From 2749e091c76d8447470cbf56d5b17b95a02cfcdf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 30 Sep 2024 22:10:00 -0400 Subject: [PATCH] update nemd example so it is reproducible --- examples/nemd/in.nemd | 48 +++++----- examples/nemd/log.27Nov18.nemd.g++.1 | 137 --------------------------- examples/nemd/log.27Nov18.nemd.g++.4 | 137 --------------------------- examples/nemd/log.30Sep24.g++.1 | 111 ++++++++++++++++++++++ examples/nemd/log.30Sep24.g++.4 | 111 ++++++++++++++++++++++ 5 files changed, 246 insertions(+), 298 deletions(-) delete mode 100644 examples/nemd/log.27Nov18.nemd.g++.1 delete mode 100644 examples/nemd/log.27Nov18.nemd.g++.4 create mode 100644 examples/nemd/log.30Sep24.g++.1 create mode 100644 examples/nemd/log.30Sep24.g++.4 diff --git a/examples/nemd/in.nemd b/examples/nemd/in.nemd index af3e4bed82..fb66e3fd3d 100644 --- a/examples/nemd/in.nemd +++ b/examples/nemd/in.nemd @@ -1,37 +1,37 @@ # 2d NEMD simulation -units lj -atom_style atomic -dimension 2 +units lj +atom_style atomic +dimension 2 -lattice sq2 0.8442 -region box prism 0 10 0 8 -0.5 0.5 0 0 0 -create_box 2 box -create_atoms 1 box -mass * 1.0 +lattice sq2 0.8442 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +create_atoms 1 box +mass * 1.0 -velocity all create 1.44 87287 loop geom +velocity all create 1.44 87287 loop geom -region slice block 4 6 INF INF INF INF -set region slice type 2 +region slice block 4 6 INF INF INF INF +set region slice type 2 -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 1.0 +pair_style lj/cut 4.0 +pair_coeff * * 1.0 1.0 -neighbor 0.3 bin -neigh_modify delay 0 every 1 +neighbor 0.3 bin +neigh_modify delay 0 every 1 -fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 -fix 2 all deform 1 xy erate 0.01 remap v +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v -#dump 1 all custom 5000 dump.nemd id type x y z +#dump 1 all custom 500 dump.nemd id type x y z -#dump 2 all image 1000 image.*.jpg type type adiam 1.2 -#dump_modify 2 pad 5 +#dump 2 all image 100 image.*.jpg type type adiam 1.2 +#dump_modify 2 pad 5 -#dump 3 all movie 1000 movie.mpg type type adiam 1.2 -#dump_modify 3 pad 5 +#dump 3 all movie 100 movie.mpg type type adiam 1.2 +#dump_modify 3 pad 5 -thermo 1000 +thermo 50 -run 50000 +run 1000 diff --git a/examples/nemd/log.27Nov18.nemd.g++.1 b/examples/nemd/log.27Nov18.nemd.g++.1 deleted file mode 100644 index c0989db969..0000000000 --- a/examples/nemd/log.27Nov18.nemd.g++.1 +++ /dev/null @@ -1,137 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 2d NEMD simulation - -units lj -atom_style atomic -dimension 2 - -lattice sq2 0.8442 -Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 -region box prism 0 10 0 8 -0.5 0.5 0 0 0 -create_box 2 box -Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 160 atoms - Time spent = 0.000332355 secs -mass * 1.0 - -velocity all create 1.44 87287 loop geom - -region slice block 4 6 INF INF INF INF -set region slice type 2 - 40 settings made for type - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 1.0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 - -fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 -fix 2 all deform 1 xy erate 0.01 remap v - -#dump 1 all custom 5000 dump.nemd id type x y z - -#dump 2 all image 1000 image.