Loading examples/peptide/log.5Oct16.peptide.g++.1→examples/peptide/log.27Nov18.peptide.g++.1 +50 −44 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real Loading Loading @@ -70,7 +71,7 @@ group peptide type <= 12 run 300 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading @@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 10648 3375 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 Loading @@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Memory usage per processor = 15.5934 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 ---------------- Step 50 ----- CPU = 0.9457 (sec) ---------------- ---------------- Step 50 ----- CPU = 1.0190 (sec) ---------------- TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 Loading @@ -114,77 +120,77 @@ SHAKE stats (type/ave/delta) on step 100 14 0.96 0 18 0.957201 5.3796e-06 31 104.52 0.000502278 ---------------- Step 100 ----- CPU = 1.9163 (sec) ---------------- ---------------- Step 100 ----- CPU = 2.0505 (sec) ---------------- TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 ---------------- Step 150 ----- CPU = 2.9286 (sec) ---------------- TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 ---------------- Step 150 ----- CPU = 3.1208 (sec) ---------------- TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1829 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18698e-07 6 0.997 1.50562e-07 8 1.08 6.57498e-08 6 0.997 1.50563e-07 8 1.08 6.57499e-08 10 1.111 5.54188e-07 12 1.08 1.98839e-07 12 1.08 1.9884e-07 14 0.96 0 18 0.957201 3.59627e-06 31 104.52 0.000388335 ---------------- Step 200 ----- CPU = 3.8703 (sec) ---------------- TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 ---------------- Step 200 ----- CPU = 4.1320 (sec) ---------------- TotEng = -5308.4468 KinEng = 1100.4873 Temp = 273.5421 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3400 ---------------- Step 250 ----- CPU = 4.8652 (sec) ---------------- TotEng = -5294.1569 KinEng = 1071.0938 Temp = 266.2359 PotEng = -6365.2507 E_bond = 14.2013 E_angle = 39.1996 E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3401 ---------------- Step 250 ----- CPU = 5.2131 (sec) ---------------- TotEng = -5294.1568 KinEng = 1071.0940 Temp = 266.2360 PotEng = -6365.2508 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4590 E_coul = 26714.0040 E_long = -33908.7139 Press = -189.6059 E_coul = 26714.0039 E_long = -33908.7139 Press = -189.6057 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.79044e-06 4 1.111 3.79043e-06 6 0.997001 3.6052e-06 8 1.08 2.09369e-06 10 1.111 5.6484e-06 12 1.08 2.10677e-06 12 1.08 2.10676e-06 14 0.96 0 18 0.957202 7.72576e-06 31 104.52 0.000806204 ---------------- Step 300 ----- CPU = 5.8596 (sec) ---------------- TotEng = -5251.3637 KinEng = 1123.7718 Temp = 279.3298 PotEng = -6375.1355 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3473 E_coul = 26745.4074 E_long = -33909.0791 Press = -471.5505 Loop time of 5.85959 on 1 procs for 300 steps with 2004 atoms Performance: 8.847 ns/day, 2.713 hours/ns, 51.198 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads 18 0.957202 7.72571e-06 31 104.52 0.000806203 ---------------- Step 300 ----- CPU = 6.2919 (sec) ---------------- TotEng = -5251.3662 KinEng = 1123.7719 Temp = 279.3299 PotEng = -6375.1381 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3476 E_coul = 26745.4045 E_long = -33909.0791 Press = -471.5904 Loop time of 6.29195 on 1 procs for 300 steps with 2004 atoms Performance: 8.239 ns/day, 2.913 hours/ns, 47.680 timesteps/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6289 | 4.6289 | 4.6289 | 0.0 | 79.00 Bond | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.23 Kspace | 0.47821 | 0.47821 | 0.47821 | 0.0 | 8.16 Neigh | 0.64447 | 0.64447 | 0.64447 | 0.0 | 11.00 Comm | 0.026137 | 