#------------------------------------------------------------------------------- # 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 1928 = # 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.999449 0.580386 5784 2 97.755 14.349 1928 Per MPI rank memory allocation (min/avg/max) = 10.93 | 12.3 | 13.51 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 -1704.8527 138406.7 0.6276451 427.16581 7.2228442 18.819759 0 0 17750.962 1686.0181 -76.429471 -152374.05 -132911.02 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.31817e-06 5784 2 103.7 0.000107738 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.36661e-06 5784 2 103.7 0.00012489 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.36426e-06 5784 2 103.7 9.86601e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.10841e-06 5784 2 103.7 9.74168e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.0749e-06 5784 2 103.7 9.48521e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.41853e-06 5784 2 103.7 0.00010815 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.11798e-06 5784 2 103.7 9.83249e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.16399e-06 5784 2 103.7 9.49998e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.33832e-06 5784 2 103.7 9.75171e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15721e-06 5784 2 103.7 9.48338e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.12695e-06 5784 2 103.7 9.64817e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.22468e-06 5784 2 103.7 9.96617e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.06358e-06 5784 2 103.7 8.99572e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20915e-06 5784 2 103.7 9.66436e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.41787e-06 5784 2 103.7 9.69278e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.29033e-06 5784 2 103.7 0.000113537 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.04101e-06 5784 2 103.7 9.86992e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.30453e-06 5784 2 103.7 0.000106087 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.30316e-06 5784 2 103.7 0.000100905 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.2435e-06 5784 2 103.7 9.41745e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.11753e-06 5784 2 103.7 9.22294e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.07998e-06 5784 2 103.7 9.71419e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.28526e-06 5784 2 103.7 0.000113469 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.36623e-06 5784 2 103.7 8.95048e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.23625e-06 5784 2 103.7 9.08929e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.22462e-06 5784 2 103.7 9.58211e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.68276e-06 5784 2 103.7 0.000103819 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.43562e-06 5784 2 103.7 0.000131193 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.39639e-06 5784 2 103.7 0.000110646 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.16925e-06 5784 2 103.7 0.000103343 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.54216e-06 5784 2 103.7 0.000109014 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.31167e-06 5784 2 103.7 9.31987e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.18642e-06 5784 2 103.7 0.000105768 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.36103e-06 5784 2 103.7 9.92297e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.25118e-06 5784 2 103.7 9.76006e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10386e-06 5784 2 103.7 9.41369e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.77635e-06 5784 2 103.7 0.000160612 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.07672e-06 5784 2 103.7 8.91168e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.2053e-06 5784 2 103.7 9.25589e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.13196e-06 5784 2 103.7 9.85645e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.10316e-06 5784 2 103.7 0.000103694 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.75767e-06 5784 2 103.7 0.000127183 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.10763e-06 5784 2 103.7 8.59543e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.16515e-06 5784 2 103.7 0.000105522 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.02864e-06 5784 2 103.7 8.59137e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.17256e-06 5784 2 103.7 9.54413e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.29674e-06 5784 2 103.7 9.76445e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.36672e-06 5784 2 103.7 0.000109577 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.42269e-06 5784 2 103.7 0.000110237 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.20314e-06 5784 2 103.7 9.4914e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.13511e-06 5784 2 103.7 0.000101109 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.19337e-06 5784 2 103.7 0.000102678 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.24889e-06 5784 2 103.7 0.000103606 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.27842e-06 5784 2 103.7 0.000100122 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.38759e-06 5784 2 103.7 8.8672e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.15481e-06 5784 2 103.7 9.99451e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.07601e-06 5784 2 103.7 9.17633e-05 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.54222e-06 5784 2 103.7 0.000112156 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.60097e-06 5784 2 103.7 0.000135819 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.13581e-06 