Loading examples/dipole/log.5Oct16.dipole.g++.1→examples/dipole/log.27Nov18.dipole.g++.1 +21 −14 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj Loading @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 200 atoms Time spent = 0.00140882 secs # need both mass settings due to hybrid atom style Loading Loading @@ -46,13 +48,18 @@ thermo 500 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 13 13 2 Memory usage per processor = 4.47689 Mbytes binsize = 1.4, bins = 13 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/dipole/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair c_erot TotEng Press 0 0 -2.1909822 0 -2.1909822 -2.5750971 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899 Loading @@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press 9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949 9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561 10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978 Loop time of 1.05484 on 1 procs for 10000 steps with 200 atoms Loop time of 0.851938 on 1 procs for 10000 steps with 200 atoms Performance: 4095400.088 tau/day, 9480.093 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 5070791.481 tau/day, 11737.943 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88325 | 0.88325 | 0.88325 | 0.0 | 83.73 Neigh | 0.038596 | 0.038596 | 0.038596 | 0.0 | 3.66 Comm | 0.034257 | 0.034257 | 0.034257 | 0.0 | 3.25 Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.01 Modify | 0.083041 | 0.083041 | 0.083041 | 0.0 | 7.87 Other | | 0.01556 | | | 1.48 Pair | 0.64889 | 0.64889 | 0.64889 | 0.0 | 76.17 Neigh | 0.04038 | 0.04038 | 0.04038 | 0.0 | 4.74 Comm | 0.058003 | 0.058003 | 0.058003 | 0.0 | 6.81 Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02 Modify | 0.083454 | 0.083454 | 0.083454 | 0.0 | 9.80 Other | | 0.021 | | | 2.47 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -101,4 +108,4 @@ Total # of neighbors = 1625 Ave neighs/atom = 8.125 Neighbor list builds = 673 Dangerous builds = 0 Total wall time: 0:00:01 Total wall time: 0:00:00 examples/dipole/log.5Oct16.dipole.g++.4→examples/dipole/log.27Nov18.dipole.g++.4 +20 −13 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj Loading @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 200 atoms Time spent = 0.00139761 secs # need both mass settings due to hybrid atom style Loading Loading @@ -46,13 +48,18 @@ thermo 500 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 13 13 2 Memory usage per processor = 4.47621 Mbytes binsize = 1.4, bins = 13 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/dipole/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair c_erot TotEng Press 0 0 -2.1909822 0 -2.1909822 -2.5750971 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899 Loading @@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press 9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391 9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721 10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509 Loop time of 0.406978 on 4 procs for 10000 steps with 200 atoms Loop time of 0.396069 on 4 procs for 10000 steps with 200 atoms Performance: 10614834.981 tau/day, 24571.377 timesteps/s 99.5% CPU use with 4 MPI tasks x no OpenMP threads Performance: 10907185.759 tau/day, 25248.115 timesteps/s 96.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18518 | 0.23558 | 0.25487 | 6.0 | 57.88 Neigh | 0.0090437 | 0.011033 | 0.011971 | 1.1 | 2.71 Comm | 0.086857 | 0.10807 | 0.16262 | 9.6 | 26.56 Output | 0.00029182 | 0.00031263 | 0.00035739 | 0.1 | 0.08 Modify | 0.022396 | 0.025649 | 0.026865 | 1.2 | 6.30 Other | | 0.02633 | | | 6.47 Pair | 0.13746 | 0.17338 | 0.19067 | 5.1 | 43.77 Neigh | 0.0096052 | 0.011424 | 0.012275 | 1.0 | 2.88 Comm | 0.12394 | 0.14718 | 0.1914 | 7.1 | 37.16 Output | 0.00037861 | 0.00056618 | 0.0011225 | 0.0 | 0.14 Modify | 0.021838 | 0.024665 | 0.026625 | 1.1 | 6.23 Other | | 0.03886 | | | 9.81 Nlocal: 50 ave 53 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 3 Loading examples/dreiding/in.dreiding +22 −18 Original line number Diff line number Diff line Loading @@ -23,7 +23,7 @@ pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.93 pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4 pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 pair_modify mix arithmetic neighbor 2.0 multi neigh_modify every 2 delay 4 check yes Loading @@ -36,4 +36,8 @@ variable E_hbond equal c_hb[2] #hbond energy thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol thermo_modify line multi format float %14.6f run 0 fix 1 all nve thermo 10 run 100 examples/dreiding/log.5Oct16.dreiding.g++.1→examples/dreiding/log.27Nov18.dreiding.g++.1 +198 −0 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full boundary p p p Loading Loading @@ -43,7 +44,7 @@ pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.93 pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4 pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 pair_modify mix arithmetic neighbor 2.0 multi neigh_modify every 2 delay 4 check yes Loading @@ -56,11 +57,14 @@ variable E_hbond equal c_hb[2] #hbond energy thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol thermo_modify line multi format float %14.6f run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) fix 1 all nve thermo 10 run 100 PPPM initialization ... WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297) WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.142073 grid = 3 3 3 stencil order = 5 Loading @@ -69,34 +73,110 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 512 27 Neighbor list info ... 