Loading examples/rigid/in.rigid.early 0 → 100644 +83 −0 Original line number Diff line number Diff line # Simple rigid body system units lj atom_style atomic pair_style lj/cut 2.5 read_data data.rigid velocity all create 100.0 4928459 # unconnected bodies group clump1 id <> 1 9 group clump2 id <> 10 18 group clump3 id <> 19 27 group clump4 id <> 28 36 group clump5 id <> 37 45 group clump6 id <> 46 54 group clump7 id <> 55 63 group clump8 id <> 64 72 group clump9 id <> 73 81 fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 & clump6 clump7 clump8 clump9 fix_modify 1 bodyforces early # 1 chain of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 36 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & # clump6 clump7 clump8 clump9 # 2 chains of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 37 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 #fix 2 all poems group clump5 clump6 clump7 clump8 clump9 neigh_modify exclude group clump1 clump1 neigh_modify exclude group clump2 clump2 neigh_modify exclude group clump3 clump3 neigh_modify exclude group clump4 clump4 neigh_modify exclude group clump5 clump5 neigh_modify exclude group clump6 clump6 neigh_modify exclude group clump7 clump7 neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump9 clump9 thermo 100 #dump 1 all atom 50 dump.rigid #dump 2 all image 100 image.*.jpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 5 #dump 3 all movie 100 movie.mpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 5 timestep 0.0001 thermo 50 run 10000 examples/rigid/in.rigid.nve.early 0 → 100644 +83 −0 Original line number Diff line number Diff line # Simple rigid body system units lj atom_style atomic pair_style lj/cut 2.5 read_data data.rigid velocity all create 100.0 4928459 # unconnected bodies group clump1 id <> 1 9 group clump2 id <> 10 18 group clump3 id <> 19 27 group clump4 id <> 28 36 group clump5 id <> 37 45 group clump6 id <> 46 54 group clump7 id <> 55 63 group clump8 id <> 64 72 group clump9 id <> 73 81 fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 & clump6 clump7 clump8 clump9 fix_modify 1 bodyforces early # 1 chain of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 36 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & # clump6 clump7 clump8 clump9 # 2 chains of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 37 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 #fix 2 all poems group clump5 clump6 clump7 clump8 clump9 neigh_modify exclude group clump1 clump1 neigh_modify exclude group clump2 clump2 neigh_modify exclude group clump3 clump3 neigh_modify exclude group clump4 clump4 neigh_modify exclude group clump5 clump5 neigh_modify exclude group clump6 clump6 neigh_modify exclude group clump7 clump7 neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump9 clump9 thermo 100 #dump 1 all atom 50 dump.rigid #dump 2 all image 100 image.*.jpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 5 #dump 3 all movie 100 movie.mpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 5 timestep 0.0001 thermo 50 run 10000 examples/rigid/log.20Apr18.rigid.atomfile.g++.1 +9 −9 Original line number Diff line number Diff line Loading @@ -309,20 +309,20 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 Loop time of 0.13941 on 1 procs for 10000 steps with 81 atoms Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms Performance: 619755.656 tau/day, 71730.979 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 615179.112 tau/day, 71201.286 timesteps/s 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010763 | 0.010763 | 0.010763 | 0.0 | 7.72 Neigh | 0.037528 | 0.037528 | 0.037528 | 0.0 | 26.92 Comm | 0.0093656 | 0.0093656 | 0.0093656 | 0.0 | 6.72 Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 1.72 Modify | 0.073635 | 0.073635 | 0.073635 | 0.0 | 52.82 Other | | 0.005718 | | | 4.10 Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37 Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06 Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58 Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70 Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01 Other | | 0.006017 | | | 4.28 Nlocal: 81 ave 81 max 81 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading examples/rigid/log.20Apr18.rigid.atomfile.g++.4 +9 −9 Original line number Diff line number Diff line Loading @@ -309,20 +309,20 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 Loop time of 0.202573 on 4 procs for 10000 steps