#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 1 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # of frozen angles find clusters CPU = 0.001 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 100000 100000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension file 2.5_averages.txt off 1 fix 3 movable ave/time 100 1 100 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension file 2.5_instantaneous.txt restart 1000000 2.5.restart dump sci all custom 100000 2.5.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32360719 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032437318 estimated relative force accuracy = 9.768402e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.03073e-13 8304 2 103.7 7.91687e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.55 | 13.04 | 13.3 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 -406.38622 120592.96 1.006734 303.42795 37.951939 60.352827 0 0 21214.213 88469.32 -345.28628 -270630.28 -160848.45 5727.0476 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.13507e-06 8304 2 103.7 0.000132483 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.10002e-06 8304 2 103.7 0.000101952 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.30006e-06 8304 2 103.7 9.67536e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.29746e-06 8304 2 103.7 0.000102053 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.41922e-06 8304 2 103.7 0.000103867 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.08719e-06 8304 2 103.7 8.75445e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.9722e-06 8304 2 103.7 0.000120743 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.27851e-06 8304 2 103.7 0.000121115 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.17257e-06 8304 2 103.7 9.28088e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.13264e-06 8304 2 103.7 9.13413e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.21219e-06 8304 2 103.7 9.57724e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.17603e-06 8304 2 103.7 8.86931e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.20066e-06 8304 2 103.7 9.32643e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.17885e-06 8304 2 103.7 9.6708e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.26268e-06 8304 2 103.7 9.6589e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.21803e-06 8304 2 103.7 0.000109047 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.16721e-06 8304 2 103.7 9.63451e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.03663e-06 8304 2 103.7 9.11941e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.13e-06 8304 2 103.7 0.000138895 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.24481e-06 8304 2 103.7 9.39521e-05 2768 1000000 1000000 -878.64063 120592.96 1.006734 303.96246 52.213622 64.652174 0 0 20821.498 89007.492 -345.28628 -270627.25 -160681.39 5737.1361 Loop time of 5811.89 on 32 procs for 1000000 steps with 9101 atoms Performance: 14.866 ns/day, 1.614 hours/ns, 172.061 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 600.34 | 2084.3 | 2726.8 |1799.1 | 35.86 Bond | 1.0451 | 2.5548 | 4.7472 | 72.1 | 0.04 Kspace | 2219.6 | 2868.7 | 4358.4 |1541.1 | 49.36 Neigh | 169.61 | 170.45 | 171.48 | 4.9 | 2.93 Comm | 238.38 | 298.96 | 325.78 | 196.0 | 5.14 Output | 0.010006 | 0.012269 | 0.014375 | 1.2 | 0.00 Modify | 348.42 | 368.9 | 419.96 | 151.0 | 6.35 Other | | 18 | | | 0.31 Nlocal: 284.406 ave 367 max 73 min Histogram: 2 5 1 0 0 0 0 0 6 18 Nghost: 4151.84 ave 5094 max 3588 min Histogram: 8 2 14 0 0 0 0 0 0 8 Neighs: 76770.5 ave 101977 max 15132 min Histogram: 6 2 0 0 0 0 0 0 9 15 Total # of neighbors = 2456656 Ave neighs/atom = 269.93253 Ave special neighs/atom = 1.8929788 Neighbor list builds = 49760 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.5.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32360719 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032437318 estimated relative force accuracy = 9.768402e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.24481e-06 8304 2 103.7 9.39521e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.55 | 13.05 | 13.3 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 1000000 1000000 -877.93043 120592.96 1.006734 303.96246 52.213622 64.652174 0 0 20821.498 89007.492 -345.28628 -270627.25 -160681.39 5737.1361 Loop time of 8.78934e-06 on 32 procs for 0 steps with 9101 atoms 115.2% CPU use with 32 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 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 | | 8.789e-06 | | |100.00 Nlocal: 284.406 ave 367 max 73 min Histogram: 2 5 1 0 0 0 0 0 6 18 Nghost: 4151.84 ave 5094 max 3588 min Histogram: 8 2 14 0 0 0 0 0 0 8 Neighs: 76770.5 ave 101977 max 15132 min Histogram: 6 2 0 0 0 0 0 0 9 15 Total # of neighbors = 2456656 Ave neighs/atom = 269.93253 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 4:51:27