create 300.0 761341 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 202.37482 -138029.39 0 -137175.59 -7622.7319 90 194.90628 -137997.05 0 -137174.75 -32267.471 100 185.17818 -137954.51 0 -137173.26 -6901.7499 -Loop time of 4.96341 on 1 procs for 100 steps with 32640 atoms +Loop time of 9.44819 on 1 procs for 100 steps with 32640 atoms -Performance: 0.870 ns/day, 27.574 hours/ns, 20.147 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.457 ns/day, 52.490 hours/ns, 10.584 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.4476 | 3.4476 | 3.4476 | 0.0 | 69.46 -Neigh | 1.4692 | 1.4692 | 1.4692 | 0.0 | 29.60 -Comm | 0.015226 | 0.015226 | 0.015226 | 0.0 | 0.31 -Output | 0.00098777 | 0.00098777 | 0.00098777 | 0.0 | 0.02 -Modify | 0.021646 | 0.021646 | 0.021646 | 0.0 | 0.44 -Other | | 0.008718 | | | 0.18 +Pair | 7.037 | 7.037 | 7.037 | 0.0 | 74.48 +Neigh | 2.3182 | 2.3182 | 2.3182 | 0.0 | 24.54 +Comm | 0.029898 | 0.029898 | 0.029898 | 0.0 | 0.32 +Output | 0.0014331 | 0.0014331 | 0.0014331 | 0.0 | 0.02 +Modify | 0.043851 | 0.043851 | 0.043851 | 0.0 | 0.46 +Other | | 0.01774 | | | 0.19 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -84,4 +86,4 @@ Total # of neighbors = 4902134 Ave neighs/atom = 150.188 Neighbor list builds = 9 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:09 diff --git a/examples/airebo/log.12Dec18.rebo2.g++.4 b/examples/airebo/log.30Apr2019.rebo2.g++.4 similarity index 73% rename from examples/airebo/log.12Dec18.rebo2.g++.4 rename to examples/airebo/log.30Apr2019.rebo2.g++.4 index f38f484238..14086fbf40 100644 --- a/examples/airebo/log.12Dec18.rebo2.g++.4 +++ b/examples/airebo/log.30Apr2019.rebo2.g++.4 @@ -1,6 +1,7 @@ -LAMMPS (12 Dec 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task -# AIREBO polyethelene benchmark +# REBO polyethelene benchmark units metal atom_style atomic @@ -10,19 +11,20 @@ read_data data.airebo 1 by 1 by 4 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000682831 secs replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms - Time spent = 0.000644684 secs + replicate CPU = 0.00221777 secs neighbor 0.5 bin neigh_modify delay 5 every 1 pair_style rebo -pair_coeff * * ../../potentials/CH.rebo C H -Reading potential file ../../potentials/CH.rebo with DATE: 2018-7-3 +pair_coeff * * CH.rebo C H +Reading potential file CH.rebo with DATE: 2018-7-3 velocity all create 300.0 761341 @@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 80 202.37482 -138029.39 0 -137175.59 -7622.7319 90 194.90628 -137997.05 0 -137174.75 -32267.471 100 185.17818 -137954.51 0 -137173.26 -6901.7499 -Loop time of 1.4517 on 4 procs for 100 steps with 32640 atoms +Loop time of 6.35645 on 4 procs for 100 steps with 32640 atoms -Performance: 2.976 ns/day, 8.065 hours/ns, 68.885 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.680 ns/day, 35.314 hours/ns, 15.732 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.92079 | 0.93883 | 0.95524 | 1.6 | 64.67 -Neigh | 0.45826 | 0.46013 | 0.46316 | 0.3 | 31.70 -Comm | 0.02183 | 0.038046 | 0.052974 | 7.5 | 2.62 -Output | 0.00044131 | 0.00057179 | 0.00093198 | 0.0 | 0.04 -Modify | 0.0088243 | 0.0089917 | 0.0092998 | 0.2 | 0.62 -Other | | 0.005127 | | | 0.35 +Pair | 4.4335 | 4.5041 | 4.56 | 2.1 | 70.86 +Neigh | 1.5332 | 1.5919 | 1.6466 | 3.6 | 25.04 +Comm | 0.098299 | 0.20854 | 0.26277 | 14.2 | 3.28 +Output | 0.0011072 | 0.0018047 | 0.0037503 | 2.6 | 0.03 +Modify | 0.028811 | 0.030358 | 0.031516 | 0.6 | 0.48 +Other | | 0.01977 | | | 0.31 Nlocal: 8160 ave 8163 max 8157 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -84,4 +86,4 @@ Total # of neighbors = 4902134 Ave neighs/atom = 150.188 Neighbor list builds = 9 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:06