0.026137 | 0.026137 | 0.0 | 0.45 Output | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.00 Modify | 0.062095 | 0.062095 | 0.062095 | 0.0 | 1.06 Other | | 0.006195 | | | 0.11 Pair | 4.8228 | 4.8228 | 4.8228 | 0.0 | 76.65 Bond | 0.0094063 | 0.0094063 | 0.0094063 | 0.0 | 0.15 Kspace | 0.523 | 0.523 | 0.523 | 0.0 | 8.31 Neigh | 0.82602 | 0.82602 | 0.82602 | 0.0 | 13.13 Comm | 0.03742 | 0.03742 | 0.03742 | 0.0 | 0.59 Output | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.00 Modify | 0.068182 | 0.068182 | 0.068182 | 0.0 | 1.08 Other | | 0.00493 | | | 0.08 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11185 ave 11185 max 11185 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 708018 ave 708018 max 708018 min Neighs: 708019 ave 708019 max 708019 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 708018 Ave neighs/atom = 353.302 Total # of neighbors = 708019 Ave neighs/atom = 353.303 Ave special neighs/atom = 2.34032 Neighbor list builds = 26 Dangerous builds = 0 Total wall time: 0:00:05 Total wall time: 0:00:06 examples/peptide/log.5Oct16.peptide.g++.4→examples/peptide/log.27Nov18.peptide.g++.4 +54 −48 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real Loading Loading @@ -70,7 +71,7 @@ group peptide type <= 12 run 300 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading @@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 4312 960 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 Loading @@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Memory usage per processor = 14.8928 Mbytes Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 ---------------- Step 50 ----- CPU = 0.2741 (sec) ---------------- ---------------- Step 50 ----- CPU = 0.2858 (sec) ---------------- TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 Loading @@ -114,65 +120,65 @@ SHAKE stats (type/ave/delta) on step 100 14 0.96 0 18 0.957201 5.3796e-06 31 104.52 0.000502278 ---------------- Step 100 ----- CPU = 0.5371 (sec) ---------------- ---------------- Step 100 ----- CPU = 0.5744 (sec) ---------------- TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 ---------------- Step 150 ----- CPU = 0.8054 (sec) ---------------- TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6820 ---------------- Step 150 ----- CPU = 0.8756 (sec) ---------------- TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8826 E_bond = 17.4925 E_angle = 32.8594 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1830 E_coul = 26717.2656 E_long = -33907.2821 Press = -333.1828 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18699e-07 6 0.997 1.50563e-07 8 1.08 6.57501e-08 10 1.111 5.54188e-07 12 1.08 1.98841e-07 8 1.08 6.575e-08 10 1.111 5.54187e-07 12 1.08 1.9884e-07 14 0.96 0 18 0.957201 3.59627e-06 31 104.52 0.000388336 ---------------- Step 200 ----- CPU = 1.0652 (sec) ---------------- TotEng = -5308.4465 KinEng = 1100.4875 Temp = 273.5422 PotEng = -6408.9340 E_bond = 18.2714 E_angle = 33.3040 31 104.52 0.000388335 ---------------- Step 200 ----- CPU = 1.1602 (sec) ---------------- TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 E_coul = 26736.1321 E_long = -33902.3837 Press = -1470.3400 ---------------- Step 250 ----- CPU = 1.3409 (sec) ---------------- TotEng = -5294.1570 KinEng = 1071.0939 Temp = 266.2360 PotEng = -6365.2509 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4591 E_coul = 26714.0037 E_long = -33908.7139 Press = -189.6059 E_coul = 26736.1320 E_long = -33902.3837 Press = -1470.3400 ---------------- Step 250 ----- CPU = 1.4629 (sec) ---------------- TotEng = -5294.1567 KinEng = 1071.0938 Temp = 266.2359 PotEng = -6365.2505 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4589 E_coul = 26714.0043 E_long = -33908.7139 Press = -189.6068 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.79043e-06 6 