#------------------------------------------------------------------------------- # 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) = 0.25031202 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033302856 estimated relative force accuracy = 1.0029056e-05 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 5.93747e-13 6027 2 103.7 7.34701e-11 2009 Per MPI rank memory allocation (min/avg/max) = 10.96 | 12.45 | 13.55 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 -371.24485 140334.36 0.61135344 293.33833 28.518017 43.608414 0 0 13053.486 31787.438 -75.27119 -144664.24 -99751.192 3981.0787 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.09784e-06 6027 2 103.7 9.52169e-05 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.25432e-06 6027 2 103.7 9.71963e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.21366e-06 6027 2 103.7 9.16122e-05 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.30664e-06 6027 2 103.7 8.9166e-05 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.2236e-06 6027 2 103.7 0.000100508 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.18802e-06 6027 2 103.7 9.48454e-05 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.15984e-06 6027 2 103.7 9.05385e-05 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.27119e-06 6027 2 103.7 0.000111773 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.53361e-06 6027 2 103.7 0.000115913 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.18537e-06 6027 2 103.7 9.18601e-05 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.55397e-06 6027 2 103.7 0.00010211 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.09323e-06 6027 2 103.7 9.99723e-05 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.16686e-06 6027 2 103.7 0.000100384 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.32877e-06 6027 2 103.7 0.000107105 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.20848e-06 6027 2 103.7 9.17812e-05 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.20885e-06 6027 2 103.7 9.58611e-05 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.14614e-06 6027 2 103.7 9.02552e-05 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 2.18342e-06 6027 2 103.7 0.000161582 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.14519e-06 6027 2 103.7 9.52496e-05 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.7382e-06 6027 2 103.7 0.000139023 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.11867e-06 6027 2 103.7 8.94075e-05 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.1509e-06 6027 2 103.7 9.50095e-05 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.68229e-06 6027 2 103.7 0.000121997 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.10866e-06 6027 2 103.7 0.000100099 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.50421e-06 6027 2 103.7 0.000105024 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.39969e-06 6027 2 103.7 9.38701e-05 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.20645e-06 6027 2 103.7 9.88796e-05 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.84136e-06 6027 2 103.7 0.000109963 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.05109e-06 6027 2 103.7 9.83585e-05 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.28459e-06 6027 2 103.7 9.65921e-05 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.17295e-06 6027 2 103.7 9.13301e-05 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.42555e-06 6027 2 103.7 9.66847e-05 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.35039e-06 6027 2 103.7 0.00014174 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.26072e-06 6027 2 103.7 0.000104729 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.15889e-06 6027 2 103.7 0.00012514 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.28376e-06 6027 2 103.7 9.82963e-05 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.16556e-06 6027 2 103.7 9.07699e-05 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.22972e-06 6027 2 103.7 0.00010295 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.24814e-06 6027 2 103.7 0.000112253 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.11965e-06 6027 2 103.7 9.10057e-05 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.23324e-06 6027 2 103.7 0.000100893 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.16252e-06 6027 2 103.7 0.00010207 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.44505e-06 6027 2 103.7 0.000106921 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.37785e-06 6027 2 103.7 9.28958e-05 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.14232e-06 6027 2 103.7 9.24413e-05 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.19579e-06 6027 2 103.7 9.73166e-05 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.20842e-06 6027 2 103.7 9.48374e-05 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.23001e-06 6027 2 103.7 0.000106473 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.27686e-06 6027 2 103.7 0.000111228 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.21974e-06 6027 2 103.7 0.000121246 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.1403e-06 6027 2 103.7 9.0568e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.21463e-06 6027 2 103.7 0.000101974 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.18751e-06 6027 2 103.7 9.60462e-05 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.90747e-06 6027 2 103.7 0.000120333 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.28523e-06 6027 2 103.7 9.60248e-05 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.23544e-06 6027 2 103.7 0.000105263 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.28172e-06 6027 2 103.7 0.000105321 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.34241e-06 6027 2 103.7 0.000114454 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.89787e-06 6027 2 103.7 0.000112294 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.45801e-06 6027 2 103.7 8.86975e-05 2009 3000000 3000000 -285.57179 140334.36 0.61135344 297.26712 36.700041 39.515088 0 0 13207.889 31481.17 -75.27119 -144650.36 -99885.088 4034.3989 Loop time of 26320.7 on 32 procs for 3000000 steps with 6563 atoms Performance: 9.848 ns/day, 2.437 hours/ns, 113.979 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0219 | 8002.1 | 18950 |8758.5 | 30.40 Bond | 2.803 | 5.7428 | 24.758 | 174.5 | 0.02 Kspace | 4292.4 | 15308 | 23458 |6373.8 | 58.16 Neigh | 1135 | 1142 | 1153.5 | 17.9 | 4.34 Comm | 261.83 | 668.59 | 910.32 | 896.0 | 2.54 Output | 0.01038 | 0.012208 | 0.013841 | 0.9 | 0.00 Modify | 967.53 | 1143.4 | 1389.2 | 493.3 | 4.34 Other | | 51 | | | 0.19 Nlocal: 205.094 ave 424 max 0 min Histogram: 12 0 3 0 1 0 0 4 1 11 Nghost: 3998.56 ave 7766 max 193 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 95063.9 ave 230338 max 0 min Histogram: 16 0 0 0 0 0 5 2 4 5 Total # of neighbors = 3042044 Ave neighs/atom = 463.51425 Ave special neighs/atom = 1.9037026 Neighbor list builds = 146498 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) = 0.25031202 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033302856 estimated relative force accuracy = 1.0029056e-05 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 1.45801e-06 6027 2 103.7 8.86975e-05 2009 Per MPI rank memory allocation (min/avg/max) = 11.09 | 12.45 | 13.55 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 -285.18312 140334.36 0.61135344 297.26712 36.700041 39.515088 0 0 13207.889 31481.17 -75.27119 -144650.36 -99885.088 4034.3989 Loop time of 8.12841e-06 on 32 procs for 0 steps with 6563 atoms 106.1% 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 | | 8.128e-06 | | |100.00 Nlocal: 205.094 ave 424 max 0 min Histogram: 12 0 3 0 1 0 0 4 1 11 Nghost: 3998.56 ave 7766 max 193 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 95063.9 ave 230338 max 0 min Histogram: 16 0 0 0 0 0 5 2 4 5 Total # of neighbors = 3042044 Ave neighs/atom = 463.51425 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: 14:34:19