Loading examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle→examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 +38 −26 Original line number Diff line number Diff line LAMMPS (20 Mar 2014-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading @@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... Loading Loading @@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 12.4188 Mbytes Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 ---------------- Step 200 ----- CPU = 8.7547 (sec) ---------------- ---------------- Step 200 ----- CPU = 11.2079 (sec) ---------------- TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 ---------------- Step 400 ----- CPU = 17.7479 (sec) ---------------- ---------------- Step 400 ----- CPU = 22.6137 (sec) ---------------- TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 ---------------- Step 600 ----- CPU = 26.7299 (sec) ---------------- ---------------- Step 600 ----- CPU = 33.9441 (sec) ---------------- TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 ---------------- Step 800 ----- CPU = 35.8941 (sec) ---------------- ---------------- Step 800 ----- CPU = 45.4291 (sec) ---------------- TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 ---------------- Step 1000 ----- CPU = 45.1542 (sec) ---------------- ---------------- Step 1000 ----- CPU = 56.9328 (sec) ---------------- TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 Loop time of 56.9329 on 1 procs for 1000 steps with 40140 atoms Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms 99.5% CPU use with 2 MPI tasks x 1 OpenMP threads Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s Performance: 7.588 ns/day, 3.163 hours/ns, 17.565 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timings breakdown: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27 Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14 Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34 Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49 Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00 Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19 Other | | 0.2571 | | | 0.57 Pair | 50.734 | 50.734 | 50.734 | 0.0 | 89.11 Bond | 0.94032 | 0.94032 | 0.94032 | 0.0 | 1.65 Neigh | 4.5195 | 4.5195 | 4.5195 | 0.0 | 7.94 Comm | 0.15045 | 0.15045 | 0.15045 | 0.0 | 0.26 Output | 0.00056767 | 0.00056767 | 0.00056767 | 0.0 | 0.00 Modify | 0.47228 | 0.47228 | 0.47228 | 0.0 | 0.83 Other | | 0.1154 | | | 0.20 Nlocal: 20070 ave 20100 max 20040 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 20230.5 ave 20241 max 20220 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nlocal: 40140 ave 40140 max 40140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25966 ave 25966 max 25966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.68676e+06 ave 5.68676e+06 max 5.68676e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5686756 Ave neighs/atom = 141.673 Loading @@ -113,3 +124,4 @@ Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:57 examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 0 → 100644 +127 −0 Original line number Diff line number Diff line LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real dimension 3 atom_style angle # enforce that in z-direction there is only one # processor (could be two) for optimal performance processors * * 1 # read topology and force field pair_style lj/sdk 15.0 bond_style harmonic angle_style sdk special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 2 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... 40140 velocities scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 13284 bonds reading angles ... 12177 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of special neighbors neighbor 3.0 bin neigh_modify delay 5 timestep 5.0 #dump 1 all xtc 200 pegc12e8-1.xtc #dump_modify 1 unwrap yes #dump 2 all dcd 200 pegc12e8-1.dcd unwrap #dump_modify 2 unwrap yes velocity all create 303.0 46659 mom yes rot yes dist gaussian fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 ---------------- Step 200 ----- CPU = 3.0597 (sec) ---------------- TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 ---------------- Step 400 ----- CPU = 6.2514 (sec) ---------------- TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 ---------------- Step 600 ----- CPU = 9.4073 (sec) ---------------- TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 ---------------- Step 800 ----- CPU = 12.6096 (sec) ---------------- TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 ---------------- Step 1000 ----- CPU = 15.9134 (sec) ---------------- TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 timesteps/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.325 | 13.6 | 13.755 | 4.7 | 85.46 Bond | 0.2432 | 0.25007 | 0.25671 | 1.0 | 1.57 Neigh | 1.2394 | 1.2399 | 1.2402 | 0.0 | 7.79 Comm | 0.41026 | 0.5737 | 0.85471 | 23.4 | 3.61 Output | 0.00025368 | 0.0004195 | 0.00091338 | 0.0 | 0.00 Modify | 0.17159 | 0.17316 | 0.17459 | 0.3 | 1.09 Other | | 0.0768 | | | 0.48 Nlocal: 10035 ave 10084 max 9971 min Histogram: 1 0 0 1 0 0 0 0 1 1 Nghost: 14548.8 ave 14610 max 14509 min Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min Histogram: 1 0 0 0 0 0 1 0 1 1 Total # of neighbors = 5686756 Ave neighs/atom = 141.673 Ave special neighs/atom = 1.26861 Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:16 examples/USER/cgsdk/peg-verlet/log.pegc12e8→examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 +38 −26 Original line number Diff line number Diff line LAMMPS (20 Mar 2014-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading @@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... Loading Loading @@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 12.4188 Mbytes Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 105.8245 ---------------- Step 200 ----- CPU = 8.6552 (sec) ---------------- ---------------- Step 200 ----- CPU = 11.2074 (sec) ---------------- TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441 PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608 E_coul = 0.0000 E_long = 0.0000 Press = 29.3660 ---------------- Step 400 ----- CPU = 17.5807 (sec) ---------------- ---------------- Step 400 ----- CPU = 22.6113 (sec) ---------------- TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316 PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067 E_coul = 0.0000 E_long = 0.0000 Press = 16.4419 ---------------- Step 600 ----- CPU = 28.1043 (sec) ---------------- ---------------- Step 600 ----- CPU = 34.0551 (sec) ---------------- TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478 PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435 E_coul = 0.0000 E_long = 0.0000 Press = 14.0304 ---------------- Step 800 ----- CPU = 40.5132 (sec) ---------------- ---------------- Step 800 ----- CPU = 45.5316 (sec) ---------------- TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372 PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910 E_coul = 0.0000 E_long = 0.0000 Press = -6.8312 ---------------- Step 1000 ----- CPU = 52.8166 (sec) ---------------- ---------------- Step 1000 ----- CPU = 56.9111 (sec) ---------------- TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800 PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639 E_coul = 0.0000 E_long = 0.0000 Press = 0.0980 Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms 99.6% CPU use with 2 MPI tasks x 1 OpenMP threads Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timings breakdown: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79 Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88 Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42 Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27 Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00 Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12 Other | | 0.2731 | | | 0.52 Pair | 50.775 | 50.775 | 50.775 | 0.0 | 89.22 Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55 Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94 Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26 Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00 Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83 Other | | 0.1127 | | | 0.20 Nlocal: 20070 ave 20109 max 20031 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 20234 ave 20281 max 20187 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nlocal: 40140 ave 40140 max 40140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25968 ave 25968 max 25968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5691680 Ave neighs/atom = 141.796 Loading @@ -113,3 +124,4 @@ Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:57 examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 0 → 100644 +127 −0 Original line number Diff line number Diff line LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real dimension 3 atom_style angle # enforce that in z-direction there is only one # processor (could be two) for optimal performance processors * * 1 # read topology and force field pair_style lj/sdk 15.0 bond_style harmonic angle_style harmonic special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 2 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... 40140 velocities scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 13284 bonds reading angles ... 12177 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of special neighbors neighbor 3.0 bin neigh_modify delay 5 timestep 5.0 #dump 1 all xtc 200 pegc12e8-1.xtc #dump_modify 1 unwrap yes #dump 2 all dcd 200 pegc12e8-1.dcd unwrap #dump_modify 2 unwrap yes velocity all create 303.0 46659 mom yes rot yes dist gaussian fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 105.8245 ---------------- Step 200 ----- CPU = 3.0107 (sec) ---------------- TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441 PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608 E_coul = 0.0000 E_long = 0.0000 Press = 29.3660 ---------------- Step 400 ----- CPU = 6.1324 (sec) ---------------- TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316 PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067 E_coul = 0.0000 E_long = 0.0000 Press = 16.4419 ---------------- Step 600 ----- CPU = 9.3443 (sec) ---------------- TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478 PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435 E_coul = 0.0000 E_long = 0.0000 Press = 14.0304 ---------------- Step 800 ----- CPU = 12.5388 (sec) ---------------- TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372 PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910 E_coul = 0.0000 E_long = 0.0000 Press = -6.8312 ---------------- Step 1000 ----- CPU = 15.7416 (sec) ---------------- TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800 PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639 E_coul = 0.0000 E_long = 0.0000 Press = 0.0980 Loop time of 15.7417 on 4 procs for 1000 steps with 40140 atoms Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 timesteps/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.591 | 13.612 | 13.626 | 0.4 | 86.47 Bond | 0.22508 | 0.23213 | 0.23791 | 1.0 | 1.47 Neigh | 1.2257 | 1.2261 | 1.2266 | 0.0 | 7.79 Comm | 0.39628 | 0.41769 | 0.44666 | 2.9 | 2.65 Output | 0.000247 | 0.00041109 | 0.00090098 | 0.0 | 0.00 Modify | 0.17674 | 0.17803 | 0.17952 | 0.2 | 1.13 Other | | 0.07576 | | | 0.48 Nlocal: 10035 ave 10098 max 10004 min Histogram: 2 0 1 0 0 0 0 0 0 1 Nghost: 14546.5 ave 14564 max 14503 min Histogram: 1 0 0 0 0 0 0 0 0 3 Neighs: 1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min Histogram: 1 1 0 1 0 0 0 0 0 1 Total # of neighbors = 5691680 Ave neighs/atom = 141.796 Ave special neighs/atom = 1.26861 Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:15 examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 0 → 100644 +145 −0 File added.Preview size limit exceeded, changes collapsed. 