0.997001 3.60519e-06 8 1.08 2.09368e-06 10 1.111 5.64839e-06 12 1.08 2.10676e-06 6 0.997001 3.6052e-06 8 1.08 2.09369e-06 10 1.111 5.6484e-06 12 1.08 2.10677e-06 14 0.96 0 18 0.957202 7.72573e-06 31 104.52 0.000806208 ---------------- Step 300 ----- CPU = 1.6199 (sec) ---------------- TotEng = -5251.3639 KinEng = 1123.7721 Temp = 279.3299 PotEng = -6375.1360 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3470 E_coul = 26745.4071 E_long = -33909.0790 Press = -471.5569 Loop time of 1.61992 on 4 procs for 300 steps with 2004 atoms Performance: 32.002 ns/day, 0.750 hours/ns, 185.194 timesteps/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads 18 0.957202 7.72579e-06 31 104.52 0.000806203 ---------------- Step 300 ----- CPU = 1.7662 (sec) ---------------- TotEng = -5251.3662 KinEng = 1123.7712 Temp = 279.3297 PotEng = -6375.1374 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3474 E_coul = 26745.4053 E_long = -33909.0790 Press = -471.5904 Loop time of 1.76629 on 4 procs for 300 steps with 2004 atoms Performance: 29.350 ns/day, 0.818 hours/ns, 169.847 timesteps/s 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1484 | 1.17 | 1.1865 | 1.5 | 72.23 Bond | 0.0011752 | 0.003831 | 0.0069602 | 4.0 | 0.24 Kspace | 0.16316 | 0.1798 | 0.20413 | 3.9 | 11.10 Neigh | 0.16885 | 0.16895 | 0.16902 | 0.0 | 10.43 Comm | 0.046479 | 0.047215 | 0.047759 | 0.2 | 2.91 Output | 0.00024033 | 0.00025702 | 0.00030375 | 0.2 | 0.02 Modify | 0.04556 | 0.045949 | 0.046353 | 0.2 | 2.84 Other | | 0.003923 | | | 0.24 Pair | 1.2044 | 1.2351 | 1.2721 | 2.3 | 69.92 Bond | 0.0013924 | 0.0034139 | 0.0057151 | 3.2 | 0.19 Kspace | 0.17476 | 0.21195 | 0.2407 | 5.3 | 12.00 Neigh | 0.21273 | 0.21286 | 0.21293 | 0.0 | 12.05 Comm | 0.042942 | 0.046074 | 0.047584 | 0.9 | 2.61 Output | 0.00025845 | 0.00033492 | 0.00055695 | 0.0 | 0.02 Modify | 0.049944 | 0.051619 | 0.054278 | 0.8 | 2.92 Other | | 0.004988 | | | 0.28 Nlocal: 501 ave 508 max 490 min Histogram: 1 0 0 0 0 0 1 1 0 1 Loading examples/peri/log.6Jul17.peri.eps.g++.1→examples/peri/log.27Nov18.peri.eps.g++.1 +24 −23 Original line number Diff line number Diff line LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile Loading @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 1 by 1 by 1 MPI processor grid create_atoms 1 region target Created 3487 atoms Time spent = 0.00100374 secs pair_style peri/eps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 Loading Loading @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 50.29 | 50.29 | 50.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 900 1.3166045e+28 1911868.6 0 9.524241e+08 1.9729649e+14 3.2117896e-06 1000 1.3159578e+28 1995827.6 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 Loop time of 72.5574 on 1 procs for 1000 steps with 3487 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 100 9.7403734e+24 248692.93 0 951891.49 9.3703576e+11 5.0030006e-07 200 1.220493e+27 1011231.9 0 89123756 1.0636834e+14 5.5224782e-07 300 2.7274231e+27 4549425.2 0 2.0145358e+08 1.7250255e+14 7.6097098e-07 400 3.3665092e+27 13347641 0 2.5639011e+08 1.5828139e+14 1.0236725e-06 500 3.8995641e+27 14196430 0 2.9572238e+08 1.5145191e+14 1.2392314e-06 600 4.6668832e+27 23135807 0 3.6005775e+08 1.478168e+14 1.5195473e-06 700 1.1847301e+28 8126622 0 8.6343315e+08 2.9204301e+14 1.9524671e-06 800 1.2328889e+28 4646514.3 0 8.9472087e+08 2.2467312e+14 2.6410944e-06 900 1.2277283e+28 2668877.7 0 8.8901759e+08 1.671177e+14 3.5358262e-06 1000 1.2260912e+28 1587002.9 0 8.8675386e+08 1.29707e+14 4.5495712e-06 Loop time of 34.8143 on 1 procs for 1000 steps with 3487 atoms 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 71.779 | 71.779 | 71.779 | 0.0 | 98.93 Neigh | 0.5596 | 0.5596 | 0.5596 | 0.0 | 0.77 Comm | 0.0040631 | 0.0040631 | 0.0040631 | 0.0 | 0.01 Output | 