#------------------------------------------------------------------------------- # Stage 2.6: NVT integration for 2 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 2768 = # 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 200000 200000 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 2.6_averages.txt off 1 fix 3 movable ave/time 200 1 200 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 2.6_instantaneous.txt restart 2000000 2.6.restart dump sci all custom 200000 2.6.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.20391866 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0031570161 estimated relative force accuracy = 9.5072601e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.09546e-12 8304 2 103.7 8.31477e-11 2768 Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.74 | 13.84 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 85.570754 97473.161 1.2455227 302.98529 41.730137 64.181103 0 0 21437.339 -11719.031 -110.80248 -171336.38 -161512.17 5718.6926 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.27726e-06 8304 2 103.7 9.75992e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.12277e-06 8304 2 103.7 9.55443e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.27434e-06 8304 2 103.7 0.000112892 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.2012e-06 8304 2 103.7 9.14573e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.4854e-06 8304 2 103.7 0.00013623 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.51582e-06 8304 2 103.7 9.50853e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.14507e-06 8304 2 103.7 9.88084e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.10117e-06 8304 2 103.7 9.25548e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.16802e-06 8304 2 103.7 8.96583e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.2659e-06 8304 2 103.7 9.76666e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.55828e-06 8304 2 103.7 0.00011652 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.15636e-06 8304 2 103.7 0.000108352 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.22777e-06 8304 2 103.7 0.000102929 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.27576e-06 8304 2 103.7 9.88636e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.22248e-06 8304 2 103.7 9.10915e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.28045e-06 8304 2 103.7 0.000101789 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.24494e-06 8304 2 103.7 9.34794e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.50103e-06 8304 2 103.7 0.000106091 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.39191e-06 8304 2 103.7 9.60676e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.28174e-06 8304 2 103.7 9.94695e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.61973e-06 8304 2 103.7 0.0001148 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.20383e-06 8304 2 103.7 8.82991e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.16269e-06 8304 2 103.7 0.000105443 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.1625e-06 8304 2 103.7 0.000119452 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.39776e-06 8304 2 103.7 9.58691e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.52673e-06 8304 2 103.7 0.000102516 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.53559e-06 8304 2 103.7 9.89416e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.07768e-06 8304 2 103.7 9.32605e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.34233e-06 8304 2 103.7 9.30627e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.29103e-06 8304 2 103.7 9.92135e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.46143e-06 8304 2 103.7 0.000115521 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.01034e-06 8304 2 103.7 8.60456e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.11219e-06 8304 2 103.7 0.000100331 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.63093e-06 8304 2 103.7 9.71549e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.28385e-06 8304 2 103.7 9.32164e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.53954e-06 8304 2 103.7 0.000114425 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.25666e-06 8304 2 103.7 9.61119e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.37003e-06 8304 2 103.7 0.000102888 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.31111e-06 8304 2 103.7 0.000102117 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.71311e-06 8304 2 103.7 0.000100529 2768 2000000 2000000 164.8026 97473.161 1.2455227 297.65081 41.771242 61.09674 0 0 21445.532 -11647.523 -110.80248 -171330.05 -161429.17 5618.0069 Loop time of 22648.7 on 32 procs for 2000000 steps with 9101 atoms Performance: 7.630 ns/day, 3.146 hours/ns, 88.305 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 | 14923 | 16020 | 17453 | 554.1 | 70.73 Bond | 2.5271 | 5.9665 | 12.195 | 119.6 | 0.03 Kspace | 2049.5 | 3491.2 | 4577.6 |1186.1 | 15.41 Neigh | 774.39 | 774.93 | 775.63 | 1.2 | 3.42 Comm | 1060.6 | 1075.2 | 1084.4 | 19.4 | 4.75 Output | 0.0090603 | 0.011383 | 0.013573 | 1.3 | 0.00 Modify | 1186.9 | 1193.9 | 1201.6 | 10.2 | 5.27 Other | | 87.65 | | | 0.39 Nlocal: 284.406 ave 310 max 259 min Histogram: 1 0 3 5 7 9 4 1 0 2 Nghost: 10727 ave 10775 max 10680 min Histogram: 1 0 3 5 9 6 2 4 1 1 Neighs: 273166 ave 308135 max 242763 min Histogram: 3 3 2 4 5 5 5 2 2 1 Total # of neighbors = 8741304 Ave neighs/atom = 960.47731 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98866 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.6.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) = 0.20391866 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0031570161 estimated relative force accuracy = 9.5072601e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.71311e-06 8304 2 103.7 0.000100529 2768 Per MPI rank memory allocation (min/avg/max) = 13.46 | 13.75 | 13.85 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 2000000 2000000 165.76063 97473.161 1.2455227 297.65081 41.771242 61.09674 0 0 21445.532 -11647.523 -110.80248 -171330.05 -161429.17 5618.0069 Loop time of 8.01731e-06 on 32 procs for 0 steps with 9101 atoms 112.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.017e-06 | | |100.00 Nlocal: 284.406 ave 310 max 259 min Histogram: 1 0 3 5 7 9 4 1 0 2 Nghost: 10727 ave 10775 max 10680 min Histogram: 1 0 3 5 9 6 2 4 1 1 Neighs: 273166 ave 308135 max 242763 min Histogram: 3 3 2 4 5 5 5 2 2 1 Total # of neighbors = 8741304 Ave neighs/atom = 960.47731 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 28:14:54