Loading examples/USER/misc/momb/log.17Mar2017.system.g++.1 +21 −18 Original line number Diff line number Diff line Loading @@ -239,9 +239,9 @@ Per MPI rank memory allocation (min/avg/max) = 99.82 | 99.82 | 99.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10035.476 218.18376 -9817.2917 -1066.914 9 0 -10244.892 211.35072 -10033.541 -3283.8636 Loop time of 2.65996 on 1 procs for 9 steps with 18146 atoms Loop time of 2.6765 on 1 procs for 9 steps with 18146 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Loading @@ -255,14 +255,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2936 | 2.2936 | 2.2936 | 0.0 | 86.23 Bond | 0.08754 | 0.08754 | 0.08754 | 0.0 | 3.29 Kspace | 0.2664 | 0.2664 | 0.2664 | 0.0 | 10.02 Pair | 2.3191 | 2.3191 | 2.3191 | 0.0 | 86.65 Bond | 0.084626 | 0.084626 | 0.084626 | 0.0 | 3.16 Kspace | 0.2622 | 0.2622 | 0.2622 | 0.0 | 9.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041108 | 0.0041108 | 0.0041108 | 0.0 | 0.15 Comm | 0.0033448 | 0.0033448 | 0.0033448 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008299 | | | 0.31 Other | | 0.007261 | | | 0.27 Nlocal: 18146 ave 18146 max 18146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading Loading @@ -325,22 +325,22 @@ Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz 80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477 90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058 100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357 Loop time of 18.4128 on 1 procs for 100 steps with 18146 atoms Loop time of 18.5289 on 1 procs for 100 steps with 18146 atoms Performance: 0.469 ns/day, 51.147 hours/ns, 5.431 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 0.466 ns/day, 51.469 hours/ns, 5.397 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.225 | 14.225 | 14.225 | 0.0 | 77.26 Bond | 0.65464 | 0.65464 | 0.65464 | 0.0 | 3.56 Kspace | 2.22 | 2.22 | 2.22 | 0.0 | 12.06 Neigh | 1.1926 | 1.1926 | 1.1926 | 0.0 | 6.48 Comm | 0.040519 | 0.040519 | 0.040519 | 0.0 | 0.22 Output | 0.0023048 | 0.0023048 | 0.0023048 | 0.0 | 0.01 Modify | 0.058326 | 0.058326 | 0.058326 | 0.0 | 0.32 Other | | 0.01913 | | | 0.10 Pair | 14.326 | 14.326 | 14.326 | 0.0 | 77.31 Bond | 0.65294 | 0.65294 | 0.65294 | 0.0 | 3.52 Kspace | 2.2291 | 2.2291 | 2.2291 | 0.0 | 12.03 Neigh | 1.2037 | 1.2037 | 1.2037 | 0.0 | 6.50 Comm | 0.038561 | 0.038561 | 0.038561 | 0.0 | 0.21 Output | 0.0022585 | 0.0022585 | 0.0022585 | 0.0 | 0.01 Modify | 0.058746 | 0.058746 | 0.058746 | 0.0 | 0.32 Other | | 0.018 | | | 0.10 Nlocal: 18146 ave 18146 max 18146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -354,4 +354,7 @@ Ave neighs/atom = 24.3524 Ave special neighs/atom = 5.92362 Neighbor list builds = 5 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:22 examples/USER/misc/momb/log.17Mar2017.system.g++.4 +21 −18 Original line number Diff line number Diff line Loading @@ -239,9 +239,9 @@ Per MPI rank memory allocation (min/avg/max) = 21.64 | 38.62 | 61.37 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10035.476 218.18376 -9817.2917 -1066.914 9 0 -10244.892 211.35072 -10033.541 -3283.8636 Loop time of 1.5282 on 4 procs for 9 steps with 18146 atoms Loop time of 1.52429 on 4 procs for 9 steps with 18146 atoms 98.9% CPU use with 4 MPI tasks x 1 OpenMP threads 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Loading @@ -255,14 +255,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13991 | 0.61651 | 1.354 | 63.8 | 40.34 Bond | 0.00096774 | 0.021362 | 0.048298 | 13.1 | 1.40 Kspace | 0.11483 | 0.87954 | 1.3772 | 55.5 | 57.55 Pair | 0.13871 | 0.61412 | 1.3512 | 63.6 | 40.29 Bond | 0.0010097 | 0.021249 | 0.047945 | 13.0 | 1.39 Kspace | 0.11351 | 0.87771 | 1.3739 | 55.2 | 57.