3 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.5 ghost atom cutoff = 13.5 binsize = 6.75 -> bins = 3 3 3 Memory usage per processor = 9.19186 Mbytes binsize = 6.75, bins = 3 3 3 3 neighbor lists, perpetual/occasional/extra = 3 0 0 (1) pair hbond/dreiding/lj, perpetual, skip from (3) attributes: full, newton on pair build: skip stencil: none bin: none (2) pair lj/cut/coul/long, perpetual, half/full from (3) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) neighbor class addition, perpetual attributes: full, newton on pair build: full/multi stencil: full/multi/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000 PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880 E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324 E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152 v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335 Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 atoms ---------------- Step 10 ----- CPU = 0.0306 (sec) ---------------- TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522 PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481 E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883 E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278 v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335 ---------------- Step 20 ----- CPU = 0.0597 (sec) ---------------- TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407 PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582 E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103 E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343 v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335 ---------------- Step 30 ----- CPU = 0.0889 (sec) ---------------- TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412 PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630 E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697 E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068 v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335 ---------------- Step 40 ----- CPU = 0.1178 (sec) ---------------- TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037 PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583 E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713 E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393 v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335 ---------------- Step 50 ----- CPU = 0.1467 (sec) ---------------- TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734 PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041 E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518 E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967 v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335 ---------------- Step 60 ----- CPU = 0.1755 (sec) ---------------- TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489 PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008 E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312 E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165 v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335 ---------------- Step 70 ----- CPU = 0.2044 (sec) ---------------- TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019 PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999 E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572 E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544 v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335 ---------------- Step 80 ----- CPU = 0.2333 (sec) ---------------- TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689 PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918 E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346 E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370 v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335 ---------------- Step 90 ----- CPU = 0.2622 (sec) ---------------- TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574 PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914 E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267 E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223 v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335 ---------------- Step 100 ----- CPU = 0.2911 (sec) ---------------- TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054 PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059 E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719 E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795 v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335 Loop time of 0.291149 on 1 procs for 100 steps with 384 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads Performance: 29.676 ns/day, 0.809 hours/ns, 343.467 timesteps/s 99.9% 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 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0.255 | 0.255 | 0.255 | 0.0 | 87.59 Bond | 0.0042725 | 0.0042725 | 0.0042725 | 0.0 | 1.47 Kspace | 0.027151 | 0.027151 | 0.027151 | 0.0 | 9.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Comm | 0.0034399 | 0.0034399 | 0.0034399 | 0.0 | 1.18 Output | 0.00025988 | 0.00025988 | 0.00025988 | 0.0 | 0.09 Modify | 0.00059223 | 0.00059223 | 0.00059223 | 0.0 | 0.20 Other | | 0.0004294 | | | 0.15 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -104,11 +184,11 @@ Nghost: 4637 ave 4637 max 4637 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101854 ave 101854 max 101854 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203708 ave 203708 max 203708 min FullNghs: 5624 ave 5624 max 5624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203708 Ave neighs/atom = 530.49 Total # of neighbors = 101854 Ave neighs/atom = 265.245 Ave special neighs/atom = 4 Neighbor list builds = 0 Dangerous builds = 0 Loading examples/dreiding/log.5Oct16.dreiding.g++.4→examples/dreiding/log.27Nov18.dreiding.g++.4 +198 −0 File changed and moved.Preview size limit exceeded, changes collapsed. Show changes Loading