0.00056624 | 0.00056624 | 0.00056624 | 0.0 | 0.00 Modify | 0.18403 | 0.18403 | 0.18403 | 0.0 | 0.25 Other | | 0.03016 | | | 0.04 Pair | 34.045 | 34.045 | 34.045 | 0.0 | 97.79 Neigh | 0.63254 | 0.63254 | 0.63254 | 0.0 | 1.82 Comm | 0.0025852 | 0.0025852 | 0.0025852 | 0.0 | 0.01 Output | 0.00035906 | 0.00035906 | 0.00035906 | 0.0 | 0.00 Modify | 0.11784 | 0.11784 | 0.11784 | 0.0 | 0.34 Other | | 0.01593 | | | 0.05 Nlocal: 3487 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 569177 ave 569177 max 569177 min Neighs: 546591 ave 546591 max 546591 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 Neighbor list builds = 40 Neighbor list builds = 45 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:12 Total wall time: 0:00:34 examples/peri/log.6Jul17.peri.eps.g++.4→examples/peri/log.27Nov18.peri.eps.g++.4 +29 −28 Original line number Diff line number Diff line LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile Loading @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 2 by 1 by 2 MPI processor grid create_atoms 1 region target Created 3487 atoms Time spent = 0.000587225 secs pair_style peri/eps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 Loading Loading @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 44.77 | 45.04 | 45.14 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 900 1.3166045e+28 1911869.3 0 9.524241e+08 1.9729649e+14 3.2117896e-06 1000 1.3159578e+28 1995833.9 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 Loop time of 29.6266 on 4 procs for 1000 steps with 3487 atoms 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads 100 2.3613868e+26 2297417.8 0 19345263 2.2716828e+13 5.0030006e-07 200 3.9573281e+27 28896934 0 3.1459311e+08 3.6928392e+14 5.1576607e-07 300 8.7809254e+27 38915502 0 6.7284747e+08 6.4053658e+14 6.5979263e-07 400 1.3210949e+28 35344681 0 9.8909868e+08 7.0953264e+14 8.9613355e-07 500 1.7324732e+28 21092574 0 1.2718379e+09 7.4083646e+14 1.1255254e-06 600 2.1194595e+28 11349855 0 1.5414769e+09 6.6250164e+14 1.5397467e-06 700 2.316318e+28 2515600.8 0 1.6747631e+09 5.0111859e+14 2.2246862e-06 800 2.363319e+28 1731461.2 0 1.7079109e+09 4.0277805e+14 2.8240193e-06 900 2.3668922e+28 870525.69 0 1.7096296e+09 3.1718257e+14 3.5915363e-06 1000 2.3654433e+28 789707.52 0 1.7085028e+09 2.5538989e+14 4.4577935e-06 Loop time of 5.11902 on 4 procs for 1000 steps with 3487 atoms 90.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.905 | 26.18 | 26.326 | 3.2 | 88.37 Neigh | 0.15352 | 0.1872 | 0.22394 | 7.6 | 0.63 Comm | 3.0374 | 3.1471 | 3.3731 | 7.5 | 10.62 Output | 0.00047588 | 0.00062978 | 0.00097752 | 0.0 | 0.00 Modify | 0.073521 | 0.081854 | 0.093222 | 2.7 | 0.28 Other | | 0.02989 | | | 0.10 Nlocal: 871.75 ave 908 max 838 min Histogram: 1 0 0 0 1 1 0 0 0 1 Nghost: 1368.25 ave 1402 max 1332 min Histogram: 1 0 0 0 1 1 0 0 0 1 Neighs: 142294 ave 159233 max 124729 min Pair | 3.1161 | 3.9019 | 4.7582 | 30.3 | 76.22 Neigh | 0.0701 | 0.080061 | 0.089326 | 3.0 | 1.56 Comm | 0.22296 | 1.0644 | 1.8357 | 57.0 | 20.79 Output | 0.00028729 | 0.00058514 | 0.0013847 | 0.0 | 0.01 Modify | 0.041605 | 0.043229 | 0.044626 | 0.6 | 0.84 Other | | 0.02887 | | | 0.56 Nlocal: 871.75 ave 947 max 799 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1011 ave 1087 max 936 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 91271.8 ave 92650 max 90045 min Histogram: 1 1 0 0 0 0 1 0 0 1 FullNghs: 302269 ave 346070 max 260820 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 Neighbor list builds = 40 Neighbor list builds = 24 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:29 Total wall time: 0:00:05 examples/peri/log.6Jul17.peri.lps.g++.1→examples/peri/log.27Nov18.peri.lps.g++.1 +23 −22 File changed and moved.Preview size limit exceeded, changes collapsed. 