#------------------------------------------------------------------------------- # Stage 2.6: NVT integration for 5 ns with a timestep of 1 fs # Temperature 298.15 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 8303 = # 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 298.15 298.15 100 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 v_surfacetension file 2.6_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 v_surfacetension file 2.6_instantaneous.txt restart 5000000 2.6.restart dump sci all custom 500000 2.6.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) = 0.32366646 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0035958189 estimated relative force accuracy = 1.0828702e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.79043e-13 24909 2 103.7 7.94529e-11 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.66 | 15.2 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 32.601549 292264.88 1.246085 298.64773 136.9999 186.87536 0 0 63288.258 265025.96 -1281.9531 -811973.81 -483335.71 16910.47 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 2.04892e-06 24909 2 103.7 0.000134964 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.159e-06 24909 2 103.7 9.37757e-05 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.33058e-06 24909 2 103.7 9.76985e-05 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.38116e-06 24909 2 103.7 9.8671e-05 8303 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.26073e-06 24909 2 103.7 0.000114575 8303 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.27692e-06 24909 2 103.7 0.00011107 8303 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.44694e-06 24909 2 103.7 0.000110042 8303 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.55934e-06 24909 2 103.7 0.000110489 8303 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.43505e-06 24909 2 103.7 0.000102812 8303 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.1781e-06 24909 2 103.7 0.000106283 8303 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.38096e-06 24909 2 103.7 0.000109432 8303 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21495e-06 24909 2 103.7 0.000109564 8303 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.36448e-06 24909 2 103.7 0.000101667 8303 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.4825e-06 24909 2 103.7 0.000109764 8303 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.36814e-06 24909 2 103.7 9.64935e-05 8303 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.83179e-06 24909 2 103.7 0.000110045 8303 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21413e-06 24909 2 103.7 9.54098e-05 8303 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.95751e-06 24909 2 103.7 0.00012231 8303 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.20965e-06 24909 2 103.7 0.00010552 8303 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.21653e-06 24909 2 103.7 9.85103e-05 8303 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.21164e-06 24909 2 103.7 0.000103405 8303 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.70538e-06 24909 2 103.7 0.000111454 8303 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.19225e-06 24909 2 103.7 9.32853e-05 8303 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.37508e-06 24909 2 103.7 9.77008e-05 8303 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.36273e-06 24909 2 103.7 0.000125292 8303 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.25114e-06 24909 2 103.7 0.000112264 8303 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.29153e-06 24909 2 103.7 0.000109888 8303 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.37922e-06 24909 2 103.7 0.000105304 8303 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.49907e-06 24909 2 103.7 0.000100225 8303 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.46312e-06 24909 2 103.7 0.000108805 8303 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.38786e-06 24909 2 103.7 0.000106983 8303 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.47189e-06 24909 2 103.7 0.000108913 8303 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.42528e-06 24909 2 103.7 9.88793e-05 8303 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.22042e-06 24909 2 103.7 0.000106294 8303 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.4413e-06 24909 2 103.7 9.74406e-05 8303 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.37365e-06 24909 2 103.7 9.7777e-05 8303 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.41149e-06 24909 2 103.7 0.000115423 8303 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.32547e-06 24909 2 103.7 9.63303e-05 8303 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.16471e-06 24909 2 103.7 9.81066e-05 8303 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.17087e-06 24909 2 103.7 0.000111158 8303 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.4221e-06 24909 2 103.7 9.35789e-05 8303 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.28875e-06 24909 2 103.7 0.000102905 8303 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.46759e-06 24909 2 103.7 9.9504e-05 8303 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.29651e-06 24909 2 103.7 9.49658e-05 8303 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.38817e-06 24909 2 103.7 0.000107233 8303 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.20992e-06 24909 2 103.7 0.000104909 8303 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.22526e-06 24909 2 103.7 0.000117764 8303 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.30676e-06 24909 2 103.7 9.83054e-05 8303 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.41072e-06 24909 2 103.7 0.000108791 8303 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.17782e-06 24909 2 103.7 0.000102014 8303 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.31979e-06 24909 2 103.7 9.61093e-05 8303 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.39045e-06 24909 2 103.7 0.000103601 8303 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.93318e-06 24909 2 103.7 0.000129916 8303 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.34707e-06 24909 2 103.7 0.000100649 8303 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.29573e-06 24909 2 103.7 9.96028e-05 8303 