with 81 atoms Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms Performance: 426512.281 tau/day, 49364.847 timesteps/s 97.1% CPU use with 4 MPI tasks x 1 OpenMP threads Performance: 451214.099 tau/day, 52223.854 timesteps/s 96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0024269 | 0.0037646 | 0.0050037 | 1.5 | 1.86 Neigh | 0.011164 | 0.012023 | 0.014231 | 1.2 | 5.94 Comm | 0.08759 | 0.090238 | 0.091749 | 0.5 | 44.55 Output | 0.004354 | 0.0046349 | 0.0054095 | 0.7 | 2.29 Modify | 0.080237 | 0.081892 | 0.083034 | 0.4 | 40.43 Other | | 0.01002 | | | 4.95 Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91 Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27 Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59 Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38 Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82 Other | | 0.009611 | | | 5.02 Nlocal: 20.25 ave 38 max 3 min Histogram: 1 0 1 0 0 0 1 0 0 1 Loading examples/rigid/log.20Apr18.rigid.atomvar.g++.1 +9 −9 Original line number Diff line number Diff line Loading @@ -309,20 +309,20 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 Loop time of 0.139487 on 1 procs for 10000 steps with 81 atoms Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms Performance: 619413.496 tau/day, 71691.377 timesteps/s 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 621477.474 tau/day, 71930.263 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 | 0.010553 | 0.010553 | 0.010553 | 0.0 | 7.57 Neigh | 0.036803 | 0.036803 | 0.036803 | 0.0 | 26.38 Comm | 0.0091739 | 0.0091739 | 0.0091739 | 0.0 | 6.58 Output | 0.0023518 | 0.0023518 | 0.0023518 | 0.0 | 1.69 Modify | 0.074784 | 0.074784 | 0.074784 | 0.0 | 53.61 Other | | 0.005822 | | | 4.17 Pair | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40 Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59 Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57 Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73 Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24 Other | | 0.006207 | | | 4.46 Nlocal: 81 ave 81 max 81 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading Loading
examples/rigid/in.rigid.early 0 → 100644 +83 −0 Original line number Diff line number Diff line # Simple rigid body system units lj atom_style atomic pair_style lj/cut 2.5 read_data data.rigid velocity all create 100.0 4928459 # unconnected bodies group clump1 id <> 1 9 group clump2 id <> 10 18 group clump3 id <> 19 27 group clump4 id <> 28 36 group clump5 id <> 37 45 group clump6 id <> 46 54 group clump7 id <> 55 63 group clump8 id <> 64 72 group clump9 id <> 73 81 fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 & clump6 clump7 clump8 clump9 fix_modify 1 bodyforces early # 1 chain of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 36 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & # clump6 clump7 clump8 clump9 # 2 chains of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 37 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 #fix 2 all poems group clump5 clump6 clump7 clump8 clump9 neigh_modify exclude group clump1 clump1 neigh_modify exclude group clump2 clump2 neigh_modify exclude group clump3 clump3 neigh_modify exclude group clump4 clump4 neigh_modify exclude group clump5 clump5 neigh_modify exclude group clump6 clump6 neigh_modify exclude group clump7 clump7 neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump9 clump9 thermo 100 #dump 1 all atom 50 dump.rigid #dump 2 all image 100 image.*.jpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 5 #dump 3 all movie 100 movie.mpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 5 timestep 0.0001 thermo 50 run 10000
examples/rigid/in.rigid.nve.early 0 → 100644 +83 −0 Original line number Diff line number Diff line # Simple rigid body system units lj atom_style atomic pair_style lj/cut 2.5 read_data data.rigid velocity all create 100.0 4928459 # unconnected bodies group clump1 id <> 1 9 group clump2 id <> 10 18 group clump3 id <> 19 27 group clump4 id <> 28 36 group clump5 id <> 37 45 group clump6 id <> 46 54 group clump7 id <> 55 63 group clump8 id <> 64 72 group clump9 id <> 73 81 fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 & clump6 clump7 clump8 clump9 fix_modify 1 bodyforces early # 1 chain of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 36 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & # clump6 clump7 clump8 clump9 # 2 chains of connected bodies #group clump1 id <> 1 9 #group