*.jpg type type adiam 1.2 -#dump_modify 2 pad 5 - -#dump 3 all movie 1000 movie.mpg type type adiam 1.2 -#dump_modify 3 pad 5 - -thermo 1000 - -run 50000 -Neighbor list info ... - update every 1 steps, delay 0 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 = 24 19 3 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/2d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 1.44 0 0 1.431 1.2080502 189.52855 - 1000 1.1326992 0.25863754 0 1.3842573 6.0588079 189.52855 - 2000 0.99104643 0.37634349 0 1.3611959 7.8993387 189.52855 - 3000 1.0749743 0.21908728 0 1.2873429 6.2659517 189.52855 - 4000 1.0986742 0.27147022 0 1.3632777 5.8778262 189.52855 - 5000 1.071838 0.23413372 0 1.2992728 5.9120887 189.52855 - 6000 1.0013194 0.26923671 0 1.2642979 6.2802759 189.52855 - 7000 0.94110685 0.3224557 0 1.2576806 6.1864166 189.52855 - 8000 0.97391513 0.28793383 0 1.255762 6.5071893 189.52855 - 9000 0.95346063 0.31050593 0 1.2580074 6.3321512 189.52855 - 10000 0.96236447 0.26298203 0 1.2193317 6.4083918 189.52855 - 11000 0.9511149 0.27571527 0 1.2208857 6.0949768 189.52855 - 12000 1.0186935 0.18134918 0 1.1936758 5.1269128 189.52855 - 13000 0.96350682 0.23171507 0 1.1892 5.7367267 189.52855 - 14000 0.94740402 0.27357945 0 1.2150622 6.0156532 189.52855 - 15000 0.87951545 0.27745111 0 1.1514696 6.297405 189.52855 - 16000 0.93216196 0.27020559 0 1.1965415 6.6188833 189.52855 - 17000 0.94109936 0.24756193 0 1.1827794 5.8993088 189.52855 - 18000 0.97325239 0.27996398 0 1.2471335 6.1486561 189.52855 - 19000 1.0494686 0.27132686 0 1.3142363 6.6757065 189.52855 - 20000 1.0391862 0.25195457 0 1.2846459 6.143235 189.52855 - 21000 0.96407137 0.27359166 0 1.2316376 5.9577116 189.52855 - 22000 0.97954534 0.31920255 0 1.2926257 6.5320163 189.52855 - 23000 0.97585473 0.24154424 0 1.2112999 6.0839179 189.52855 - 24000 1.0522109 0.1646952 0 1.2103298 5.0388687 189.52855 - 25000 0.93707172 0.25655806 0 1.1877731 5.819887 189.52855 - 26000 0.89798775 0.26629627 0 1.1586716 6.0393558 189.52855 - 27000 0.93259926 0.24542428 0 1.1721948 5.3560986 189.52855 - 28000 0.8428223 0.20784302 0 1.0453977 4.956911 189.52855 - 29000 0.81653505 0.21924932 0 1.030681 5.271501 189.52855 - 30000 0.90157811 0.15070734 0 1.0466506 4.476142 189.52855 - 31000 0.86580039 0.21115151 0 1.0715407 5.0056915 189.52855 - 32000 0.89768096 0.28377249 0 1.1758429 5.8449711 189.52855 - 33000 1.0504011 0.29009694 0 1.333933 6.1319155 189.52855 - 34000 1.2009765 0.19137934 0 1.3848498 4.9643885 189.52855 - 35000 1.208705 0.27071222 0 1.4718628 6.2162389 189.52855 - 36000 1.2211309 0.28389521 0 1.497394 6.5090715 189.52855 - 37000 1.1384381 0.42795547 0 1.5592783 8.5129272 189.52855 - 38000 1.2198334 0.34335732 0 1.5555668 7.2940883 189.52855 - 39000 1.1562045 0.35783089 0 1.5068091 7.340999 189.52855 - 40000 1.2145924 0.28410558 0 1.4911068 6.234986 189.52855 - 41000 1.1240878 0.34663237 0 1.4636946 7.1720193 189.52855 - 42000 1.2491422 0.26815889 0 1.509494 6.1390803 189.52855 - 43000 1.1387564 0.33755832 0 1.4691975 7.0577597 189.52855 - 44000 1.0031598 0.4081807 0 1.4050708 8.2732113 189.52855 - 45000 1.0166213 0.29131017 0 1.3015776 6.1907807 189.52855 - 46000 0.96251302 0.31483519 0 1.2713325 6.6987235 189.52855 - 47000 0.89809294 0.30909884 