#------------------------------------------------------------------------------- # 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 2009 = # 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) = 0.25058007 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.003281826 estimated relative force accuracy = 9.8831215e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.34302e-13 6027 2 103.7 7.84866e-11 2009 Per MPI rank memory allocation (min/avg/max) = 11.04 | 12.55 | 13.54 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 -6.4673413 139013.56 0.61716203 301.83191 22.369986 42.49659 0 0 13351.425 31742.941 -75.986356 -144791.13 -99631.898 4096.3504 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.21552e-06 6027 2 103.7 0.000106622 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.20636e-06 6027 2 103.7 9.51553e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.43165e-06 6027 2 103.7 9.73091e-05 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.2015e-06 6027 2 103.7 0.000108123 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.55727e-06 6027 2 103.7 0.000109206 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.5634e-06 6027 2 103.7 0.00010881 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.18626e-06 6027 2 103.7 8.88081e-05 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.25149e-06 6027 2 103.7 8.47839e-05 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.53548e-06 6027 2 103.7 0.00011644 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.13794e-06 6027 2 103.7 9.29401e-05 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.12283e-06 6027 2 103.7 9.12352e-05 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.39574e-06 6027 2 103.7 0.000101472 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.48361e-06 6027 2 103.7 0.000117573 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.04277e-06 6027 2 103.7 8.98829e-05 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.22585e-06 6027 2 103.7 0.000102121 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.58502e-06 6027 2 103.7 0.000121121 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.33602e-06 6027 2 103.7 9.80473e-05 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.57038e-06 6027 2 103.7 0.000104978 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.08158e-06 6027 2 103.7 0.000104043 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.2054e-06 6027 2 103.7 0.000113892 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.30873e-06 6027 2 103.7 9.20964e-05 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.53393e-06 6027 2 103.7 0.000114203 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.79156e-06 6027 2 103.7 0.00011496 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.37338e-06 6027 2 103.7 0.000104109 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.18989e-06 6027 2 103.7 9.99768e-05 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.17224e-06 6027 2 103.7 9.65254e-05 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.21557e-06 6027 2 103.7 9.42771e-05 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.29248e-06 6027 2 103.7 0.000100417 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.42219e-06 6027 2 103.7 9.84405e-05 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.13156e-06 6027 2 103.7 0.000107209 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.28482e-06 6027 2 103.7 0.000102204 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.29227e-06 6027 2 103.7 9.17304e-05 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.25166e-06 6027 2 103.7 9.80948e-05 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.29625e-06 6027 2 103.7 9.5149e-05 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.11561e-06 6027 2 103.7 9.84092e-05 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.22599e-06 6027 2 103.7 0.000138007 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.38615e-06 6027 2 103.7 0.000126664 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.26668e-06 6027 2 103.7 0.000101293 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.36635e-06 6027 2 103.7 0.000102072 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.52077e-06 6027 2 103.7 0.000119673 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.89908e-06 6027 2 103.7 0.000142741 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.34921e-06 6027 2 103.7 0.000102824 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.05033e-06 6027 2 103.7 8.74594e-05 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.30139e-06 6027 2 103.7 9.36579e-05 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.31324e-06 6027 2 103.7 0.000109691 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.18896e-06 6027 2 103.7 8.75183e-05 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.24588e-06 6027 2 103.7 8.83132e-05 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.66096e-06 6027 2 103.7 0.000118141 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.16789e-06 6027 2 103.7 9.79766e-05 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.13656e-06 6027 2 103.7 0.000115217 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.13026e-06 6027 2 103.7 9.37069e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.18141e-06 6027 2 103.7 9.21466e-05 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.64597e-06 6027 2 103.7 0.00012753 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.10181e-06 6027 2 103.7 9.46295e-05 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.32841e-06 6027 2 103.7 9.16104e-05 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.52896e-06 6027 2 103.7 0.000115281 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.27439e-06 6027 2 103.7 9.2153e-05 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.12568e-06 6027 2 103.7 9.83933e-05 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.32692e-06 6027 2 103.7 9.96208e-05 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.70588e-06 6027 2 103.7 0.000130068 2009 3000000 3000000 -403.62294 139013.56 0.61716203 295.30135 29.594365 49.441856 0 0 13065.636 31877.913 -75.986356 -144795.92 -99773.334 4007.7201 Loop time of 26437.2 on 32 procs for 3000000 steps with 6563 atoms Performance: 9.804 ns/day, 2.448 hours/ns, 113.477 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 | 15.388 | 8027.6 | 19073 |8765.5 | 30.36 Bond | 2.5047 | 5.8059 | 14.966 | 146.6 | 0.02 Kspace | 4061.3 | 15160 | 23258 |6413.4 | 57.34 Neigh | 1323.4 | 1329.9 | 1339.6 | 14.1 | 5.03 Comm | 363.26 | 684.84 | 894.38 | 780.2 | 2.59 Output | 0.012153 | 0.013927 | 0.015523 | 0.8 | 0.00 Modify | 1019.3 | 1175.3 | 1403.2 | 445.2 | 4.45 Other | | 54.05 | | | 0.20 Nlocal: 205.094 ave 427 max 0 min Histogram: 15 1 0 0 0 0 0 0 4 12 Nghost: 4057.91 ave 7355 max 775 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 94837.3 ave 227612 max 0 min Histogram: 16 0 0 0 0 2 2 0 8 4 Total # of neighbors = 3034793 Ave neighs/atom = 462.40942 Ave special neighs/atom = 1.9037026 Neighbor list builds = 146447 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) = 0.25058007 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.003281826 estimated relative force accuracy = 9.8831215e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.70588e-06 6027 2 103.7 0.000130068 2009 Per MPI rank memory allocation (min/avg/max) = 11.04 | 12.55 | 13.54 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 -403.30205 139013.56 0.61716203 295.30135 29.594365 49.441856 0 0 13065.636 31877.913 -75.986356 -144795.92 -99773.334 4007.7201 Loop time of 7.48334e-06 on 32 procs for 0 steps with 6563 atoms 109.8% 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 | | 7.483e-06 | | |100.00 Nlocal: 205.094 ave 427 max 0 min Histogram: 15 1 0 0 0 0 0 0 4 12 Nghost: 4057.91 ave 7355 max 775 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 94837.3 ave 227612 max 0 min Histogram: 16 0 0 0 0 2 2 0 8 4 Total # of neighbors = 3034793 Ave neighs/atom = 462.40942 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 14:45:59