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examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle→examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 +38 −26 Original line number Diff line number Diff line LAMMPS (20 Mar 2014-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading @@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... Loading Loading @@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 12.4188 Mbytes Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 ---------------- Step 200 ----- CPU = 8.7547 (sec) ---------------- ---------------- Step 200 ----- CPU = 11.2079 (sec) ---------------- TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 ---------------- Step 400 ----- CPU = 17.7479 (sec) ---------------- ---------------- Step 400 ----- CPU = 22.6137 (sec) ---------------- TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 ---------------- Step 600 ----- CPU = 26.7299 (sec) ---------------- ---------------- Step 600 ----- CPU = 33.9441 (sec) ---------------- TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 ---------------- Step 800 ----- CPU = 35.8941 (sec) ---------------- ---------------- Step 800 ----- CPU = 45.4291 (sec) ---------------- TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 ---------------- Step 1000 ----- CPU = 45.1542 (sec) ---------------- ---------------- Step 1000 ----- CPU = 56.9328 (sec) ---------------- TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 Loop time of 56.9329 on 1 procs for 1000 steps with 40140 atoms Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms 99.5% CPU use with 2 MPI tasks x 1 OpenMP threads Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s Performance: 7.588 ns/day, 3.163 hours/ns, 17.565 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timings breakdown: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27 Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14 Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34 Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49 Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00 Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19 Other | | 0.2571 | | | 0.57 Pair | 50.734 | 50.734 | 50.734 | 0.0 | 89.11 Bond | 0.94032 | 0.94032 | 0.94032 | 0.0 | 1.65 Neigh | 4.5195 | 4.5195 | 4.5195 | 0.0 | 7.94 Comm | 0.15045 | 0.15045 | 0.15045 | 0.0 | 0.26 Output | 0.00056767 | 0.00056767 | 0.00056767 | 0.0 | 0.00 Modify | 0.47228 | 0.47228 | 0.47228 | 0.0 | 0.83 Other | | 0.1154 | | | 0.20 Nlocal: 20070 ave 20100 max 20040 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 20230.5 ave 20241 max 20220 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nlocal: 40140 ave 40140 max 40140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25966 ave 25966 max 25966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.68676e+06 ave 5.68676e+06 max 5.68676e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5686756 Ave neighs/atom = 141.673 Loading @@ -113,3 +124,4 @@ Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:57
examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 0 → 100644 +127 −0 Original line number Diff line number Diff line LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real dimension 3 atom_style angle # enforce that in z-direction there is only one # processor (could be two) for optimal performance processors * * 1 # read topology and force field pair_style lj/sdk 15.0 bond_style harmonic angle_style sdk special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 2 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... 40140 velocities scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 13284 bonds reading angles ... 12177 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of special neighbors neighbor 3.0 bin neigh_modify delay 5 timestep 5.0 #dump 1 all xtc 200 pegc12e8-1.xtc #dump_modify 1 unwrap yes #dump 2 all dcd 200 pegc12e8-1.dcd unwrap #dump_modify 2 unwrap yes velocity all create 303.0 46659 mom yes rot yes dist gaussian fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 ---------------- Step 200 ----- CPU = 3.0597 (sec) ---------------- TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 ---------------- Step 400 ----- CPU = 6.2514 (sec) ---------------- TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 ---------------- Step 600 ----- CPU = 9.4073 (sec) ---------------- TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 ---------------- Step 800 ----- CPU = 12.6096 (sec) ---------------- TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 ---------------- Step 1000 ----- CPU = 15.9134 (sec) ---------------- TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 timesteps/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.325 | 13.6 | 13.755 | 4.7 | 85.46 Bond | 0.2432 | 0.25007 | 0.25671 | 1.0 | 1.57 Neigh | 1.2394 | 1.2399 | 1.2402 | 0.0 | 7.79 Comm | 0.41026 | 0.5737 | 0.85471 | 23.4 | 3.61 Output | 0.00025368 | 0.0004195 | 0.00091338 | 0.0 | 0.00 Modify | 0.17159 | 0.17316 | 0.17459 | 0.3 | 1.09 Other | | 0.0768 | | | 0.48 Nlocal: 10035 ave 10084 max 9971 min Histogram: 1 0 0 1 0 0 0 0 1 1 Nghost: 14548.8 ave 14610 max 14509 min Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min Histogram: 1 0 0 0 0 0 1 0 1 1 Total # of neighbors = 5686756 Ave neighs/atom = 141.673 Ave special neighs/atom = 1.26861 Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:16