examples/dipole/log.5Oct16.dipole.g++.1→examples/dipole/log.27Nov18.dipole.g++.1 +21 −14 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj Loading @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 200 atoms Time spent = 0.00140882 secs # need both mass settings due to hybrid atom style Loading Loading @@ -46,13 +48,18 @@ thermo 500 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 13 13 2 Memory usage per processor = 4.47689 Mbytes binsize = 1.4, bins = 13 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/dipole/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair c_erot TotEng Press 0 0 -2.1909822 0 -2.1909822 -2.5750971 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899 Loading @@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press 9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949 9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561 10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978 Loop time of 1.05484 on 1 procs for 10000 steps with 200 atoms Loop time of 0.851938 on 1 procs for 10000 steps with 200 atoms Performance: 4095400.088 tau/day, 9480.093 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 5070791.481 tau/day, 11737.943 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88325 | 0.88325 | 0.88325 | 0.0 | 83.73 Neigh | 0.038596 | 0.038596 | 0.038596 | 0.0 | 3.66 Comm | 0.034257 | 0.034257 | 0.034257 | 0.0 | 3.25 Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.01 Modify | 0.083041 | 0.083041 | 0.083041 | 0.0 | 7.87 Other | | 0.01556 | | | 1.48 Pair | 0.64889 | 0.64889 | 0.64889 | 0.0 | 76.17 Neigh | 0.04038 | 0.04038 | 0.04038 | 0.0 | 4.74 Comm | 0.058003 | 0.058003 | 0.058003 | 0.0 | 6.81 Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02 Modify | 0.083454 | 0.083454 | 0.083454 | 0.0 | 9.80 Other | | 0.021 | | | 2.47 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -101,4 +108,4 @@ Total # of neighbors = 1625 Ave neighs/atom = 8.125 Neighbor list builds = 673 Dangerous builds = 0 Total wall time: 0:00:01 Total wall time: 0:00:00
examples/dipole/log.5Oct16.dipole.g++.4→examples/dipole/log.27Nov18.dipole.g++.4 +20 −13 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj Loading @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 200 atoms Time spent = 0.00139761 secs # need both mass settings due to hybrid atom style Loading Loading @@ -46,13 +48,18 @@ thermo 500 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 13 13 2 Memory usage per processor = 4.47621 Mbytes binsize = 1.4, bins = 13 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/dipole/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair c_erot TotEng Press 0 0 -2.1909822 0 -2.1909822 -2.5750971 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899 Loading @@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press 9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391 9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721 10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509 Loop time of 0.406978 on 4 procs for 10000 steps with 200 atoms Loop time of 0.396069 on 4 procs for 10000 steps with 200 atoms Performance: 10614834.981 tau/day, 24571.377 timesteps/s 99.5% CPU use with 4 MPI tasks x no OpenMP threads Performance: 10907185.759 tau/day, 25248.115 timesteps/s 96.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18518 | 0.23558 | 0.25487 | 6.0 | 57.88 Neigh | 0.0090437 | 0.011033 | 0.011971 | 1.1 | 2.71 Comm | 0.086857 | 0.10807 | 0.16262 | 9.6 | 26.56 Output | 0.00029182 | 0.00031263 | 0.00035739 | 0.1 | 0.08 Modify | 0.022396 | 0.025649 | 0.026865 | 1.2 | 6.30 Other | | 0.02633 | | | 6.47 Pair | 0.13746 | 0.17338 | 0.19067 | 5.1 | 43.77 Neigh | 0.0096052 | 0.011424 | 0.012275 | 1.0 | 2.88 Comm | 0.12394 | 0.14718 | 0.1914 | 7.1 | 37.16 Output | 0.00037861 | 0.00056618 | 0.0011225 | 0.0 | 0.14 Modify | 0.021838 | 0.024665 | 0.026625 | 1.1 | 6.23 Other | | 0.03886 | | | 9.81 Nlocal: 50 ave 53 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 3 Loading
examples/dreiding/in.dreiding +22 −18 Original line number Diff line number Diff line Loading @@ -23,7 +23,7 @@ pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.93 pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4 pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 pair_modify mix arithmetic neighbor 2.0 multi neigh_modify every 2 delay 4 check yes Loading @@ -36,4 +36,8 @@ variable E_hbond equal c_hb[2] #hbond energy thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol thermo_modify line multi format float %14.6f run 0 fix 1 all nve thermo 10 run 100
examples/dreiding/log.5Oct16.dreiding.g++.1→examples/dreiding/log.27Nov18.dreiding.g++.1 +198 −0 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full boundary p p p Loading Loading @@ -43,7 +44,7 @@ pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.93 pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4 pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 pair_modify mix arithmetic neighbor 2.0 multi neigh_modify every 2 delay 4 check yes Loading @@ -56,11 +57,14 @@ variable E_hbond equal c_hb[2] #hbond energy thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol thermo_modify line multi format float %14.6f run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) fix 1 all nve thermo 10 run 100 PPPM initialization ... WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297) WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.142073 grid = 3 3 3 stencil order = 5 Loading @@ -69,34 +73,110 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 512 27 Neighbor list info ... 