#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 9.52793e-13 6000 1 103.7 8.22808e-11 2000 Per MPI rank memory allocation (min/avg/max) = 8.324 | 9.602 | 10.26 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 -96.76961 119078.03 0.50244692 295.37591 0 0 0 0 5036.3999 96267.866 -89.819258 -122205.7 -20901.434 3520.9575 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.46139e-06 6000 1 103.7 0.000103146 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 2.1926e-06 6000 1 103.7 0.000164455 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.36137e-06 6000 1 103.7 0.000102074 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.14225e-06 6000 1 103.7 9.74416e-05 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.22553e-06 6000 1 103.7 9.67326e-05 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.17359e-06 6000 1 103.7 0.000102713 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.26013e-06 6000 1 103.7 0.000111252 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.23432e-06 6000 1 103.7 9.62705e-05 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.25581e-06 6000 1 103.7 0.000104315 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.10336e-06 6000 1 103.7 9.55114e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.28142e-06 6000 1 103.7 9.50839e-05 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.96068e-06 6000 1 103.7 0.000137271 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.31079e-06 6000 1 103.7 0.000107939 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.29895e-06 6000 1 103.7 0.000119359 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.2824e-06 6000 1 103.7 0.000113046 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.58279e-06 6000 1 103.7 0.000126447 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.34964e-06 6000 1 103.7 0.000109969 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.14931e-06 6000 1 103.7 9.03273e-05 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.4505e-06 6000 1 103.7 0.000118073 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.26823e-06 6000 1 103.7 9.45842e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.13741e-06 6000 1 103.7 9.29437e-05 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.55196e-06 6000 1 103.7 0.00010406 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.01403e-06 6000 1 103.7 0.000100515 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.24935e-06 6000 1 103.7 0.000111527 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.23059e-06 6000 1 103.7 8.78107e-05 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.18939e-06 6000 1 103.7 9.17583e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.33773e-06 6000 1 103.7 9.90691e-05 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.4827e-06 6000 1 103.7 0.000127839 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.77389e-06 6000 1 103.7 0.000144628 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.33586e-06 6000 1 103.7 9.97768e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.17411e-06 6000 1 103.7 9.34783e-05 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.14785e-06 6000 1 103.7 0.000103166 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.10792e-06 6000 1 103.7 0.000103084 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.12924e-06 6000 1 103.7 8.99836e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.63609e-06 6000 1 103.7 0.000132006 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.02072e-06 6000 1 103.7 9.76674e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.71462e-06 6000 1 103.7 0.000139297 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.23374e-06 6000 1 103.7 9.51996e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.52905e-06 6000 1 103.7 0.000111863 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.27142e-06 6000 1 103.7 0.000102916 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.29526e-06 6000 1 103.7 0.000101663 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.3135e-06 6000 1 103.7 9.10851e-05 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.74451e-06 6000 1 103.7 0.000152869 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.81328e-06 6000 1 103.7 0.000122246 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.67451e-06 6000 1 103.7 0.000117725 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.58414e-06 6000 1 103.7 0.000130764 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.20573e-06 6000 1 103.7 9.45233e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.47346e-06 6000 1 103.7 0.000128107 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.13253e-06 6000 1 103.7 0.000100003 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.38071e-06 6000 1 103.7 9.17527e-05 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.10132e-06 6000 1 103.7 8.89913e-05 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.29754e-06 6000 1 103.7 9.55223e-05 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.84876e-06 6000 1 103.7 0.000147116 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.97562e-06 6000 1 103.7 0.000142496 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.14992e-06 6000 1 103.7 9.27487e-05 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.13325e-06 6000 1 103.7 8.63945e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.17636e-06 6000 1 103.7 0.000105984 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.27489e-06 6000 1 103.7 0.000113782 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.39124e-06 6000 1 103.7 9.56189e-05 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.21183e-06 6000 1 103.7 0.000118257 2000 3000000 3000000 -289.97081 119078.03 0.50244692 298.35535 0 0 0 0 5002.2482 96013.892 -89.819258 -122205.2 -21189.058 3556.4731 Loop time of 17204 on 32 procs for 3000000 steps with 6000 atoms Performance: 15.066 ns/day, 1.593 hours/ns, 174.378 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3901 | 4922.9 | 10429 |6809.5 | 28.61 Bond | 2.1445 | 3.1664 | 4.9335 | 25.5 | 0.02 Kspace | 4694 | 10290 | 15418 |4789.7 | 59.81 Neigh | 556.87 | 567.49 | 600.58 | 58.0 | 3.30 Comm | 15.954 | 430.58 | 648.89 |1158.9 | 2.50 Output | 0.011031 | 0.012672 | 0.014069 | 0.8 | 0.00 Modify | 817.98 | 940.35 | 1115.5 | 406.3 | 5.47 Other | | 49.95 | | | 0.29 Nlocal: 187.5 ave 379 max 0 min Histogram: 12 4 0 0 0 0 0 0 1 15 Nghost: 2899.97 ave 5749 max 0 min Histogram: 8 0 1 7 0 0 4 4 0 8 Neighs: 61896.2 ave 134766 max 0 min Histogram: 16 0 0 0 0 0 0 1 5 10 Total # of neighbors = 1980680 Ave neighs/atom = 330.11333 Ave special neighs/atom = 2 Neighbor list builds = 148544 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) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.21183e-06 6000 1 103.7 0.000118257 2000 Per MPI rank memory allocation (min/avg/max) = 8.337 | 9.61 | 10.26 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 -289.54477 119078.03 0.50244692 298.35535 0 0 0 0 5002.2482 96013.892 -89.819258 -122205.2 -21189.058 3556.4731 Loop time of 8.28891e-06 on 32 procs for 0 steps with 6000 atoms 113.1% 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 | | 8.289e-06 | | |100.00 Nlocal: 187.5 ave 379 max 0 min Histogram: 12 4 0 0 0 0 0 0 1 15 Nghost: 2899.97 ave 5749 max 0 min Histogram: 8 0 1 7 0 0 4 4 0 8 Neighs: 61896.2 ave 134766 max 0 min Histogram: 16 0 0 0 0 0 0 1 5 10 Total # of neighbors = 1980680 Ave neighs/atom = 330.11333 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 7:58:04