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examples/peptide/log.5Oct16.peptide.g++.1→examples/peptide/log.27Nov18.peptide.g++.1 +50 −44 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real Loading Loading @@ -70,7 +71,7 @@ group peptide type <= 12 run 300 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading @@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 10648 3375 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 Loading @@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Memory usage per processor = 15.5934 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 ---------------- Step 50 ----- CPU = 0.9457 (sec) ---------------- ---------------- Step 50 ----- CPU = 1.0190 (sec) ---------------- TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 Loading @@ -114,77 +120,77 @@ SHAKE stats (type/ave/delta) on step 100 14 0.96 0 18 0.957201 5.3796e-06 31 104.52 0.000502278 ---------------- Step 100 ----- CPU = 1.9163 (sec) ---------------- ---------------- Step 100 ----- CPU = 2.0505 (sec) ---------------- TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 ---------------- Step 150 ----- CPU = 2.9286 (sec) ---------------- TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 ---------------- Step 150 ----- CPU = 3.1208 (sec) ---------------- TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1829 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18698e-07 6 0.997 1.50562e-07 8 1.08 6.57498e-08 6 0.997 1.50563e-07 8 1.08 6.57499e-08 10 1.111 5.54188e-07 12 1.08 1.98839e-07 12 1.08 1.9884e-07 14 0.96 0 18 0.957201 3.59627e-06 31 104.52 0.000388335 ---------------- Step 200 ----- CPU = 3.8703 (sec) ---------------- TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 ---------------- Step 200 ----- CPU = 4.1320 (sec) ---------------- TotEng = -5308.4468 KinEng = 1100.4873 Temp = 273.5421 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3400 ---------------- Step 250 ----- CPU = 4.8652 (sec) ---------------- TotEng = -5294.1569 KinEng = 1071.0938 Temp = 266.2359 PotEng = -6365.2507 E_bond = 14.2013 E_angle = 39.1996 E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3401 ---------------- Step 250 ----- CPU = 5.2131 (sec) ---------------- TotEng = -5294.1568 KinEng = 1071.0940 Temp = 266.2360 PotEng = -6365.2508 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4590 E_coul = 26714.0040 E_long = -33908.7139 Press = -189.6059 E_coul = 26714.0039 E_long = -33908.7139 Press = -189.6057 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.79044e-06 4 1.111 3.79043e-06 6 0.997001 3.6052e-06 8 1.08 2.09369e-06 10 1.111 5.6484e-06 12 1.08 2.10677e-06 12 1.08 2.10676e-06 14 0.96 0 18 0.957202 7.72576e-06 31 104.52 0.000806204 ---------------- Step 300 ----- CPU = 5.8596 (sec) ---------------- TotEng = -5251.3637 KinEng = 1123.7718 Temp = 279.3298 PotEng = -6375.1355 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3473 E_coul = 26745.4074 E_long = -33909.0791 Press = -471.5505 Loop time of 5.85959 on 1 procs for 300 steps with 2004 atoms Performance: 8.847 ns/day, 2.713 hours/ns, 51.198 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads 18 0.957202 7.72571e-06 31 104.52 0.000806203 ---------------- Step 300 ----- CPU = 6.2919 (sec) ---------------- TotEng = -5251.3662 KinEng = 1123.7719 Temp = 279.3299 PotEng = -6375.1381 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3476 E_coul = 26745.4045 E_long = -33909.0791 Press = -471.5904 Loop time of 6.29195 on 1 procs for 300 steps with 2004 atoms Performance: 8.239 ns/day, 2.913 hours/ns, 47.680 timesteps/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6289 | 4.6289 | 4.6289 | 0.0 | 79.00 Bond | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.23 Kspace | 0.47821 | 0.47821 | 0.47821 | 0.0 | 8.16 Neigh | 0.64447 | 0.64447 | 0.64447 | 0.0 | 11.00 