#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 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 0.97 8.26228e-13 5784 2 103.7 7.72218e-11 1928 Per MPI rank memory allocation (min/avg/max) = 10.96 | 12.41 | 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 -137.95457 138406.7 0.6276451 297.01815 27.997386 32.187726 0 0 16300.985 11236.046 -76.429471 -152471.54 -124874.32 3946.9113 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.34391e-06 5784 2 103.7 0.00010418 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.51411e-06 5784 2 103.7 9.55646e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.20803e-06 5784 2 103.7 0.000102269 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.66937e-06 5784 2 103.7 0.00011287 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.17151e-06 5784 2 103.7 9.80177e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.21257e-06 5784 2 103.7 0.000105761 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.21005e-06 5784 2 103.7 0.000104967 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.12687e-06 5784 2 103.7 0.000106467 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.21671e-06 5784 2 103.7 0.000112908 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.09594e-06 5784 2 103.7 9.56894e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.33545e-06 5784 2 103.7 0.000106849 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.20199e-06 5784 2 103.7 9.50032e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.25861e-06 5784 2 103.7 0.00010414 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.41775e-06 5784 2 103.7 0.000122935 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.13793e-06 5784 2 103.7 8.68964e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.18897e-06 5784 2 103.7 9.47629e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.30412e-06 5784 2 103.7 9.70001e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.15497e-06 5784 2 103.7 9.14404e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.19462e-06 5784 2 103.7 0.000103248 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.31558e-06 5784 2 103.7 9.15993e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.13557e-06 5784 2 103.7 0.000118107 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.18597e-06 5784 2 103.7 9.78564e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.29367e-06 5784 2 103.7 0.000101657 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.02663e-06 5784 2 103.7 9.42343e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.42098e-06 5784 2 103.7 0.000101042 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.74584e-06 5784 2 103.7 0.000141214 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.54044e-06 5784 2 103.7 0.000115475 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.49598e-06 5784 2 103.7 9.80487e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.33848e-06 5784 2 103.7 9.63241e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.21299e-06 5784 2 103.7 0.000101093 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.22477e-06 5784 2 103.7 9.8838e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.37096e-06 5784 2 103.7 0.000126296 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.31318e-06 5784 2 103.7 9.87271e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.094e-06 5784 2 103.7 9.08592e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.3259e-06 5784 2 103.7 0.000104433 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.87993e-06 5784 2 103.7 0.000166517 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.0676e-06 5784 2 103.7 9.18458e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.08032e-06 5784 2 103.7 9.09858e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.38808e-06 5784 2 103.7 0.000111631 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.23172e-06 5784 2 103.7 8.81758e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.29701e-06 5784 2 103.7 0.000101425 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 9.75216e-07 5784 2 103.7 9.31554e-05 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.14052e-06 5784 2 103.7 0.000103553 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.17497e-06 5784 2 103.7 0.00012247 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.27227e-06 5784 2 103.7 8.88804e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.52335e-06 5784 2 103.7 0.000110392 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.81772e-06 5784 2 103.7 0.000130742 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.17831e-06 5784 2 103.7 9.99299e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.28427e-06 5784 2 103.7 0.000112938 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.14432e-06 5784 2 103.7 0.000101751 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.12084e-06 5784 2 103.7 9.87225e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.21626e-06 5784 2 103.7 0.000103252 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.20363e-06 5784 2 103.7 0.000107871 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.16822e-06 5784 2 103.7 0.000100165 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.19332e-06 5784 2 103.7 9.31013e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.1625e-06 5784 2 103.7 0.000104889 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.29882e-06 5784 2 103.7 0.000113245 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.04907e-06 5784 2 103.7 9.0938e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.70482e-06 5784 2 103.7 0.000116538 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.72363e-06 5784 2 103.7 0.00012866 1928 3000000 3000000 -258.81094 138406.7 0.6276451 297.7878 31.347267 43.505609 0 0 16212.366 11149.182 -76.429471 -152486.27 -125049.87 3957.1387 Loop time of 25706.3 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.083 ns/day, 2.380 hours/ns, 116.703 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.591 | 7675.3 | 18477 |8426.9 | 29.86 Bond | 2.561 | 5.4895 | 16.423 | 159.0 | 0.02 Kspace | 3935.9 | 14790 | 22624 |6113.6 | 57.53 Neigh | 1368.7 | 1374.7 | 1381.7 | 12.1 | 5.35 Comm | 237.33 | 644.81 | 898.82 | 917.9 | 2.51 Output | 0.010975 | 0.012824 | 0.014495 | 0.9 | 0.00 Modify | 977.43 | 1164.3 | 1408.1 | 497.0 | 4.53 Other | | 51.98 | | | 0.20 Nlocal: 199.594 ave 402 max 0 min Histogram: 12 0 0 0 2 6 0 0 0 12 Nghost: 3938.12 ave 7760 max 17 min Histogram: 4 0 8 0 0 8 0 8 0 4 Neighs: 91264.5 ave 225138 max 0 min Histogram: 12 4 0 1 3 0 0 0 8 4 Total # of neighbors = 2920463 Ave neighs/atom = 457.25114 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145343 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25049777 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 3000000 2 0.97 1.72363e-06 5784 2 103.7 0.00012866 1928 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.42 | 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 3000000 3000000 -258.48332 138406.7 0.6276451 297.7878 31.347267 43.505609 0 0 16212.366 11149.182 -76.429471 -152486.27 -125049.87 3957.1387 Loop time of 7.73316e-06 on 32 procs for 0 steps with 6387 atoms 117.2% 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 | | 7.733e-06 | | |100.00 Nlocal: 199.594 ave 402 max 0 min Histogram: 12 0 0 0 2 6 0 0 0 12 Nghost: 3938.12 ave 7760 max 17 min Histogram: 4 0 8 0 0 8 0 8 0 4 Neighs: 91264.5 ave 225138 max 0 min Histogram: 12 4 0 1 3 0 0 0 8 4 Total # of neighbors = 2920463 Ave neighs/atom = 457.25114 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 14:15:07