#------------------------------------------------------------------------------- # 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 2812 = # 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 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 file 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.16902e-13 8436 2 103.7 8.08029e-11 2812 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.45 | 17.64 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 -211.37391 141184.09 1.4079299 298.95645 46.592795 92.883496 0 0 31903.702 -35612.092 -312.04795 -284079.21 -287648.13 6835.8766 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.15316e-06 8436 2 103.7 9.93486e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.56485e-06 8436 2 103.7 9.61717e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.20027e-06 8436 2 103.7 9.97623e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.09828e-06 8436 2 103.7 9.08304e-05 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.27561e-06 8436 2 103.7 9.59695e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.24722e-06 8436 2 103.7 9.48723e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.21192e-06 8436 2 103.7 9.60934e-05 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.36132e-06 8436 2 103.7 0.000116069 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.2842e-06 8436 2 103.7 0.00011604 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.14223e-06 8436 2 103.7 0.000102196 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.23959e-06 8436 2 103.7 0.000106802 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.39234e-06 8436 2 103.7 9.35888e-05 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.22388e-06 8436 2 103.7 9.96524e-05 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.21349e-06 8436 2 103.7 9.42103e-05 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.13469e-06 8436 2 103.7 9.04487e-05 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.21844e-06 8436 2 103.7 0.000100388 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.24941e-06 8436 2 103.7 0.000100738 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.10409e-06 8436 2 103.7 9.04969e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.54531e-06 8436 2 103.7 0.00010963 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.29791e-06 8436 2 103.7 0.000100085 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.28649e-06 8436 2 103.7 0.00010168 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.15395e-06 8436 2 103.7 9.61597e-05 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.21755e-06 8436 2 103.7 0.000103315 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.24983e-06 8436 2 103.7 9.44468e-05 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.09785e-06 8436 2 103.7 0.000103604 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.18593e-06 8436 2 103.7 9.89815e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.14321e-06 8436 2 103.7 9.55967e-05 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.24461e-06 8436 2 103.7 0.000108131 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.1695e-06 8436 2 103.7 0.000100996 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.3945e-06 8436 2 103.7 0.000114262 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.32276e-06 8436 2 103.7 9.52439e-05 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.14925e-06 8436 2 103.7 0.000106787 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.26661e-06 8436 2 103.7 9.86521e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.4473e-06 8436 2 103.7 0.00011279 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.27738e-06 8436 2 103.7 9.34861e-05 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.23378e-06 8436 2 103.7 9.47137e-05 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.84298e-06 8436 2 103.7 0.000109601 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.047e-06 8436 2 103.7 9.79665e-05 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.31639e-06 8436 2 103.7 9.52399e-05 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.02806e-06 8436 2 103.7 8.88557e-05 2812 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.07174e-06 8436 2 103.7 9.94204e-05 2812 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.13399e-06 8436 2 103.7 0.000104257 2812 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.45282e-06 8436 2 103.7 9.4275e-05 2812 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.07073e-06 8436 2 103.7 0.000103456 2812 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.18167e-06 8436 2 103.7 9.52747e-05 2812 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.2622e-06 8436 2 103.7 0.000100914 2812 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.49805e-06 8436 2 103.7 0.00012205 2812 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.22652e-06 8436 2 103.7 9.54596e-05 2812 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.10146e-06 8436 2 103.7 8.81551e-05 2812 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.46553e-06 8436 2 103.7 0.000112757 2812 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.52566e-06 8436 2 103.7 9.61706e-05 2812 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.21705e-06 8436 2 103.7 8.98664e-05 2812 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.03277e-06 8436 2 103.7 0.000106817 2812 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.72355e-06 8436 2 103.7 0.000114461 2812 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.36991e-06 8436 2 103.7 0.000107361 2812 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.61084e-06 8436 2 103.7 0.000121713 2812 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.30595e-06 8436 2 103.7 9.17271e-05 2812 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.08655e-06 8436 2 103.7 9.78215e-05 2812 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.11046e-06 8436 2 103.7 0.000111105 2812 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.40863e-06 8436 2 103.7 0.000118938 2812 3000000 3000000 -462.61693 141184.09 1.4079299 301.37294 43.715645 78.280656 0 0 31784.297 -35475.491 -312.04795 -284078.34 -287647.54 6891.1316 Loop time of 64432.3 on 8 procs for 3000000 steps with 10808 atoms Performance: 4.023 ns/day, 5.966 hours/ns, 46.561 timesteps/s 98.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11163 | 39155 | 50753 |8189.1 | 60.77 Bond | 2.8763 | 13.989 | 26.985 | 216.3 | 0.02 Kspace | 8884.7 | 20494 | 48521 |11330.3 | 31.81 Neigh | 2672.6 | 2676.4 | 2680.8 | 5.3 | 4.15 Comm | 691.82 | 767.07 | 848.43 | 185.6 | 1.19 Output | 0.023172 | 0.026227 | 0.028959 | 1.2 | 0.00 Modify | 1184.2 | 1248.6 | 1290.2 | 107.9 | 1.94 Other | | 77.34 | | | 0.12 Nlocal: 1351 ave 1613 max 711 min Histogram: 2 0 0 0 0 0 0 0 1 5 Nghost: 11080.4 ave 13277 max 9597 min Histogram: 2 0 2 2 0 0 0 0 0 2 Neighs: 633326 ave 814413 max 177618 min Histogram: 2 0 0 0 0 0 0 0 1 5 Total # of neighbors = 5066607 Ave neighs/atom = 468.78303 Ave special neighs/atom = 1.6184308 Neighbor list builds = 149354 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.40863e-06 8436 2 103.7 0.000118938 2812 Per MPI rank memory allocation (min/avg/max) = 14.06 | 16.45 | 17.64 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 -462.09858 141184.09 1.4079299 301.37294 43.715645 78.280656 0 0 31784.297 -35475.491 -312.04795 -284078.34 -287647.54 6891.1316 Loop time of 3.08662e-06 on 8 procs for 0 steps with 10808 atoms 137.7% CPU use with 8 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 | | 3.087e-06 | | |100.00 Nlocal: 1351 ave 1613 max 711 min Histogram: 2 0 0 0 0 0 0 0 1 5 Nghost: 11080.4 ave 13277 max 9597 min Histogram: 2 0 2 2 0 0 0 0 0 2 Neighs: 633326 ave 814413 max 177618 min Histogram: 2 0 0 0 0 0 0 0 1 5 Total # of neighbors = 5066607 Ave neighs/atom = 468.78303 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out