From f28b103beec30cbbd6d8aa4ec1c5d97f9e4b4131 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 May 2010 14:48:21 -0400 Subject: [PATCH] improved & expanded test for tabulated potentials now testing all variants with r, r**2 and bitmap storage and using lookup, linear, and spline interpolation methods. --- examples/USER/openmp/in.melt-table | 37 ++++- examples/USER/openmp/log.melt-table | 245 +++++++++++++++++++++++++--- 2 files changed, 251 insertions(+), 31 deletions(-) diff --git a/examples/USER/openmp/in.melt-table b/examples/USER/openmp/in.melt-table index 923a53403f..28524efd40 100644 --- a/examples/USER/openmp/in.melt-table +++ b/examples/USER/openmp/in.melt-table @@ -11,15 +11,44 @@ mass 1 1.0 velocity all create 3.0 87287 -pair_style table/omp bitmap 12 -pair_coeff 1 1 lj_table.txt lj_bitmap 2.5 +pair_style table/omp lookup 1000 +pair_coeff 1 1 lj_table.txt lj_rsq 2.5 neighbor 0.3 bin neigh_modify every 20 delay 0 check no fix 1 all nve -dump id all atom 50 dump.melt - thermo 50 + +run 250 + +pair_style table/omp linear 1000 +pair_coeff 1 1 lj_table.txt lj_rsq 2.5 + +run 250 + +pair_style table/omp spline 1000 +pair_coeff 1 1 lj_table.txt lj_rsq 2.5 + +run 250 + +pair_style table/omp lookup 1000 +pair_coeff 1 1 lj_table.txt lj_r 2.5 + +run 250 + +pair_style table/omp linear 1000 +pair_coeff 1 1 lj_table.txt lj_r 2.5 + +run 250 + +pair_style table/omp spline 1000 +pair_coeff 1 1 lj_table.txt lj_r 2.5 + +run 250 + +pair_style table/omp bitmap 12 +pair_coeff 1 1 lj_table.txt lj_bitmap 2.5 + run 250 diff --git a/examples/USER/openmp/log.melt-table b/examples/USER/openmp/log.melt-table index 35fd64811d..f2c595ef49 100644 --- a/examples/USER/openmp/log.melt-table +++ b/examples/USER/openmp/log.melt-table @@ -9,50 +9,241 @@ Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) - 1 by 1 by 2 processor grid - using 8 OpenMP thread(s) per MPI task + 2 by 2 by 2 processor grid + using 2 OpenMP thread(s) per MPI task create_atoms 1 box Created 32000 atoms mass 1 1.0 velocity all create 3.0 87287 -pair_style table/omp bitmap 12 -pair_coeff 1 1 lj_table.txt lj_bitmap 2.5 +pair_style table/omp lookup 1000 +pair_coeff 1 1 lj_table.txt lj_rsq 2.5 neighbor 0.3 bin neigh_modify every 20 delay 0 check no fix 1 all nve -dump id all atom 50 dump.melt - thermo 50 + run 250 -Memory usage per processor = 6.94424 Mbytes +Memory usage per processor = 2.04461 Mbytes Step Temp E_pair E_mol TotEng Press - 0 3 -6.7733728 0 -2.2735134 -3.7027346 - 50 1.6634081 -4.7759661 0 -2.2809319 5.7074352 - 100 1.6411543 -4.7410379 0 -2.2793834 5.8716813 - 150 1.6433225 -4.7439798 0 -2.279073 5.8706212 - 200 1.642771 -4.7429978 0 -2.2789182 5.8815586 - 250 1.6366989 -4.7346105 0 -2.2796389 5.904304 -Loop time of 2.53542 on 2 procs / 8 threads for 250 steps with 32000 atoms + 0 3 -6.7637051 0 -2.2638457 -3.7196088 + 50 1.6668891 -4.7807849 0 -2.2805293 5.690735 + 100 1.6517887 -4.7566813 0 -2.2790757 5.8026657 + 150 1.6521143 -4.7564656 0 -2.2783717 5.821308 + 200 1.6443947 -4.744167 0 -2.2776521 5.8745814 + 250 1.6449933 -4.7446526 0 -2.2772398 5.8838204 +Loop time of 1.00595 on 8 procs / 2 threads for 250 steps with 32000 atoms -Pair time (%) = 1.25123 (49.3502) -Neigh time (%) = 0.570161 (22.4879) -Comm time (%) = 0.287084 (11.323) -Outpt time (%) = 0.274688 (10.834) -Other time (%) = 0.152251 (6.00495) +Pair time (%) = 0.640826 (63.7036) +Neigh time (%) = 0.11874 (11.8038) +Comm time (%) = 0.209618 (20.8379) +Outpt time (%) = 0.000472963 (0.0470165) +Other time (%) = 0.0362921 (3.60775) -Nlocal: 16000 ave 16023 max 15977 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 13071.5 ave 13076 max 13067 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 606412 ave 612209 max 600615 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 4000 ave 4026 max 3974 min +Histogram: 1 0 2 0 0 2 1 1 0 1 +Nghost: 5485.25 ave 5503 max 5473 min +Histogram: 2 2 0 0 1 0 0 1 1 1 +Neighs: 151540 ave 152449 max 150271 min +Histogram: 1 0 0 1 1 1 1 1 0 2 -Total # of neighbors = 1212824 -Ave neighs/atom = 37.9008 +Total # of neighbors = 1212320 +Ave neighs/atom = 37.885 +Neighbor list builds = 12 +Dangerous builds = 0 + +pair_style table/omp linear 1000 +pair_coeff 1 1 lj_table.txt lj_rsq 2.5 + +run 250 +Memory usage per processor = 2.04461 Mbytes +Step Temp E_pair E_mol TotEng Press + 250 1.6449933 -4.744272 0 -2.2768591 5.8860557 + 300 1.6390267 -4.735735 0 -2.2772718 5.9225893 + 350 1.6496467 -4.7517624 0 -2.2773697 5.8597313 + 400 1.6464054 -4.7474729 0 -2.2779419 5.8678018 + 450 1.6471441 -4.7488835 0 -2.2782445 5.8576003 + 500 1.6429156 -4.7427993 0 -2.278503 5.9022982 +Loop time of 1.14394 on 8 procs / 2 threads for 250 steps with 32000 atoms + +Pair time (%) = 0.770431 (67.3489) +Neigh time (%) = 0.117043 (10.2316) +Comm time (%) = 0.220681 (19.2913) +Outpt time (%) = 0.000401378 (0.0350873) +Other time (%) = 0.0353838 (3.09315) + +Nlocal: 4000 ave 4015 max 3986 min +Histogram: 1 1 2 0 0 0 1 1 1 1 +Nghost: 5492.12 ave 5534 max 5453 min +Histogram: 1 1 0 1 1 2 0 1 0 1 +Neighs: 151564 ave 153889 max 149973 min +Histogram: 2 1 0 2 0 0 1 1 0 1 + +Total # of neighbors = 1212511 +Ave neighs/atom = 37.891 +Neighbor list builds = 12 +Dangerous builds = 0 + +pair_style table/omp spline 1000 +pair_coeff 1 1 lj_table.txt lj_rsq 2.5 + +run 250 +Memory usage per processor = 2.04461 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 1.6429156 -4.7433947 0 -2.2790983 5.8990032 + 550 1.6405054 -4.7399746 0 -2.2792934 5.9099298 + 600 1.6470431 -4.7502838 0 -2.2797963 5.8646675 + 650 1.6494374 -4.7541076 0 -2.2800289 5.8422356 + 700 1.6386636 -4.7386414 0 -2.2807229 5.8972449 + 750 1.6403779 -4.7412456 0 -2.2807557 5.8876867 +Loop time of 1.23384 on 8 procs / 2 threads for 250 steps with 32000 atoms + +Pair time (%) = 0.854802 (69.28) +Neigh time (%) = 0.11736 (9.51182) +Comm time (%) = 0.225617 (18.2858) +Outpt time (%) = 0.000406504 (0.0329463) +Other time (%) = 0.0356504 (2.8894) + +Nlocal: 4000 ave 4012 max 3981 min +Histogram: 1 1 0 0 0 1 1 1 1 2 +Nghost: 5493.75 ave 5510 max 5471 min +Histogram: 1 0 0 1 1 0 3 1 0 1 +Neighs: 151580 ave 153823 max 149054 min +Histogram: 1 0 2 1 0 0 1 1 0 2 + +Total # of neighbors = 1212640 +Ave neighs/atom = 37.895 +Neighbor list builds = 12 +Dangerous builds = 0 + +pair_style table/omp lookup 1000 +pair_coeff 1 1 lj_table.txt lj_r 2.5 + +run 250 +Memory usage per processor = 2.04461 Mbytes +Step Temp E_pair E_mol TotEng Press + 750 1.6403779 -4.7410243 0 -2.2805344 5.8887421 + 800 1.6433307 -4.7452637 0 -2.2803447 5.8784851 + 850 1.6399884 -4.7398109 0 -2.2799052 5.8889271 + 900 1.6403131 -4.7402343 0 -2.2798415 5.8989758 + 950 1.6425157 -4.7433702 0 -2.2796736 5.879569 + 1000 1.642171 -4.7429316 0 -2.2797521 5.8852123 +Loop time of 0.986443 on 8 procs / 2 threads for 250 steps with 32000 atoms + +Pair time (%) = 0.618168 (62.6664) +Neigh time (%) = 0.117748 (11.9367) +Comm time (%) = 0.215395 (21.8355) +Outpt time (%) = 0.000415891 (0.0421607) +Other time (%) = 0.0347156 (3.51927) + +Nlocal: 4000 ave 4015 max 3983 min +Histogram: 2 0 1 0 0 0 1 2 1 1 +Nghost: 5475.12 ave 5499 max 5461 min +Histogram: 1 2 0 2 1 1 0 0 0 1 +Neighs: 151526 ave 153077 max 148725 min +Histogram: 1 0 1 1 0 0 1 0 0 4 + +Total # of neighbors = 1212211 +Ave neighs/atom = 37.8816 +Neighbor list builds = 12 +Dangerous builds = 0 + +pair_style table/omp linear 1000 +pair_coeff 1 1 lj_table.txt lj_r 2.5 + +run 250 +Memory usage per processor = 2.04461 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 1.642171 -4.7422506 0 -2.2790711 5.889006 + 1050 1.6343428 -4.7301701 0 -2.2787325 5.93429 + 1100 1.6465123 -4.7491667 0 -2.2794755 5.8698345 + 1150 1.6476593 -4.7510989 0 -2.2796872 5.855273 + 1200 1.6494782 -4.7540825 0 -2.2799426 5.8447346 + 1250 1.6456816 -4.7487388 0 -2.2802934 5.865547 +Loop time of 1.14093 on 8 procs / 2 threads for 250 steps with 32000 atoms + +Pair time (%) = 0.765485 (67.093) +Neigh time (%) = 0.117306 (10.2816) +Comm time (%) = 0.222228 (19.4777) +Outpt time (%) = 0.00041908 (0.0367314) +Other time (%) = 0.0354944 (3.11101) + +Nlocal: 4000 ave 4039 max 3963 min +Histogram: 1 1 1 0 0 2 1 1 0 1 +Nghost: 5486.5 ave 5510 max 5460 min +Histogram: 2 1 0 0 0 0 1 2 1 1 +Neighs: 151607 ave 152618 max 150228 min +Histogram: 1 1 0 0 1 1 1 0 1 2 + +Total # of neighbors = 1212854 +Ave neighs/atom = 37.9017 +Neighbor list builds = 12 +Dangerous builds = 0 + +pair_style table/omp spline 1000 +pair_coeff 1 1 lj_table.txt lj_r 2.5 + +run 250 +Memory usage per processor = 2.04461 Mbytes +Step Temp E_pair E_mol TotEng Press + 1250 1.6456816 -4.749325 0 -2.2808797 5.8622739 + 1300 1.637551 -4.7374686 0 -2.2812189 5.9062773 + 1350 1.6469218 -4.7517796 0 -2.2814742 5.8615876 + 1400 1.6375887 -4.7380421 0 -2.2817358 5.9032243 + 1450 1.6393448 -4.7415226 0 -2.2825823 5.881546 + 1500 1.6433388 -4.7471781 0 -2.2822469 5.8488637 +Loop time of 1.24799 on 8 procs / 2 threads for 250 steps with 32000 atoms + +Pair time (%) = 0.85371 (68.407) +Neigh time (%) = 0.117516 (9.41649) +Comm time (%) = 0.238137 (19.0817) +Outpt time (%) = 0.00346574 (0.277707) +Other time (%) = 0.0351564 (2.81705) + +Nlocal: 4000 ave 4023 max 3977 min +Histogram: 2 0 1 0 1 0 1 1 1 1 +Nghost: 5495.5 ave 5517 max 5472 min +Histogram: 1 1 0 1 1 0 1 1 1 1 +Neighs: 151674 ave 152578 max 150755 min +Histogram: 1 0 3 0 0 0 0 2 1 1 + +Total # of neighbors = 1213396 +Ave neighs/atom = 37.9186 +Neighbor list builds = 12 +Dangerous builds = 0 + +pair_style table/omp bitmap 12 +pair_coeff 1 1 lj_table.txt lj_bitmap 2.5 + +run 250 +Memory usage per processor = 2.04461 Mbytes +Step Temp E_pair E_mol TotEng Press + 1500 1.6433388 -4.7465997 0 -2.2816686 5.8504474 + 1550 1.6364098 -4.7366789 0 -2.2821409 5.9056544 + 1600 1.6365458 -4.737108 0 -2.282366 5.8907653 + 1650 1.6394524 -4.7419358 0 -2.282834 5.8982579 + 1700 1.6415454 -4.7452399 0 -2.2829988 5.8709923 + 1750 1.6400308 -4.743288 0 -2.2833187 5.8906805 +Loop time of 1.27882 on 8 procs / 2 threads for 250 steps with 32000 atoms + +Pair time (%) = 0.750027 (58.65) +Neigh time (%) = 0.117702 (9.20394) +Comm time (%) = 0.374876 (29.3143) +Outpt time (%) = 0.000406325 (0.0317735) +Other time (%) = 0.0358061 (2.79994) + +Nlocal: 4000 ave 4022 max 3987 min +Histogram: 2 1 0 1 1 2 0 0 0 1 +Nghost: 5487.62 ave 5511 max 5465 min +Histogram: 2 0 0 0 1 2 1 1 0 1 +Neighs: 151558 ave 154215 max 149672 min +Histogram: 3 0 0 0 2 1 0 1 0 1 + +Total # of neighbors = 1212466 +Ave neighs/atom = 37.8896 Neighbor list builds = 12 Dangerous builds = 0