clump2 id <> 9 18 #group clump3 id <> 18 27 #group clump4 id <> 27 36 #group clump5 id <> 37 45 #group clump6 id <> 45 54 #group clump7 id <> 54 63 #group clump8 id <> 63 72 #group clump9 id <> 72 81 #fix 1 all poems group clump1 clump2 clump3 clump4 #fix 2 all poems group clump5 clump6 clump7 clump8 clump9 neigh_modify exclude group clump1 clump1 neigh_modify exclude group clump2 clump2 neigh_modify exclude group clump3 clump3 neigh_modify exclude group clump4 clump4 neigh_modify exclude group clump5 clump5 neigh_modify exclude group clump6 clump6 neigh_modify exclude group clump7 clump7 neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump9 clump9 thermo 100 #dump 1 all atom 50 dump.rigid #dump 2 all image 100 image.*.jpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 5 #dump 3 all movie 100 movie.mpg type type & # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 5 timestep 0.0001 thermo 50 run 10000
examples/rigid/log.20Apr18.rigid.atomfile.g++.1 +9 −9 Original line number Diff line number Diff line Loading @@ -309,20 +309,20 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 Loop time of 0.13941 on 1 procs for 10000 steps with 81 atoms Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms Performance: 619755.656 tau/day, 71730.979 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 615179.112 tau/day, 71201.286 timesteps/s 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010763 | 0.010763 | 0.010763 | 0.0 | 7.72 Neigh | 0.037528 | 0.037528 | 0.037528 | 0.0 | 26.92 Comm | 0.0093656 | 0.0093656 | 0.0093656 | 0.0 | 6.72 Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 1.72 Modify | 0.073635 | 0.073635 | 0.073635 | 0.0 | 52.82 Other | | 0.005718 | | | 4.10 Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37 Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06 Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58 Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70 Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01 Other | | 0.006017 | | | 4.28 Nlocal: 81 ave 81 max 81 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading
examples/rigid/log.20Apr18.rigid.atomfile.g++.4 +9 −9 Original line number Diff line number Diff line Loading @@ -309,20 +309,20 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 Loop time of 0.202573 on 4 procs for 10000 steps with 81 atoms Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms Performance: 426512.281 tau/day, 49364.847 timesteps/s 97.1% CPU use with 4 MPI tasks x 1 OpenMP threads Performance: 451214.099 tau/day, 52223.854 timesteps/s 96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0024269 | 0.0037646 | 0.0050037 | 1.5 | 1.86 Neigh | 0.011164 | 0.012023 | 0.014231 | 1.2 | 5.94 Comm | 0.08759 | 0.090238 | 0.091749 | 0.5 | 44.55 Output | 0.004354 | 0.0046349 | 0.0054095 | 0.7 | 2.29 Modify | 0.080237 | 0.081892 | 0.083034 | 0.4 | 40.43 Other | | 0.01002 | | | 4.95 Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91 Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27 Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59 Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38 Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82 Other | | 0.009611 | | | 5.02 Nlocal: 20.25 ave 38 max 3 min Histogram: 1 0 1 0 0 0 1 0 0 1 Loading
examples/rigid/log.20Apr18.rigid.atomvar.g++.1 +9 −9 Original line number Diff line number Diff line Loading @@ -309,20 +309,20 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 Loop time of 0.139487 on 1 procs for 10000 steps with 81 atoms Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms Performance: 619413.496 tau/day, 71691.377 timesteps/s 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 621477.474 tau/day, 71930.263 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 | 0.010553 | 0.010553 | 0.010553 | 0.0 | 7.57 Neigh | 0.036803 | 0.036803 | 0.036803 | 0.0 | 26.38 Comm | 0.0091739 | 0.0091739 | 0.0091739 | 0.0 | 6.58 Output | 0.0023518 | 0.0023518 | 0.0023518 | 0.0 | 1.69 Modify | 0.074784 | 0.074784 | 0.074784 | 0.0 | 53.61 Other | | 0.005822 | | | 4.17 Pair | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40 Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59 Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57 Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73 Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24 Other | | 0.006207 | | | 4.46 Nlocal: 81 ave 81 max 81 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading