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038254 | 0.0055712 | 0.0068097 | 1.6 | 0.36 Comm | 0.0040638 | 0.0056078 | 0.0067704 | 1.6 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005224 | | | 0.34 Other | | 0.005606 | | | 0.37 Nlocal: 4536.5 ave 8000 max 700 min Histogram: 1 0 0 0 1 0 1 0 0 1 Loading Loading @@ -325,22 +325,22 @@ Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz 80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477 90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058 100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357 Loop time of 10.6429 on 4 procs for 100 steps with 18146 atoms Loop time of 10.6085 on 4 procs for 100 steps with 18146 atoms Performance: 0.812 ns/day, 29.564 hours/ns, 9.396 timesteps/s 98.7% CPU use with 4 MPI tasks x 1 OpenMP threads Performance: 0.814 ns/day, 29.468 hours/ns, 9.426 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 | 1.1093 | 3.9562 | 8.5073 | 153.7 | 37.17 Bond | 0.0072014 | 0.1612 | 0.36361 | 36.2 | 1.51 Kspace | 0.96559 | 5.5587 | 8.4333 | 131.1 | 52.23 Neigh | 0.70939 | 0.70989 | 0.7104 | 0.0 | 6.67 Comm | 0.057808 | 0.21244 | 0.39607 | 26.3 | 2.00 Output | 0.0013831 | 0.0014417 | 0.001529 | 0.1 | 0.01 Modify | 0.023245 | 0.028182 | 0.038124 | 3.5 | 0.26 Other | | 0.0148 | | | 0.14 Pair | 1.1362 | 3.9541 | 8.4741 | 152.5 | 37.27 Bond | 0.0070739 | 0.16051 | 0.36228 | 36.1 | 1.51 Kspace | 0.96032 | 5.5204 | 8.3734 | 130.4 | 52.04 Neigh | 0.70817 | 0.7087 | 0.70915 | 0.0 | 6.68 Comm | 0.061705 | 0.2165 | 0.40455 | 26.6 | 2.04 Output | 0.0013981 | 0.001441 | 0.0015171 | 0.1 | 0.01 Modify | 0.024801 | 0.030292 | 0.039353 | 3.1 | 0.29 Other | | 0.01646 | | | 0.16 Nlocal: 4536.5 ave 8016 max 572 min Histogram: 1 0 0 0 1 0 1 0 0 1 Loading @@ -354,4 +354,7 @@ Ave neighs/atom = 24.3524 Ave special neighs/atom = 5.92362 Neighbor list builds = 5 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:12 src/USER-MISC/pair_momb.cpp +20 −1 Original line number Diff line number Diff line Loading @@ -23,12 +23,31 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" #include "citeme.h" using namespace LAMMPS_NS; static const char cite_momb[] = "Pair style momb:\n\n" "@Article{pair_momb_2015,\n" "title = {A force field for describing the polyvinylpyrrolidone-mediated" " solution-phase synthesis of shape-selective Ag nanoparticles.},\n" "volume = {118},\n" "number = {6},\n" "url = {http://dx.doi.org/10.1021/jp412098n},\n" "doi = {10.1021/jp412098n},\n" "journal = {J. Phys. Chem. C},\n" "author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n" "year = {2014},\n" "pages = {3366--3374}\n" "}\n\n"; /* ---------------------------------------------------------------------- */ PairMomb::PairMomb(LAMMPS *lmp) : Pair(lmp) {} PairMomb::PairMomb(LAMMPS *lmp) : Pair(lmp) { if (lmp->citeme) lmp->citeme->add(cite_momb); } /* ---------------------------------------------------------------------- */ Loading Loading
examples/USER/misc/momb/log.17Mar2017.system.g++.1 +21 −18 Original line number Diff line number Diff line Loading @@ -239,9 +239,9 @@ Per MPI rank memory allocation (min/avg/max) = 99.82 | 99.82 | 99.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10035.476 218.18376 -9817.2917 -1066.914 9 0 -10244.892 211.35072 -10033.541 -3283.8636 Loop time of 2.65996 on 1 procs for 9 steps with 18146 atoms Loop time of 2.6765 on 1 procs for 9 steps with 18146 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Loading @@ -255,14 +255,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2936 | 2.2936 | 2.2936 | 0.0 | 86.23 Bond | 0.08754 | 0.08754 | 0.08754 | 0.0 | 3.29 Kspace | 0.2664 | 0.2664 | 0.2664 | 0.0 | 10.02 Pair | 2.3191 | 2.3191 | 2.3191 | 0.0 | 86.65 Bond | 0.084626 | 0.084626 | 0.084626 | 0.0 | 3.16 Kspace | 0.2622 | 0.2622 | 0.2622 | 0.0 | 9.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041108 | 0.0041108 | 0.0041108 | 0.0 | 0.15 Comm | 0.0033448 | 0.0033448 | 0.0033448 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008299 | | | 0.31 Other | | 0.007261 | | | 0.27 Nlocal: 18146 ave 18146 max 18146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading Loading @@ -325,22 +325,22 @@ Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz 80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477 90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058 100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357 Loop time of 18.4128 on 1 procs for 100 steps with 18146 atoms Loop time of 18.5289 on 1 procs for 100 steps with 18146 atoms Performance: 0.469 ns/day, 51.147 hours/ns, 5.431 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 0.466 ns/day, 51.469 hours/ns, 5.397 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.225 | 14.225 | 14.225 | 0.0 | 77.26 Bond | 0.65464 | 0.65464 | 0.65464 | 0.0 | 3.56 Kspace | 2.22 | 2.22 | 2.22 | 0.0 | 12.06 Neigh | 1.1926 | 1.1926 | 1.1926 | 0.0 | 6.48 Comm | 0.040519 | 0.040519 | 0.040519 | 0.0 | 0.22 Output | 0.0023048 | 0.0023048 | 0.0023048 | 0.0 | 0.01 Modify | 0.058326 | 0.058326 | 0.058326 | 0.0 | 0.32 Other | | 0.01913 | | | 0.10 Pair | 14.326 | 14.326 | 14.326 | 0.0 | 77.31 Bond | 0.65294 | 0.65294 | 0.65294 | 0.0 | 3.52 Kspace | 2.2291 | 2.2291 | 2.2291 | 0.0 | 12.03 Neigh | 1.2037 | 1.2037 | 1.2037 | 0.0 | 6.50 Comm | 0.038561 | 0.038561 | 0.038561 | 0.0 | 0.21 Output | 0.0022585 | 0.0022585 | 0.0022585 | 0.0 | 0.01 Modify | 0.058746 | 0.058746 | 0.058746 | 0.0 | 0.32 Other | | 0.018 | | | 0.10 Nlocal: 18146 ave 18146 max 18146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -354,4 +354,7 @@ Ave neighs/atom = 24.3524 Ave special neighs/atom = 5.92362 Neighbor list builds = 5 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:22
examples/USER/misc/momb/log.17Mar2017.system.g++.4 +21 −18 Original line number Diff line number Diff line Loading @@ -239,9 +239,9 @@ Per MPI rank memory allocation (min/avg/max) = 21.64 | 38.62 | 61.37 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10035.476 218.18376 -9817.2917 -1066.914 9 0 -10244.892 211.35072 -10033.541 -3283.8636 Loop time of 1.5282 on 4 procs for 9 steps with 18146 atoms Loop time of 1.52429 on 4 procs for 9 steps with 18146 atoms 98.9% CPU use with 4 MPI tasks x 1 OpenMP threads 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Loading @@ -255,14 +255,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13991 | 0.61651 | 1.354 | 63.8 | 40.34 Bond | 0.00096774 | 0.021362 | 0.048298 | 13.1 | 1.40 Kspace | 0.11483 | 0.87954 | 1.3772 | 55.5 | 57.55 Pair | 0.13871 | 0.61412 | 1.3512 | 63.6 | 40.29 Bond | 0.0010097 | 0.021249 | 0.047945 | 13.0 | 1.39 Kspace | 0.11351 | 0.87771 | 1.3739 | 55.2 | 57.