3 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.5 ghost atom cutoff = 13.5 binsize = 6.75 -> bins = 3 3 3 Memory usage per processor = 9.19186 Mbytes binsize = 6.75, bins = 3 3 3 3 neighbor lists, perpetual/occasional/extra = 3 0 0 (1) pair hbond/dreiding/lj, perpetual, skip from (3) attributes: full, newton on pair build: skip stencil: none bin: none (2) pair lj/cut/coul/long, perpetual, half/full from (3) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) neighbor class addition, perpetual attributes: full, newton on pair build: full/multi stencil: full/multi/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000 PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880 E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324 E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152 v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335 Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 atoms ---------------- Step 10 ----- CPU = 0.0306 (sec) ---------------- TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522 PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481 E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883 E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278 v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335 ---------------- Step 20 ----- CPU = 0.0597 (sec) ---------------- TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407 PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582 E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103 E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343 v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335 ---------------- Step 30 ----- CPU = 0.0889 (sec) ---------------- TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412 PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630 E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697 E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068 v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335 ---------------- Step 40 ----- CPU = 0.1178 (sec) ---------------- TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037 PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583 E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713 E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393 v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335 ---------------- Step 50 ----- CPU = 0.1467 (sec) ---------------- TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734 PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041 E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518 E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967 v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335 ---------------- Step 60 ----- CPU = 0.1755 (sec) ---------------- TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489 PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008 E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312 E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165 v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335 ---------------- Step 70 ----- CPU = 0.2044 (sec) ---------------- TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019 PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999 E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572 E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544 v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335 ---------------- Step 80 ----- CPU = 0.2333 (sec) ---------------- TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689 PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918 E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346 E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370 v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335 ---------------- Step 90 ----- CPU = 0.2622 (sec) ---------------- TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574 PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914 E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267 E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223 v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335 ---------------- Step 100 ----- CPU = 0.2911 (sec) ---------------- TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054 PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059 E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719 E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795 v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335 Loop time of 0.291149 on 1 procs for 100 steps with 384 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads Performance: 29.676 ns/day, 0.809 hours/ns, 343.467 timesteps/s 99.9% 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 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0.255 | 0.255 | 0.255 | 0.0 | 87.59 Bond | 0.0042725 | 0.0042725 | 0.0042725 | 0.0 | 1.47 Kspace | 0.027151 | 0.027151 | 0.027151 | 0.0 | 9.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Comm | 0.0034399 | 0.0034399 | 0.0034399 | 0.0 | 1.18 Output | 0.00025988 | 0.00025988 | 0.00025988 | 0.0 | 0.09 Modify | 0.00059223 | 0.00059223 | 0.00059223 | 0.0 | 0.20 Other | | 0.0004294 | | | 0.15 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -104,11 +184,11 @@ Nghost: 4637 ave 4637 max 4637 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101854 ave 101854 max 101854 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203708 ave 203708 max 203708 min FullNghs: 5624 ave 5624 max 5624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203708 Ave neighs/atom = 530.49 Total # of neighbors = 101854 Ave neighs/atom = 265.245 Ave special neighs/atom = 4 Neighbor list builds = 0 Dangerous builds = 0 Loading
examples/dreiding/log.5Oct16.dreiding.g++.4→examples/dreiding/log.27Nov18.dreiding.g++.4 +198 −0 File changed and moved.Preview size limit exceeded, changes collapsed. Show changes
