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