#------------------------------------------------------------------------------- # 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 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 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) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.26783e-13 8304 2 103.7 8.92584e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.9 | 13.07 | 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 -155.84624 192519.71 0.63061093 296.60031 43.49591 73.724935 0 0 21085.411 86545.097 -216.28484 -268039.11 -160291.38 5598.1794 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.05389e-06 8304 2 103.7 0.000100103 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.06281e-06 8304 2 103.7 9.43685e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.62285e-06 8304 2 103.7 0.000108943 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.03078e-06 8304 2 103.7 9.16854e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.0682e-06 8304 2 103.7 9.78843e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.05962e-06 8304 2 103.7 9.33818e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.258e-06 8304 2 103.7 0.000101241 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.31417e-06 8304 2 103.7 9.8591e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.24756e-06 8304 2 103.7 9.53774e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21643e-06 8304 2 103.7 0.000107345 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.33902e-06 8304 2 103.7 8.91267e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.14717e-06 8304 2 103.7 9.38964e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.4148e-06 8304 2 103.7 0.000104613 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20349e-06 8304 2 103.7 9.25234e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.07103e-06 8304 2 103.7 9.08407e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.12369e-06 8304 2 103.7 9.39555e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.31574e-06 8304 2 103.7 9.60054e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.61575e-06 8304 2 103.7 0.000113447 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.29562e-06 8304 2 103.7 9.93604e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.46855e-06 8304 2 103.7 0.000107999 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.58075e-06 8304 2 103.7 0.000110195 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.09776e-06 8304 2 103.7 9.74526e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.17655e-06 8304 2 103.7 9.77407e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.42394e-06 8304 2 103.7 0.00010101 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.42869e-06 8304 2 103.7 0.000105537 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.24375e-06 8304 2 103.7 0.000100817 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.6059e-06 8304 2 103.7 9.75543e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.39755e-06 8304 2 103.7 9.78748e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.12964e-06 8304 2 103.7 9.9017e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.25529e-06 8304 2 103.7 0.000102054 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.28537e-06 8304 2 103.7 9.69939e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.25053e-06 8304 2 103.7 9.54963e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.17517e-06 8304 2 103.7 9.84415e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.2269e-06 8304 2 103.7 0.000121588 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.15775e-06 8304 2 103.7 9.67275e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19865e-06 8304 2 103.7 9.56598e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.25153e-06 8304 2 103.7 9.22284e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.41939e-06 8304 2 103.7 9.53582e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.23302e-06 8304 2 103.7 9.1287e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.29495e-06 8304 2 103.7 0.000131056 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.23817e-06 8304 2 103.7 0.000118082 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.40354e-06 8304 2 103.7 0.000105071 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.27729e-06 8304 2 103.7 9.45326e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.1844e-06 8304 2 103.7 8.7497e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.10842e-06 8304 2 103.7 9.47005e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.18356e-06 8304 2 103.7 0.000105615 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.19438e-06 8304 2 103.7 9.45105e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.67821e-06 8304 2 103.7 0.000118413 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.21891e-06 8304 2 103.7 9.82082e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.14029e-06 8304 2 103.7 9.23707e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.13141e-06 8304 2 103.7 9.14856e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.1866e-06 8304 2 103.7 9.99822e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.1192e-06 8304 2 103.7 9.08732e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.11075e-06 8304 2 103.7 9.25816e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.21635e-06 8304 2 103.7 9.80919e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.76776e-06 8304 2 103.7 0.00014332 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.18012e-06 8304 2 103.7 8.88386e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.14779e-06 8304 2 103.7 9.32647e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.32348e-06 8304 2 103.7 9.92018e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.33321e-06 8304 2 103.7 9.6409e-05 2768 3000000 3000000 -465.27143 192519.71 0.63061093 294.12437 45.937531 71.734813 0 0 20898.35 86794.706 -216.28484 -268030.46 -160219.73 5551.4473 Loop time of 24580.4 on 32 procs for 3000000 steps with 9101 atoms Performance: 10.545 ns/day, 2.276 hours/ns, 122.048 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 | 196.97 | 5992.7 | 12126 |7080.4 | 24.38 Bond | 2.8924 | 7.8486 | 22.977 | 175.3 | 0.03 Kspace | 9688.4 | 15835 | 21690 |4381.3 | 64.42 Neigh | 764.8 | 770.75 | 780.59 | 20.7 | 3.14 Comm | 409.64 | 669.73 | 853.95 | 649.7 | 2.72 Output | 0.013616 | 0.015618 | 0.017524 | 1.0 | 0.00 Modify | 1119.4 | 1242.2 | 1424.4 | 355.5 | 5.05 Other | | 62.51 | | | 0.25 Nlocal: 284.406 ave 555 max 0 min Histogram: 9 7 0 0 0 0 0 0 1 15 Nghost: 3146.84 ave 4838 max 1504 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74332 ave 158831 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 2378623 Ave neighs/atom = 261.35842 Ave special neighs/atom = 1.8929788 Neighbor list builds = 150022 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) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.33321e-06 8304 2 103.7 9.6409e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.9 | 13.13 | 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 -464.87038 192519.71 0.63061093 294.12437 45.937531 71.734813 0 0 20898.35 86794.706 -216.28484 -268030.46 -160219.73 5551.4473 Loop time of 1.35448e-05 on 32 procs for 0 steps with 9101 atoms 114.7% 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 | | 1.354e-05 | | |100.00 Nlocal: 284.406 ave 555 max 0 min Histogram: 9 7 0 0 0 0 0 0 1 15 Nghost: 3146.84 ave 4838 max 1504 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74332 ave 158831 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 2378623 Ave neighs/atom = 261.35842 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: 18:10:59