5784 2 103.7 0.000107961 1928 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.0698e-06 5784 2 103.7 8.82431e-05 1928 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.26962e-06 5784 2 103.7 8.90172e-05 1928 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.18987e-06 5784 2 103.7 9.36189e-05 1928 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.46323e-06 5784 2 103.7 0.000119371 1928 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.30384e-06 5784 2 103.7 0.00014663 1928 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.12013e-06 5784 2 103.7 9.57015e-05 1928 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.05703e-06 5784 2 103.7 9.52172e-05 1928 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.15845e-06 5784 2 103.7 9.03636e-05 1928 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.72017e-06 5784 2 103.7 0.000142025 1928 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.44811e-06 5784 2 103.7 0.000123625 1928 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.34793e-06 5784 2 103.7 9.35368e-05 1928 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.06549e-06 5784 2 103.7 8.61765e-05 1928 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.18385e-06 5784 2 103.7 9.38315e-05 1928 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.53419e-06 5784 2 103.7 0.000112559 1928 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.25982e-06 5784 2 103.7 0.000102856 1928 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.31726e-06 5784 2 103.7 0.000100033 1928 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.41786e-06 5784 2 103.7 0.000104097 1928 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.15646e-06 5784 2 103.7 0.000102535 1928 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.17635e-06 5784 2 103.7 0.00010304 1928 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.0409e-06 5784 2 103.7 0.000109249 1928 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.10607e-06 5784 2 103.7 8.82717e-05 1928 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.417e-06 5784 2 103.7 0.000103159 1928 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.02668e-06 5784 2 103.7 9.47948e-05 1928 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.13876e-06 5784 2 103.7 9.39448e-05 1928 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.52783e-06 5784 2 103.7 9.89641e-05 1928 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.20644e-06 5784 2 103.7 9.19724e-05 1928 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.0516e-06 5784 2 103.7 9.17153e-05 1928 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.10638e-06 5784 2 103.7 9.26951e-05 1928 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.28525e-06 5784 2 103.7 9.95498e-05 1928 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.32515e-06 5784 2 103.7 9.80855e-05 1928 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.24845e-06 5784 2 103.7 9.97427e-05 1928 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.03573e-06 5784 2 103.7 9.25193e-05 1928 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.15649e-06 5784 2 103.7 9.37732e-05 1928 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.11549e-06 5784 2 103.7 8.80572e-05 1928 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.40166e-06 5784 2 103.7 9.68477e-05 1928 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.31051e-06 5784 2 103.7 9.14158e-05 1928 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.13312e-06 5784 2 103.7 9.38762e-05 1928 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.2749e-06 5784 2 103.7 0.000101498 1928 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.16523e-06 5784 2 103.7 9.01502e-05 1928 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.15217e-06 5784 2 103.7 0.000109329 1928 5000000 5000000 -338.57958 138406.7 0.6276451 296.67718 29.773861 41.191761 0 0 16247.018 11137.644 -76.429471 -152455.46 -124999.83 3942.3802 Loop time of 42512.4 on 32 procs for 5000000 steps with 6387 atoms Performance: 10.162 ns/day, 2.362 hours/ns, 117.613 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.82 | 12851 | 30491 |11317.2 | 30.23 Bond | 4.3892 | 9.6516 | 23.183 | 170.4 | 0.02 Kspace | 6821.1 | 24548 | 37530 |8231.6 | 57.74 Neigh | 2045.8 | 2055.7 | 2071.3 | 18.5 | 4.84 Comm | 554.06 | 1092.6 | 1439 |1007.4 | 2.57 Output | 0.012665 | 0.014355 | 0.015804 | 0.8 | 0.00 Modify | 1603.6 | 1870.4 | 2243.1 | 582.1 | 4.40 Other | | 84.76 | | | 0.20 Nlocal: 199.594 ave 402 max 0 min Histogram: 14 2 0 0 0 0 0 0 1 15 Nghost: 3946.88 ave 7271 max 562 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 91262.3 ave 219617 max 0 min Histogram: 16 0 0 0 0 1 3 1 7 4 Total # of neighbors = 2920393 Ave neighs/atom = 457.24018 Ave special neighs/atom = 1.8738062 Neighbor list builds = 241773 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.15217e-06 5784 2 103.7 0.000109329 1928 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.55 | 13.5 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 -338.05789 138406.7 0.6276451 296.67718 29.773861 41.191761 0 0 16247.018 11137.644 -76.429471 -152455.46 -124999.83 3942.3802 Loop time of 8.49662e-06 on 32 procs for 0 steps with 6387 atoms 109.6% 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 | | 8.497e-06 | | |100.00 Nlocal: 199.594 ave 402 max 0 min Histogram: 14 2 0 0 0 0 0 0 1 15 Nghost: 3946.88 ave 7271 max 562 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 91262.3 ave 219617 max 0 min Histogram: 16 0 0 0 0 1 3 1 7 4 Total # of neighbors = 2920393 Ave neighs/atom = 457.24018 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out