#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 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 500000 500000 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 file 2.4_averages.txt off 1 fix 3 movable ave/time 500 1 500 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 file 2.4_instantaneous.txt restart 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00156 0.0787194 8304 2 97.54 9.98242 2768 Per MPI rank memory allocation (min/avg/max) = 11.79 | 12.86 | 13.53 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 -392.81718 192519.71 0.63061093 428.55654 8.0494937 44.639204 0 0 26255.647 67251.146 -216.28484 -268340.03 -174780.55 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 9.71163e-07 8304 2 103.7 9.31112e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.61447e-06 8304 2 103.7 0.000106846 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.42396e-06 8304 2 103.7 0.000108029 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.24774e-06 8304 2 103.7 9.95607e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.4174e-06 8304 2 103.7 9.93052e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.28084e-06 8304 2 103.7 9.30734e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.21026e-06 8304 2 103.7 0.000103093 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1434e-06 8304 2 103.7 9.2433e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.59298e-06 8304 2 103.7 0.00010762 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.27185e-06 8304 2 103.7 0.000109568 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.38723e-06 8304 2 103.7 0.000106033 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.20277e-06 8304 2 103.7 9.56298e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.38361e-06 8304 2 103.7 0.000136373 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.22294e-06 8304 2 103.7 9.62685e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.30813e-06 8304 2 103.7 0.000100096 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.22585e-06 8304 2 103.7 9.08152e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.36818e-06 8304 2 103.7 8.59645e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.1338e-06 8304 2 103.7 0.000127305 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.6324e-06 8304 2 103.7 0.000115001 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17905e-06 8304 2 103.7 9.82999e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.34203e-06 8304 2 103.7 9.53626e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.25256e-06 8304 2 103.7 9.31933e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.1182e-06 8304 2 103.7 0.000114079 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.08848e-06 8304 2 103.7 8.91472e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.22584e-06 8304 2 103.7 9.58545e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.12623e-06 8304 2 103.7 9.35786e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.4003e-06 8304 2 103.7 9.84279e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.11158e-06 8304 2 103.7 0.000107384 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.29323e-06 8304 2 103.7 9.49242e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.32314e-06 8304 2 103.7 9.11801e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.0555e-06 8304 2 103.7 9.31003e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.08503e-06 8304 2 103.7 8.70906e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.2144e-06 8304 2 103.7 9.51682e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.5576e-06 8304 2 103.7 0.000105215 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.45112e-06 8304 2 103.7 9.54514e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.05256e-06 8304 2 103.7 9.28872e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.36138e-06 8304 2 103.7 8.79839e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.1897e-06 8304 2 103.7 0.000111218 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.16551e-06 8304 2 103.7 0.000101277 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.29102e-06 8304 2 103.7 9.72737e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.9166e-06 8304 2 103.7 0.000142112 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.13488e-06 8304 2 103.7 8.82249e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.35692e-06 8304 2 103.7 0.000101654 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.18515e-06 8304 2 103.7 9.32016e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.14984e-06 8304 2 103.7 9.3363e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.23645e-06 8304 2 103.7 0.000103786 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.16865e-06 8304 2 103.7 9.507e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.06371e-06 8304 2 103.7 9.15022e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.35416e-06 8304 2 103.7 0.000106645 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.3294e-06 8304 2 103.7 0.000108168 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.23483e-06 8304 2 103.7 8.95189e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.204e-06 8304 2 103.7 8.92607e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.20455e-06 8304 2 103.7 9.50174e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.27221e-06 8304 2 103.7 9.23305e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.19325e-06 8304 2 103.7 9.57565e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.29862e-06 8304 2 103.7 9.13371e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.55478e-06 8304 2 103.7 9.85018e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.15298e-06 