Comm | 0.026137 | 0.026137 | 0.026137 | 0.0 | 0.45 Output | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.00 Modify | 0.062095 | 0.062095 | 0.062095 | 0.0 | 1.06 Other | | 0.006195 | | | 0.11 Pair | 4.8228 | 4.8228 | 4.8228 | 0.0 | 76.65 Bond | 0.0094063 | 0.0094063 | 0.0094063 | 0.0 | 0.15 Kspace | 0.523 | 0.523 | 0.523 | 0.0 | 8.31 Neigh | 0.82602 | 0.82602 | 0.82602 | 0.0 | 13.13 Comm | 0.03742 | 0.03742 | 0.03742 | 0.0 | 0.59 Output | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.00 Modify | 0.068182 | 0.068182 | 0.068182 | 0.0 | 1.08 Other | | 0.00493 | | | 0.08 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11185 ave 11185 max 11185 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 708018 ave 708018 max 708018 min Neighs: 708019 ave 708019 max 708019 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 708018 Ave neighs/atom = 353.302 Total # of neighbors = 708019 Ave neighs/atom = 353.303 Ave special neighs/atom = 2.34032 Neighbor list builds = 26 Dangerous builds = 0 Total wall time: 0:00:05 Total wall time: 0:00:06
examples/peptide/log.5Oct16.peptide.g++.4→examples/peptide/log.27Nov18.peptide.g++.4 +54 −48 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real Loading Loading @@ -70,7 +71,7 @@ group peptide type <= 12 run 300 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading @@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 4312 960 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 Loading @@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Memory usage per processor = 14.8928 Mbytes Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 ---------------- Step 50 ----- CPU = 0.2741 (sec) ---------------- ---------------- Step 50 ----- CPU = 0.2858 (sec) ---------------- TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 Loading @@ -114,65 +120,65 @@ SHAKE stats (type/ave/delta) on step 100 14 0.96 0 18 0.957201 5.3796e-06 31 104.52 0.000502278 ---------------- Step 100 ----- CPU = 0.5371 (sec) ---------------- ---------------- Step 100 ----- CPU = 0.5744 (sec) ---------------- TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 ---------------- Step 150 ----- CPU = 0.8054 (sec) ---------------- TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6820 ---------------- Step 150 ----- CPU = 0.8756 (sec) ---------------- TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8826 E_bond = 17.4925 E_angle = 32.8594 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1830 E_coul = 26717.2656 E_long = -33907.2821 Press = -333.1828 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18699e-07 6 0.997 1.50563e-07 8 1.08 6.57501e-08 10 1.111 5.54188e-07 12 1.08 1.98841e-07 8 1.08 6.575e-08 10 1.111 5.54187e-07 12 1.08 1.9884e-07 14 0.96 0 18 0.957201 3.59627e-06 31 104.52 0.000388336 ---------------- Step 200 ----- CPU = 1.0652 (sec) ---------------- TotEng = -5308.4465 KinEng = 1100.4875 Temp = 273.5422 PotEng = -6408.9340 E_bond = 18.2714 E_angle = 33.3040 31 104.52 0.000388335 ---------------- Step 200 ----- CPU = 1.1602 (sec) ---------------- TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 E_coul = 26736.1321 E_long = -33902.3837 Press = -1470.3400 ---------------- Step 250 ----- CPU = 1.3409 (sec) ---------------- TotEng = -5294.1570 KinEng = 1071.0939 Temp = 266.2360 PotEng = -6365.2509 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4591 E_coul = 26714.0037 E_long = -33908.7139 Press = -189.6059 E_coul = 26736.1320 E_long = -33902.3837 Press = -1470.3400 ---------------- Step 250 ----- CPU = 1.4629 (sec) ---------------- TotEng = -5294.1567 KinEng = 1071.0938 Temp = 266.2359 PotEng = -6365.2505 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4589 E_coul = 26714.0043 E_long = -33908.7139 Press = -189.6068 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.79043e-06 