0 1.2015787 6.3997583 189.52855 - 48000 0.86736217 0.31917648 0 1.1811176 7.1584774 189.52855 - 49000 0.91979053 0.21099403 0 1.1250359 5.4968259 189.52855 - 50000 0.87079959 0.24059333 0 1.1059504 5.6039305 189.52855 -Loop time of 1.54353 on 1 procs for 50000 steps with 160 atoms - -Performance: 13993916.675 tau/day, 32393.326 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 | 0.20172 | 0.20172 | 0.20172 | 0.0 | 13.07 -Neigh | 0.16634 | 0.16634 | 0.16634 | 0.0 | 10.78 -Comm | 0.068928 | 0.068928 | 0.068928 | 0.0 | 4.47 -Output | 0.00059891 | 0.00059891 | 0.00059891 | 0.0 | 0.04 -Modify | 1.0123 | 1.0123 | 1.0123 | 0.0 | 65.59 -Other | | 0.09361 | | | 6.06 - -Nlocal: 160 ave 160 max 160 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 73 ave 73 max 73 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 353 ave 353 max 353 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 353 -Ave neighs/atom = 2.20625 -Neighbor list builds = 5273 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/nemd/log.27Nov18.nemd.g++.4 b/examples/nemd/log.27Nov18.nemd.g++.4 deleted file mode 100644 index 68543882b7..0000000000 --- a/examples/nemd/log.27Nov18.nemd.g++.4 +++ /dev/null @@ -1,137 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 2d NEMD simulation - -units lj -atom_style atomic -dimension 2 - -lattice sq2 0.8442 -Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 -region box prism 0 10 0 8 -0.5 0.5 0 0 0 -create_box 2 box -Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) - 2 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 160 atoms - Time spent = 0.000308275 secs -mass * 1.0 - -velocity all create 1.44 87287 loop geom - -region slice block 4 6 INF INF INF INF -set region slice type 2 - 40 settings made for type - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 1.0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 - -fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 -fix 2 all deform 1 xy erate 0.01 remap v - -#dump 1 all custom 5000 dump.nemd id type x y z - -#dump 2 all image 1000 image.*.jpg type type adiam 1.2 -#dump_modify 2 pad 5 - -#dump 3 all movie 1000 movie.mpg type type adiam 1.2 -#dump_modify 3 pad 5 - -thermo 1000 - -run 50000 -Neighbor list info ... - update every 1 steps, delay 0 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 = 24 19 3 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/2d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 1.44 0 0 1.431 1.2080502 189.52855 - 1000 1.1682693 0.24486562 0 1.4058332 5.8092954 189.52855 - 2000 1.0928734 0.27609364 0 1.3621366 6.2237017 189.52855 - 3000 1.09088 0.24816112 0 1.3322231 5.7001547 189.52855 - 4000 1.0110684 0.29868377 0 1.303433 7.3312319 189.52855 - 5000 0.91033678 0.28330698 0 1.1879542 6.1840352 189.52855 - 6000 0.93416074 0.22661127 0 1.1549335 5.3619735 189.52855 - 7000 0.93305734 0.19203739 0 1.1192631 5.2497547 189.52855 - 8000 0.88944438 0.19421381 0 1.0780992 4.9733446 189.52855 - 9000 0.86949257 0.21207681 0 1.0761351 5.4687076 189.52855 - 10000 0.80088203 0.24071142 0 1.0365879 5.334545 189.52855 - 11000 0.88899727 0.19972767 0 1.0831687 4.8832207 189.52855 - 12000 0.93045817 0.17883252 0 1.1034753 4.9081709 189.52855 - 13000 0.9724196 0.19089684 0 1.1572388 5.3460903 