8304 2 103.7 9.79017e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.11443e-06 8304 2 103.7 0.000100113 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.57643e-06 8304 2 103.7 9.07366e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.35787e-06 8304 2 103.7 9.47287e-05 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.30663e-06 8304 2 103.7 0.00010516 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.52171e-06 8304 2 103.7 9.72985e-05 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.13881e-06 8304 2 103.7 0.000101138 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.21394e-06 8304 2 103.7 9.43595e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.21483e-06 8304 2 103.7 9.98079e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.17644e-06 8304 2 103.7 9.5377e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.23141e-06 8304 2 103.7 9.46815e-05 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.15379e-06 8304 2 103.7 9.89467e-05 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.0692e-06 8304 2 103.7 9.87644e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.22544e-06 8304 2 103.7 0.00010196 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.37817e-06 8304 2 103.7 9.86885e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.69834e-06 8304 2 103.7 0.000122656 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.83632e-06 8304 2 103.7 0.000129212 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.18085e-06 8304 2 103.7 9.67378e-05 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.69713e-06 8304 2 103.7 0.000111492 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.21028e-06 8304 2 103.7 9.87162e-05 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.27788e-06 8304 2 103.7 9.83269e-05 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.15314e-06 8304 2 103.7 0.000102771 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.17784e-06 8304 2 103.7 9.10142e-05 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.27592e-06 8304 2 103.7 0.000109394 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.97962e-06 8304 2 103.7 0.000129492 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.22265e-06 8304 2 103.7 9.78049e-05 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.59139e-06 8304 2 103.7 0.000120408 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.24118e-06 8304 2 103.7 8.74147e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.19899e-06 8304 2 103.7 9.59315e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.47127e-06 8304 2 103.7 9.72723e-05 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.17364e-06 8304 2 103.7 0.000106221 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.27548e-06 8304 2 103.7 0.000104277 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.42032e-06 8304 2 103.7 0.000133859 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.17391e-06 8304 2 103.7 9.1812e-05 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.22342e-06 8304 2 103.7 9.59416e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.47058e-06 8304 2 103.7 0.00010583 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.24825e-06 8304 2 103.7 9.2549e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.32044e-06 8304 2 103.7 9.2627e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.14579e-06 8304 2 103.7 9.26323e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.9624e-06 8304 2 103.7 0.00012514 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.2586e-06 8304 2 103.7 9.99014e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.53104e-06 8304 2 103.7 9.56391e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.4108e-06 8304 2 103.7 0.000133491 2768 5000000 5000000 -533.12967 192519.71 0.63061093 295.05328 49.918988 61.077957 0 0 20776.985 86759.919 -216.28484 -268025.54 -160377.64 5568.9799 Loop time of 41121.4 on 32 procs for 5000000 steps with 9101 atoms Performance: 10.505 ns/day, 2.285 hours/ns, 121.591 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 548.23 | 10074 | 20593 |9232.5 | 24.50 Bond | 4.691 | 12.457 | 36.761 | 241.9 | 0.03 Kspace | 16037 | 26579 | 36206 |5715.1 | 64.64 Neigh | 1299 | 1308.9 | 1324.3 | 25.6 | 3.18 Comm | 680.15 | 1101.4 | 1398.4 | 818.4 | 2.68 Output | 0.016204 | 0.018263 | 0.02017 | 0.9 | 0.00 Modify | 1744.3 | 1948.1 | 2244.2 | 465.7 | 4.74 Other | | 97.38 | | | 0.24 Nlocal: 284.406 ave 572 max 0 min Histogram: 13 3 0 0 0 0 0 0 2 14 Nghost: 3148.34 ave 4762 max 1556 min Histogram: 8 8 0 0 0 0 0 0 7 9 Neighs: 74721.9 ave 160817 max 0 min Histogram: 16 0 0 0 0 0 0 0 7 9 Total # of neighbors = 2391102 Ave neighs/atom = 262.72959 Ave special neighs/atom = 1.8929788 Neighbor list builds = 249840 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.4.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) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.4108e-06 8304 2 103.7 0.000133491 2768 Per MPI rank memory allocation (min/avg/max) = 11.91 | 13.13 | 13.54 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 5000000 5000000 -532.60369 192519.71 0.63061093 295.05328 49.918988 61.077957 0 0 20776.985 86759.919 -216.28484 -268025.54 -160377.64 5568.9799 Loop time of 1.3798e-05 on 32 procs for 0 steps with 9101 atoms 102.4% 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 | | 1.38e-05 | | |100.00 Nlocal: 284.406 ave 572 max 0 min Histogram: 13 3 0 0 0 0 0 0 2 14 Nghost: 3148.34 ave 4762 max 1556 min Histogram: 8 8 0 0 0 0 0 0 7 9 Neighs: 74721.9 ave 160817 max 0 min Histogram: 16 0 0 0 0 0 0 0 7 9 Total # of neighbors = 2391102 Ave neighs/atom = 262.72959 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out