6 0.997001 3.60519e-06 8 1.08 2.09368e-06 10 1.111 5.64839e-06 12 1.08 2.10676e-06 6 0.997001 3.6052e-06 8 1.08 2.09369e-06 10 1.111 5.6484e-06 12 1.08 2.10677e-06 14 0.96 0 18 0.957202 7.72573e-06 31 104.52 0.000806208 ---------------- Step 300 ----- CPU = 1.6199 (sec) ---------------- TotEng = -5251.3639 KinEng = 1123.7721 Temp = 279.3299 PotEng = -6375.1360 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3470 E_coul = 26745.4071 E_long = -33909.0790 Press = -471.5569 Loop time of 1.61992 on 4 procs for 300 steps with 2004 atoms Performance: 32.002 ns/day, 0.750 hours/ns, 185.194 timesteps/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads 18 0.957202 7.72579e-06 31 104.52 0.000806203 ---------------- Step 300 ----- CPU = 1.7662 (sec) ---------------- TotEng = -5251.3662 KinEng = 1123.7712 Temp = 279.3297 PotEng = -6375.1374 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3474 E_coul = 26745.4053 E_long = -33909.0790 Press = -471.5904 Loop time of 1.76629 on 4 procs for 300 steps with 2004 atoms Performance: 29.350 ns/day, 0.818 hours/ns, 169.847 timesteps/s 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1484 | 1.17 | 1.1865 | 1.5 | 72.23 Bond | 0.0011752 | 0.003831 | 0.0069602 | 4.0 | 0.24 Kspace | 0.16316 | 0.1798 | 0.20413 | 3.9 | 11.10 Neigh | 0.16885 | 0.16895 | 0.16902 | 0.0 | 10.43 Comm | 0.046479 | 0.047215 | 0.047759 | 0.2 | 2.91 Output | 0.00024033 | 0.00025702 | 0.00030375 | 0.2 | 0.02 Modify | 0.04556 | 0.045949 | 0.046353 | 0.2 | 2.84 Other | | 0.003923 | | | 0.24 Pair | 1.2044 | 1.2351 | 1.2721 | 2.3 | 69.92 Bond | 0.0013924 | 0.0034139 | 0.0057151 | 3.2 | 0.19 Kspace | 0.17476 | 0.21195 | 0.2407 | 5.3 | 12.00 Neigh | 0.21273 | 0.21286 | 0.21293 | 0.0 | 12.05 Comm | 0.042942 | 0.046074 | 0.047584 | 0.9 | 2.61 Output | 0.00025845 | 0.00033492 | 0.00055695 | 0.0 | 0.02 Modify | 0.049944 | 0.051619 | 0.054278 | 0.8 | 2.92 Other | | 0.004988 | | | 0.28 Nlocal: 501 ave 508 max 490 min Histogram: 1 0 0 0 0 0 1 1 0 1 Loading
examples/peri/log.6Jul17.peri.eps.g++.1→examples/peri/log.27Nov18.peri.eps.g++.1 +24 −23 Original line number Diff line number Diff line LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile Loading @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 1 by 1 by 1 MPI processor grid create_atoms 1 region target Created 3487 atoms Time spent = 0.00100374 secs pair_style peri/eps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 Loading Loading @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 50.29 | 50.29 | 50.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 900 1.3166045e+28 1911868.6 0 9.524241e+08 1.9729649e+14 3.2117896e-06 1000 1.3159578e+28 1995827.6 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 Loop time of 72.5574 on 1 procs for 1000 steps with 3487 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 100 9.7403734e+24 248692.93 0 951891.49 9.3703576e+11 5.0030006e-07 200 1.220493e+27 1011231.9 0 89123756 1.0636834e+14 5.5224782e-07 300 2.7274231e+27 4549425.2 0 2.0145358e+08 1.7250255e+14 7.6097098e-07 400 3.3665092e+27 13347641 0 2.5639011e+08 1.5828139e+14 1.0236725e-06 500 3.8995641e+27 14196430 0 2.9572238e+08 1.5145191e+14 1.2392314e-06 600 4.6668832e+27 23135807 0 3.6005775e+08 1.478168e+14 1.5195473e-06 700 1.1847301e+28 8126622 0 8.6343315e+08 2.9204301e+14 1.9524671e-06 800 1.2328889e+28 4646514.3 0 8.9472087e+08 2.2467312e+14 2.6410944e-06 900 1.2277283e+28 2668877.7 0 8.8901759e+08 1.671177e+14 3.5358262e-06 1000 1.2260912e+28 1587002.9 0 8.8675386e+08 1.29707e+14 4.5495712e-06 Loop time of 34.8143 on 1 procs for 1000 steps with 3487 atoms 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 71.779 | 71.779 | 71.779 | 0.0 | 98.93 Neigh | 0.5596 | 0.5596 | 0.5596 | 0.0 | 0.77 Comm | 0.0040631 | 0.0040631 | 0.0040631 | 0.0 | 0.01 Output | 0.00056624 | 0.00056624 | 0.00056624 | 0.0 | 0.00 Modify | 0.18403 | 0.18403 | 0.18403 | 0.0 | 0.25 Other | | 0.03016 | | | 0.04 Pair | 34.045 | 34.045 | 34.045 | 0.0 | 97.79 Neigh | 0.63254 | 0.63254 | 0.63254 | 0.0 | 1.82 Comm | 0.0025852 | 0.0025852 | 0.0025852 | 0.0 | 0.01 Output | 0.00035906 | 0.00035906 | 0.00035906 | 0.0 | 0.00 Modify | 0.11784 | 0.11784 | 0.11784 | 0.0 | 0.34 Other | | 0.01593 | | | 0.05 Nlocal: 3487 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 569177 ave 569177 max 569177 min Neighs: 546591 ave 546591 max 546591 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 Neighbor list builds = 40 Neighbor list builds = 45 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:12 Total wall time: 0:00:34
examples/peri/log.6Jul17.peri.eps.g++.4→examples/peri/log.27Nov18.peri.eps.g++.4 +29 −28 Original line number Diff line number Diff line LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile Loading @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 2 by 1 by 2 MPI processor grid create_atoms 1 region target Created 3487 atoms Time spent = 0.000587225 secs pair_style peri/eps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 Loading Loading @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 44.77 | 45.04 | 45.14 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 900 1.3166045e+28 1911869.3 0 9.524241e+08 1.9729649e+14 3.2117896e-06 1000 1.3159578e+28 1995833.9 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 Loop time of 29.6266 on 4 procs for 1000 steps with 3487 atoms 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads 100 2.3613868e+26 2297417.8 0 19345263 2.2716828e+13 5.0030006e-07 200 3.9573281e+27 28896934 0 3.1459311e+08 3.6928392e+14 5.1576607e-07 300 8.7809254e+27 38915502 0 6.7284747e+08 6.4053658e+14 6.5979263e-07 400 1.3210949e+28 35344681 0 9.8909868e+08 7.0953264e+14 8.9613355e-07 500 1.7324732e+28 21092574 0 1.2718379e+09 7.4083646e+14 1.1255254e-06 600 2.1194595e+28 11349855 0 1.5414769e+09 6.6250164e+14 1.5397467e-06 700 2.316318e+28 2515600.8 0 1.6747631e+09 5.0111859e+14 2.2246862e-06 800 2.363319e+28 1731461.2 0 1.7079109e+09 4.0277805e+14 2.8240193e-06 900 2.3668922e+28 870525.69 0 1.7096296e+09 3.1718257e+14 3.5915363e-06 1000 2.3654433e+28 789707.52 0 1.7085028e+09 2.5538989e+14 4.4577935e-06 Loop time of 5.11902 on 4 procs for 1000 steps with 3487 atoms 90.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.905 | 26.18 | 26.326 | 3.2 | 88.37 Neigh | 0.15352 | 0.1872 | 0.22394 | 7.6 | 0.63 Comm | 3.0374 | 3.1471 | 3.3731 | 7.5 | 10.62 Output | 0.00047588 | 0.00062978 | 0.00097752 | 0.0 | 0.00 Modify | 0.073521 | 0.081854 | 0.093222 | 2.7 | 0.28 Other | | 0.02989 | | | 0.10 Nlocal: 871.75 ave 908 max 838 min Histogram: 1 0 0 0 1 1 0 0 0 1 Nghost: 1368.25 ave 1402 max 1332 min Histogram: 1 0 0 0 1 1 0 0 0 1 Neighs: 142294 ave 159233 max 124729 min Pair | 3.1161 | 3.9019 | 4.7582 | 30.3 | 76.22 Neigh | 0.0701 | 0.080061 | 0.089326 | 3.0 | 1.56 Comm | 0.22296 | 1.0644 | 1.8357 | 57.0 | 20.79 Output | 0.00028729 | 0.00058514 | 0.0013847 | 0.0 | 0.01 Modify | 0.041605 | 0.043229 | 0.044626 | 0.6 | 0.84 Other | | 0.02887 | | | 0.56 Nlocal: 871.75 ave 947 max 799 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1011 ave 1087 max 936 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 91271.8 ave 92650 max 90045 min Histogram: 1 1 0 0 0 0 1 0 0 1 FullNghs: 302269 ave 346070 max 260820 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 Neighbor list builds = 40 Neighbor list builds = 24 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:29 Total wall time: 0:00:05
examples/peri/log.6Jul17.peri.lps.g++.1→examples/peri/log.27Nov18.peri.lps.g++.1 +23 −22 File changed and moved.Preview size limit exceeded, changes collapsed. Show changes