examples/USER/cgsdk/peg-verlet/log.pegc12e8→examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 +38 −26 Original line number Diff line number Diff line LAMMPS (20 Mar 2014-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading @@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... Loading Loading @@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 12.4188 Mbytes Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 105.8245 ---------------- Step 200 ----- CPU = 8.6552 (sec) ---------------- ---------------- Step 200 ----- CPU = 11.2074 (sec) ---------------- TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441 PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608 E_coul = 0.0000 E_long = 0.0000 Press = 29.3660 ---------------- Step 400 ----- CPU = 17.5807 (sec) ---------------- ---------------- Step 400 ----- CPU = 22.6113 (sec) ---------------- TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316 PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067 E_coul = 0.0000 E_long = 0.0000 Press = 16.4419 ---------------- Step 600 ----- CPU = 28.1043 (sec) ---------------- ---------------- Step 600 ----- CPU = 34.0551 (sec) ---------------- TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478 PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435 E_coul = 0.0000 E_long = 0.0000 Press = 14.0304 ---------------- Step 800 ----- CPU = 40.5132 (sec) ---------------- ---------------- Step 800 ----- CPU = 45.5316 (sec) ---------------- TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372 PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910 E_coul = 0.0000 E_long = 0.0000 Press = -6.8312 ---------------- Step 1000 ----- CPU = 52.8166 (sec) ---------------- ---------------- Step 1000 ----- CPU = 56.9111 (sec) ---------------- TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800 PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639 E_coul = 0.0000 E_long = 0.0000 Press = 0.0980 Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms 99.6% CPU use with 2 MPI tasks x 1 OpenMP threads Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timings breakdown: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79 Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88 Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42 Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27 Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00 Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12 Other | | 0.2731 | | | 0.52 Pair | 50.775 | 50.775 | 50.775 | 0.0 | 89.22 Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55 Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94 Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26 Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00 Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83 Other | | 0.1127 | | | 0.20 Nlocal: 20070 ave 20109 max 20031 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 20234 ave 20281 max 20187 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nlocal: 40140 ave 40140 max 40140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25968 ave 25968 max 25968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5691680 Ave neighs/atom = 141.796 Loading @@ -113,3 +124,4 @@ Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:57
examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 0 → 100644 +127 −0 Original line number Diff line number Diff line LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real dimension 3 atom_style angle # enforce that in z-direction there is only one # processor (could be two) for optimal performance processors * * 1 # read topology and force field pair_style lj/sdk 15.0 bond_style harmonic angle_style harmonic special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 2 by 2 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... 40140 velocities scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 13284 bonds reading angles ... 12177 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of special neighbors neighbor 3.0 bin neigh_modify delay 5 timestep 5.0 #dump 1 all xtc 200 pegc12e8-1.xtc #dump_modify 1 unwrap yes #dump 2 all dcd 200 pegc12e8-1.dcd unwrap #dump_modify 2 unwrap yes velocity all create 303.0 46659 mom yes rot yes dist gaussian fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 105.8245 ---------------- Step 200 ----- CPU = 3.0107 (sec) ---------------- TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441 PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608 E_coul = 0.0000 E_long = 0.0000 Press = 29.3660 ---------------- Step 400 ----- CPU = 6.1324 (sec) ---------------- TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316 PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067 E_coul = 0.0000 E_long = 0.0000 Press = 16.4419 ---------------- Step 600 ----- CPU = 9.3443 (sec) ---------------- TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478 PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435 E_coul = 0.0000 E_long = 0.0000 Press = 14.0304 ---------------- Step 800 ----- CPU = 12.5388 (sec) ---------------- TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372 PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910 E_coul = 0.0000 E_long = 0.0000 Press = -6.8312 ---------------- Step 1000 ----- CPU = 15.7416 (sec) ---------------- TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800 PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639 E_coul = 0.0000 E_long = 0.0000 Press = 0.0980 Loop time of 15.7417 on 4 procs for 1000 steps with 40140 atoms Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 timesteps/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.591 | 13.612 | 13.626 | 0.4 | 86.47 Bond | 0.22508 | 0.23213 | 0.23791 | 1.0 | 1.47 Neigh | 1.2257 | 1.2261 | 1.2266 | 0.0 | 7.79 Comm | 0.39628 | 0.41769 | 0.44666 | 2.9 | 2.65 Output | 0.000247 | 0.00041109 | 0.00090098 | 0.0 | 0.00 Modify | 0.17674 | 0.17803 | 0.17952 | 0.2 | 1.13 Other | | 0.07576 | | | 0.48 Nlocal: 10035 ave 10098 max 10004 min Histogram: 2 0 1 0 0 0 0 0 0 1 Nghost: 14546.5 ave 14564 max 14503 min Histogram: 1 0 0 0 0 0 0 0 0 3 Neighs: 1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min Histogram: 1 1 0 1 0 0 0 0 0 1 Total # of neighbors = 5691680 Ave neighs/atom = 141.796 Ave special neighs/atom = 1.26861 Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart Total wall time: 0:00:15
examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 0 → 100644 +145 −0 File added.Preview size limit exceeded, changes collapsed. Show changes