189.52855 - 14000 0.93902186 0.25513773 0 1.1882907 6.3338337 189.52855 - 15000 0.91879903 0.31605547 0 1.229112 6.2085671 189.52855 - 16000 0.9860058 0.26863362 0 1.2484769 6.514688 189.52855 - 17000 1.0354756 0.23445357 0 1.2634574 6.1519296 189.52855 - 18000 1.0244774 0.27511827 0 1.2931927 6.2230002 189.52855 - 19000 1.1581216 0.21558936 0 1.3664727 5.5458237 189.52855 - 20000 1.0552168 0.29344488 0 1.3420666 6.4880315 189.52855 - 21000 0.97925435 0.31583414 0 1.2889681 6.7584093 189.52855 - 22000 1.0112494 0.26246834 0 1.2673974 5.4112008 189.52855 - 23000 1.0463332 0.26049752 0 1.3002911 6.1359606 189.52855 - 24000 1.1130319 0.19848564 0 1.3045611 5.7088487 189.52855 - 25000 1.0355662 0.28048951 0 1.3095834 6.4596476 189.52855 - 26000 1.0823932 0.21784218 0 1.2934704 5.106334 189.52855 - 27000 0.99719525 0.32679678 0 1.3177596 6.7399277 189.52855 - 28000 1.0665868 0.25002709 0 1.3099477 6.2732557 189.52855 - 29000 1.0312798 0.30650087 0 1.3313351 7.0581024 189.52855 - 30000 1.0388277 0.29812912 0 1.3304641 6.2533028 189.52855 - 31000 1.0461658 0.21344416 0 1.2530714 5.3631154 189.52855 - 32000 1.0233681 0.27545017 0 1.2924222 5.9612896 189.52855 - 33000 1.1353086 0.20278244 0 1.3309953 5.7619128 189.52855 - 34000 1.0374791 0.29661216 0 1.327607 6.5124409 189.52855 - 35000 1.0752783 0.21684443 0 1.2854022 5.4759171 189.52855 - 36000 1.0383445 0.27068641 0 1.3025412 6.8367218 189.52855 - 37000 0.97341144 0.24034988 0 1.2076775 6.1335996 189.52855 - 38000 0.9285918 0.2737544 0 1.1965425 5.8750327 189.52855 - 39000 0.84869423 0.30079207 0 1.144182 6.8909326 189.52855 - 40000 0.88237131 0.26049171 0 1.1373482 6.3932981 189.52855 - 41000 0.90368591 0.21064132 0 1.1086792 5.5627232 189.52855 - 42000 0.93436749 0.20367569 0 1.1322034 5.1420052 189.52855 - 43000 0.91378588 0.26155533 0 1.16963 6.366756 189.52855 - 44000 0.91673608 0.25967314 0 1.1706796 6.0846334 189.52855 - 45000 1.0233334 0.25463562 0 1.2715732 6.0924255 189.52855 - 46000 0.96184729 0.35422095 0 1.3100567 7.0249175 189.52855 - 47000 1.134079 0.26196034 0 1.3889514 6.3476756 189.52855 - 48000 1.0552136 0.303812 0 1.3524305 6.6968927 189.52855 - 49000 1.1282184 0.2100955 0 1.3312626 5.8658659 189.52855 - 50000 1.0493816 0.31540438 0 1.3582274 6.6348173 189.52855 -Loop time of 1.09903 on 4 procs for 50000 steps with 160 atoms - -Performance: 19653623.953 tau/day, 45494.500 timesteps/s -94.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.057854 | 0.05974 | 0.062726 | 0.7 | 5.44 -Neigh | 0.047791 | 0.049863 | 0.054819 | 1.3 | 4.54 -Comm | 0.3581 | 0.38553 | 0.39784 | 2.6 | 35.08 -Output | 0.001116 | 0.0014414 | 0.0023859 | 1.4 | 0.13 -Modify | 0.41102 | 0.42642 | 0.4493 | 2.3 | 38.80 -Other | | 0.176 | | | 16.02 - -Nlocal: 40 ave 42 max 39 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Nghost: 36.5 ave 37 max 36 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 87.5 ave 94 max 81 min -Histogram: 1 1 0 0 0 0 0 0 1 1 - -Total # of neighbors = 350 -Ave neighs/atom = 2.1875 -Neighbor list builds = 5276 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/nemd/log.30Sep24.g++.1 b/examples/nemd/log.30Sep24.g++.1 new file mode 100644 index 0000000000..161b165a09 --- /dev/null +++ b/examples/nemd/log.30Sep24.g++.1 @@ -0,0 +1,111 @@ +LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-394-g75f86a68a7-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# 2d NEMD simulation + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.5391903 1.5391903 1.5391903 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.76959516) to (15.391903 12.313523 0.76959516) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + using lattice units in triclinic box = (0 0 -0.76959516) to (15.391903 12.313523 0.76959516) with tilt (0 0 0) + create_atoms CPU = 0.000 seconds +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 +Setting atom values ... + 40 settings made for type + +pair_style lj/cut 4.0 +pair_coeff * * 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +#dump 1 all custom 500 dump.nemd id type x y z + +#dump 2 all image 100 image.*.jpg type type adiam 1.2 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type adiam 1.2 +#dump_modify 3 pad 5 + +thermo 50 + +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 8 6 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -2.6548731 0 -1.2238731 1.9354912 189.52855 + 50 0.97904822 -2.1934929 0 -1.2205637 5.0001562 189.52855 + 100 0.96423603 -2.1711413 0 -1.2129318 5.3040025 189.52855 + 150 0.96430794 -2.153062 0 -1.194781 5.3988945 189.52855 + 200 1.056585 -2.2379316 0 -1.1879503 5.0007883 189.52855 + 250 1.0183256 -2.1921531 0 -1.1801921 5.5370076 189.52855 + 300 0.96855552 -2.140465 0 -1.177963 5.7188412 189.52855 + 350 1.0115567 -2.1883272 0 -1.1830927 5.4437104 189.52855 + 400 0.93743103 -2.1230826 0 -1.1915105 5.7059909 189.52855 + 450 1.1120368 -2.3041274 0 -1.1990408 4.646396 189.52855 + 500 0.99611106 -2.2039016 0 -1.2140162 5.1526658 189.52855 + 550 1.1075519 -2.3349751 0 -1.2343453 4.0671355 189.52855 + 600 1.0550783 -2.3126484 0 -1.2641644 4.5423735 189.52855 + 650 0.98516169 -2.2664919 0 -1.2874875 4.8365475 189.52855 + 700 0.97899201 -2.2815136 0 -1.3086403 4.5415389 189.52855 + 750 1.0107776 -2.3375258 0 -1.3330656 4.3655082 189.52855 + 800 0.97711804 -2.3221241 0 -1.3511131 4.2153988 189.52855 + 850 0.8984454 -2.258341 0 -1.3655108 4.6759265 189.52855 + 900 0.85409237 -2.2157566 0 -1.3670024 5.0180073 189.52855 + 950 0.90195434 -2.2500988 0 -1.3537817 4.8189466 189.52855 + 1000 1.0047283 -2.3359434 0 -1.3374947 4.0788763 189.52855 +Loop time of 0.0331477 on 1 procs for 1000 steps with 160 atoms + +Performance: 13032596.122 tau/day, 30168.047 timesteps/s, 4.827 Matom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.017584 | 0.017584 | 0.017584 | 0.0 | 53.05 +Neigh | 0.0080996 | 0.0080996 | 0.0080996 | 0.0 | 24.43 +Comm | 0.0010864 | 0.0010864 | 0.0010864 | 0.0 | 3.28 +Output | 9.9819e-05 | 9.9819e-05 | 9.9819e-05 | 0.0 | 0.30 +Modify | 0.0057062 | 0.0057062 | 0.0057062 | 0.0 | 17.21 +Other | | 0.0005715 | | | 1.72 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 271 ave 271 max 271 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3881 ave 3881 max 3881 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3881 +Ave neighs/atom = 24.25625 +Neighbor list builds = 106 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/nemd/log.30Sep24.g++.4 b/examples/nemd/log.30Sep24.g++.4 new file mode 100644 index 0000000000..e101d68406 --- /dev/null +++ b/examples/nemd/log.30Sep24.g++.4 @@ -0,0 +1,111 @@ +LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-394-g75f86a68a7-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# 2d NEMD simulation + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.5391903 1.5391903 1.5391903 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.76959516) to (15.391903 12.313523 0.76959516) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + using lattice units in triclinic box = (0 0 -0.76959516) to (15.391903 12.313523 0.76959516) with tilt (0 0 0) + create_atoms CPU = 0.001 seconds +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 +Setting atom values ... + 40 settings made for type + +pair_style lj/cut 4.0 +pair_coeff * * 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +#dump 1 all custom 500 dump.nemd id type x y z + +#dump 2 all image 100 image.*.jpg type type adiam 1.2 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type adiam 1.2 +#dump_modify 3 pad 5 + +thermo 50 + +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 8 6 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton/tri + stencil: half/bin/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -2.6548731 0 -1.2238731 1.9354912 189.52855 + 50 0.97904822 -2.1934929 0 -1.2205637 5.0001562 189.52855 + 100 0.96423603 -2.1711413 0 -1.2129318 5.3040025 189.52855 + 150 0.96430794 -2.153062 0 -1.194781 5.3988945 189.52855 + 200 1.056585 -2.2379316 0 -1.1879503 5.0007883 189.52855 + 250 1.0183256 -2.1921531 0 -1.1801921 5.5370076 189.52855 + 300 0.96855552 -2.140465 0 -1.177963 5.7188412 189.52855 + 350 1.0115567 -2.1883272 0 -1.1830927 5.4437104 189.52855 + 400 0.93743103 -2.1230826 0 -1.1915105 5.7059909 189.52855 + 450 1.1120368 -2.3041274 0 -1.1990408 4.646396 189.52855 + 500 0.99611106 -2.2039016 0 -1.2140162 5.1526658 189.52855 + 550 1.1075519 -2.3349751 0 -1.2343453 4.0671355 189.52855 + 600 1.0550783 -2.3126484 0 -1.2641644 4.5423735 189.52855 + 650 0.98516169 -2.2664919 0 -1.2874875 4.8365475 189.52855 + 700 0.97899201 -2.2815136 0 -1.3086403 4.5415389 189.52855 + 750 1.0107776 -2.3375258 0 -1.3330656 4.3655082 189.52855 + 800 0.97711804 -2.3221241 0 -1.3511131 4.2153988 189.52855 + 850 0.8984454 -2.258341 0 -1.3655108 4.6759265 189.52855 + 900 0.85409237 -2.2157566 0 -1.3670024 5.0180073 189.52855 + 950 0.90195434 -2.2500988 0 -1.3537817 4.8189466 189.52855 + 1000 1.0047283 -2.3359434 0 -1.3374947 4.0788763 189.52855 +Loop time of 0.0158907 on 4 procs for 1000 steps with 160 atoms + +Performance: 27185684.597 tau/day, 62929.825 timesteps/s, 10.069 Matom-step/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0044606 | 0.004562 | 0.0047619 | 0.2 | 28.71 +Neigh | 0.0023154 | 0.0023979 | 0.002494 | 0.1 | 15.09 +Comm | 0.0051743 | 0.0054807 | 0.0056638 | 0.3 | 34.49 +Output | 7.5535e-05 | 8.9889e-05 | 0.00012988 | 0.0 | 0.57 +Modify | 0.002223 | 0.0023624 | 0.0026372 | 0.3 | 14.87 +Other | | 0.0009979 | | | 6.28 + +Nlocal: 40 ave 42 max 38 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 163.5 ave 166 max 162 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 970.25 ave 1016 max 942 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 3881 +Ave neighs/atom = 24.25625 +Neighbor list builds = 106 +Dangerous builds = 0 +Total wall time: 0:00:00