#------------------------------------------------------------------------------- # 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 1928 = # 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) = 0.25063947 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035059078 estimated relative force accuracy = 1.0557937e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.76712e-13 5784 2 103.7 7.6426e-11 1928 Per MPI rank memory allocation (min/avg/max) = 10.98 | 12.46 | 13.53 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 -327.40707 137757.66 0.6306022 297.18208 32.464164 39.394204 0 0 16317.575 11106.202 -76.789562 -152574.63 -125079 3949.0896 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.10633e-06 5784 2 103.7 9.41751e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.16713e-06 5784 2 103.7 9.24423e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.65684e-06 5784 2 103.7 9.26912e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.39931e-06 5784 2 103.7 9.92564e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.22441e-06 5784 2 103.7 0.000115624 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.13368e-06 5784 2 103.7 9.45309e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.3481e-06 5784 2 103.7 0.000108091 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.17328e-06 5784 2 103.7 9.97139e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.40558e-06 5784 2 103.7 0.000111039 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.34665e-06 5784 2 103.7 0.000113273 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.6777e-06 5784 2 103.7 0.000108719 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.16508e-06 5784 2 103.7 9.19368e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.1909e-06 5784 2 103.7 0.000109731 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.2968e-06 5784 2 103.7 9.34529e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.12557e-06 5784 2 103.7 8.9082e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.17661e-06 5784 2 103.7 9.08316e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.33814e-06 5784 2 103.7 0.000106035 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.17208e-06 5784 2 103.7 8.97285e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.30881e-06 5784 2 103.7 9.98035e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.08205e-06 5784 2 103.7 9.39278e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.13754e-06 5784 2 103.7 9.06377e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.08699e-06 5784 2 103.7 9.83881e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.22433e-06 5784 2 103.7 9.8043e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.31926e-06 5784 2 103.7 8.95783e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.1646e-06 5784 2 103.7 9.06303e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.18316e-06 5784 2 103.7 9.15548e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.26505e-06 5784 2 103.7 9.37028e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.26931e-06 5784 2 103.7 9.48986e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.06824e-06 5784 2 103.7 9.32038e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.61454e-06 5784 2 103.7 0.000121517 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.25592e-06 5784 2 103.7 9.76986e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.34022e-06 5784 2 103.7 0.000102913 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.64534e-06 5784 2 103.7 0.00011079 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.2832e-06 5784 2 103.7 9.92481e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.641e-06 5784 2 103.7 0.000126514 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.12155e-06 5784 2 103.7 9.26569e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.11553e-06 5784 2 103.7 9.33575e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.18005e-06 5784 2 103.7 9.94203e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.19718e-06 5784 2 103.7 9.25603e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.21441e-06 5784 2 103.7 0.000105337 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.27526e-06 5784 2 103.7 0.000101993 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.47956e-06 5784 2 103.7 0.000108994 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.60971e-06 5784 2 103.7 0.00011368 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.18499e-06 5784 2 103.7 0.000105175 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.25927e-06 5784 2 103.7 9.35074e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.08578e-06 5784 2 103.7 0.000103948 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.47135e-06 5784 2 103.7 0.000122022 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.19171e-06 5784 2 103.7 9.52396e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.47521e-06 5784 2 103.7 9.98987e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.50157e-06 5784 2 103.7 0.000100534 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.1173e-06 5784 2 103.7 9.15767e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.15568e-06 5784 2 103.7 0.000104688 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.09913e-06 5784 2 103.7 8.20879e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.09214e-06 5784 2 103.7 9.74054e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.20249e-06 5784 2 103.7 0.000101021 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.74374e-06 5784 2 103.7 0.000134466 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.18974e-06 5784 2 103.7 9.50446e-05 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.23245e-06 5784 2 103.7 9.62645e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.07016e-06 5784 2 103.7 8.65022e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.35824e-06 5784 2 103.7 0.000110874 1928 3000000 3000000 -279.47155 137757.66 0.6306022 296.19234 25.898255 39.273191 0 0 16301.807 11019.282 -76.789562 -152562.19 -125175.93 3935.9374 Loop time of 25015.2 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.362 ns/day, 2.316 hours/ns, 119.927 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 | 5.8552 | 7673.6 | 17994 |8584.8 | 30.68 Bond | 2.5776 | 5.6902 | 12.633 | 128.9 | 0.02 Kspace | 4097.5 | 14470 | 22270 |6290.4 | 57.85 Neigh | 1059.9 | 1066.3 | 1076.8 | 17.2 | 4.26 Comm | 281.65 | 657.12 | 884.75 | 850.7 | 2.63 Output | 0.010258 | 0.012061 | 0.014023 | 0.9 | 0.00 Modify | 927.48 | 1093.1 | 1331.7 | 481.5 | 4.37 Other | | 49.07 | | | 0.20 Nlocal: 199.594 ave 422 max 0 min Histogram: 12 1 3 0 0 0 1 2 2 11 Nghost: 3937.44 ave 7611 max 234 min Histogram: 4 4 0 4 4 4 4 0 4 4 Neighs: 91648.6 ave 232089 max 0 min Histogram: 16 0 0 0 0 0 7 2 3 4 Total # of neighbors = 2932756 Ave neighs/atom = 459.17583 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145171 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) = 0.25063947 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035059078 estimated relative force accuracy = 1.0557937e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.35824e-06 5784 2 103.7 0.000110874 1928 Per MPI rank memory allocation (min/avg/max) = 11.09 | 12.44 | 13.53 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 -279.09275 137757.66 0.6306022 296.19234 25.898255 39.273191 0 0 16301.807 11019.282 -76.789562 -152562.19 -125175.93 3935.9374 Loop time of 7.17353e-06 on 32 procs for 0 steps with 6387 atoms 113.7% 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 | | 7.174e-06 | | |100.00 Nlocal: 199.594 ave 422 max 0 min Histogram: 12 1 3 0 0 0 1 2 2 11 Nghost: 3937.44 ave 7611 max 234 min Histogram: 4 4 0 4 4 4 4 0 4 4 Neighs: 91648.6 ave 232089 max 0 min Histogram: 16 0 0 0 0 0 7 2 3 4 Total # of neighbors = 2932756 Ave neighs/atom = 459.17583 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 13:55:57