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.30477e-06 24909 2 103.7 0.000107254 8303 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.76657e-06 24909 2 103.7 0.000111206 8303 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.24469e-06 24909 2 103.7 0.00010082 8303 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.41968e-06 24909 2 103.7 9.77639e-05 8303 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.49371e-06 24909 2 103.7 9.24226e-05 8303 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.36583e-06 24909 2 103.7 0.000110714 8303 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.19548e-06 24909 2 103.7 9.41384e-05 8303 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.31603e-06 24909 2 103.7 9.86482e-05 8303 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.36105e-06 24909 2 103.7 0.000101263 8303 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.33352e-06 24909 2 103.7 0.000110762 8303 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.44325e-06 24909 2 103.7 0.00010748 8303 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.40303e-06 24909 2 103.7 0.000102716 8303 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.29644e-06 24909 2 103.7 9.66788e-05 8303 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.37995e-06 24909 2 103.7 0.000109627 8303 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.53367e-06 24909 2 103.7 0.000117164 8303 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.26176e-06 24909 2 103.7 9.55366e-05 8303 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.29145e-06 24909 2 103.7 9.37647e-05 8303 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.37965e-06 24909 2 103.7 9.36203e-05 8303 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.19638e-06 24909 2 103.7 0.000100199 8303 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.24873e-06 24909 2 103.7 0.000101377 8303 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.35516e-06 24909 2 103.7 0.000100555 8303 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.35602e-06 24909 2 103.7 0.000104594 8303 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.69693e-06 24909 2 103.7 0.000108594 8303 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.3888e-06 24909 2 103.7 9.84076e-05 8303 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.57914e-06 24909 2 103.7 0.000108548 8303 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.35747e-06 24909 2 103.7 0.000105014 8303 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.19871e-06 24909 2 103.7 9.86211e-05 8303 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.25309e-06 24909 2 103.7 0.0001052 8303 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.33104e-06 24909 2 103.7 0.000112676 8303 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.3719e-06 24909 2 103.7 0.000100624 8303 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.42765e-06 24909 2 103.7 0.000101171 8303 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.38398e-06 24909 2 103.7 0.000113349 8303 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.48355e-06 24909 2 103.7 0.000114229 8303 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.29631e-06 24909 2 103.7 9.98487e-05 8303 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.18374e-06 24909 2 103.7 0.000111804 8303 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.31756e-06 24909 2 103.7 9.50281e-05 8303 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.64026e-06 24909 2 103.7 0.000111949 8303 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.66705e-06 24909 2 103.7 0.000114957 8303 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.3657e-06 24909 2 103.7 0.000102392 8303 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.77995e-06 24909 2 103.7 0.000122189 8303 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.81153e-06 24909 2 103.7 0.000112016 8303 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.40926e-06 24909 2 103.7 9.16706e-05 8303 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.29842e-06 24909 2 103.7 9.62754e-05 8303 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.30562e-06 24909 2 103.7 9.84711e-05 8303 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.23823e-06 24909 2 103.7 0.000105869 8303 5000000 5000000 51.511184 292264.88 1.246085 297.28489 137.40876 208.49738 0 0 63620.419 264236.25 -1281.9531 -811972.54 -483769.96 16833.301 Loop time of 72138 on 32 procs for 5000000 steps with 27300 atoms Performance: 5.989 ns/day, 4.008 hours/ns, 69.312 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30663 | 31682 | 32705 | 295.7 | 43.92 Bond | 14.486 | 27.266 | 50.092 | 154.0 | 0.04 Kspace | 29908 | 30938 | 31923 | 299.7 | 42.89 Neigh | 2036.8 | 2039.5 | 2042.6 | 3.3 | 2.83 Comm | 3148.5 | 3278.7 | 3341.3 | 92.8 | 4.55 Output | 0.021515 | 0.026336 | 0.03097 | 1.8 | 0.00 Modify | 3878.6 | 3919.4 | 4017.5 | 62.0 | 5.43 Other | | 253.1 | | | 0.35 Nlocal: 853.125 ave 881 max 816 min Histogram: 1 1 2 4 3 7 4 4 4 2 Nghost: 7086.16 ave 7190 max 7023 min Histogram: 6 3 5 4 3 5 2 2 0 2 Neighs: 253529 ave 264294 max 239585 min Histogram: 1 1 3 4 4 4 5 3 3 4 Total # of neighbors = 8112934 Ave neighs/atom = 297.17707 Ave special neighs/atom = 1.892967 Neighbor list builds = 269103 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.6.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) = 0.32366646 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0035958189 estimated relative force accuracy = 1.0828702e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.23823e-06 24909 2 103.7 0.000105869 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.67 | 15.2 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 52.415061 292264.88 1.246085 297.28489 137.40876 208.49738 0 0 63620.419 264236.25 -1281.9531 -811972.54 -483769.96 16833.301 Loop time of 7.2174e-06 on 32 procs for 0 steps with 27300 atoms 109.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.217e-06 | | |100.00 Nlocal: 853.125 ave 881 max 816 min Histogram: 1 1 2 4 3 7 4 4 4 2 Nghost: 7086.16 ave 7190 max 7023 min Histogram: 6 3 5 4 3 5 2 2 0 2 Neighs: 253529 ave 264294 max 239585 min Histogram: 1 1 3 4 4 4 5 3 3 4 Total # of neighbors = 8112934 Ave neighs/atom = 297.17707 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 82:26:03