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038254 | 0.0055712 | 0.0068097 | 1.6 | 0.36 Comm | 0.0040638 | 0.0056078 | 0.0067704 | 1.6 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005224 | | | 0.34 Other | | 0.005606 | | | 0.37 Nlocal: 4536.5 ave 8000 max 700 min Histogram: 1 0 0 0 1 0 1 0 0 1 Loading Loading @@ -325,22 +325,22 @@ Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz 80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477 90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058 100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357 Loop time of 10.6429 on 4 procs for 100 steps with 18146 atoms Loop time of 10.6085 on 4 procs for 100 steps with 18146 atoms Performance: 0.812 ns/day, 29.564 hours/ns, 9.396 timesteps/s 98.7% CPU use with 4 MPI tasks x 1 OpenMP threads Performance: 0.814 ns/day, 29.468 hours/ns, 9.426 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 | 1.1093 | 3.9562 | 8.5073 | 153.7 | 37.17 Bond | 0.0072014 | 0.1612 | 0.36361 | 36.2 | 1.51 Kspace | 0.96559 | 5.5587 | 8.4333 | 131.1 | 52.23 Neigh | 0.70939 | 0.70989 | 0.7104 | 0.0 | 6.67 Comm | 0.057808 | 0.21244 | 0.39607 | 26.3 | 2.00 Output | 0.0013831 | 0.0014417 | 0.001529 | 0.1 | 0.01 Modify | 0.023245 | 0.028182 | 0.038124 | 3.5 | 0.26 Other | | 0.0148 | | | 0.14 Pair | 1.1362 | 3.9541 | 8.4741 | 152.5 | 37.27 Bond | 0.0070739 | 0.16051 | 0.36228 | 36.1 | 1.51 Kspace | 0.96032 | 5.5204 | 8.3734 | 130.4 | 52.04 Neigh | 0.70817 | 0.7087 | 0.70915 | 0.0 | 6.68 Comm | 0.061705 | 0.2165 | 0.40455 | 26.6 | 2.04 Output | 0.0013981 | 0.001441 | 0.0015171 | 0.1 | 0.01 Modify | 0.024801 | 0.030292 | 0.039353 | 3.1 | 0.29 Other | | 0.01646 | | | 0.16 Nlocal: 4536.5 ave 8016 max 572 min Histogram: 1 0 0 0 1 0 1 0 0 1 Loading @@ -354,4 +354,7 @@ Ave neighs/atom = 24.3524 Ave special neighs/atom = 5.92362 Neighbor list builds = 5 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:12
src/USER-MISC/pair_momb.cpp +20 −1 Original line number Diff line number Diff line Loading @@ -23,12 +23,31 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" #include "citeme.h" using namespace LAMMPS_NS; static const char cite_momb[] = "Pair style momb:\n\n" "@Article{pair_momb_2015,\n" "title = {A force field for describing the polyvinylpyrrolidone-mediated" " solution-phase synthesis of shape-selective Ag nanoparticles.},\n" "volume = {118},\n" "number = {6},\n" "url = {http://dx.doi.org/10.1021/jp412098n},\n" "doi = {10.1021/jp412098n},\n" "journal = {J. Phys. Chem. C},\n" "author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n" "year = {2014},\n" "pages = {3366--3374}\n" "}\n\n"; /* ---------------------------------------------------------------------- */ PairMomb::PairMomb(LAMMPS *lmp) : Pair(lmp) {} PairMomb::PairMomb(LAMMPS *lmp) : Pair(lmp) { if (lmp->citeme) lmp->citeme->add(cite_momb); } /* ---------------------------------------------------------------------- */ Loading
