#------------------------------------------------------------------------------- # 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) = 0.31973058 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032868617 estimated relative force accuracy = 9.8982865e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 9.50351e-13 5784 2 103.7 8.3773e-11 1928 Per MPI rank memory allocation (min/avg/max) = 11.51 | 12.8 | 13.23 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 -465.45727 138087.51 0.62909591 296.45751 23.699029 45.117791 0 0 16055.663 53152.583 -152.16399 -193992.61 -124715.55 3939.4611 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.25094e-06 5784 2 103.7 9.4553e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.62568e-06 5784 2 103.7 0.000100444 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.08374e-06 5784 2 103.7 9.01527e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.12719e-06 5784 2 103.7 9.25756e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 9.74047e-07 5784 2 103.7 8.76072e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.21965e-06 5784 2 103.7 9.04257e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.10606e-06 5784 2 103.7 9.41736e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.30509e-06 5784 2 103.7 0.000109424 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.12632e-06 5784 2 103.7 0.000104157 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.24233e-06 5784 2 103.7 8.95431e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.72211e-06 5784 2 103.7 0.000126723 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.47453e-06 5784 2 103.7 0.000114039 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.88433e-06 5784 2 103.7 0.000143309 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.31187e-06 5784 2 103.7 9.89426e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.68111e-06 5784 2 103.7 0.00012101 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.10548e-06 5784 2 103.7 9.18465e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.40635e-06 5784 2 103.7 0.000107602 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.10759e-06 5784 2 103.7 8.80042e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.6006e-06 5784 2 103.7 0.00012443 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.27169e-06 5784 2 103.7 9.26712e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.56411e-06 5784 2 103.7 0.000109044 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.46774e-06 5784 2 103.7 0.000123203 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.48688e-06 5784 2 103.7 0.00010748 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.14626e-06 5784 2 103.7 9.50017e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.27113e-06 5784 2 103.7 0.00010846 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.66505e-06 5784 2 103.7 0.00011111 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.67885e-06 5784 2 103.7 0.000109554 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.46548e-06 5784 2 103.7 0.000111419 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.57376e-06 5784 2 103.7 0.00011034 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.35922e-06 5784 2 103.7 9.7737e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.21508e-06 5784 2 103.7 9.2148e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.23144e-06 5784 2 103.7 0.000105288 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.43576e-06 5784 2 103.7 9.11151e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.14861e-06 5784 2 103.7 9.55288e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.33642e-06 5784 2 103.7 0.000102212 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.03362e-06 5784 2 103.7 9.18348e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.21282e-06 5784 2 103.7 9.147e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.25314e-06 5784 2 103.7 0.000102928 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.80464e-06 5784 2 103.7 0.000113317 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.09841e-06 5784 2 103.7 8.95868e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.85702e-06 5784 2 103.7 0.000118453 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.25114e-06 5784 2 103.7 9.42937e-05 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.52705e-06 5784 2 103.7 0.000107587 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.26017e-06 5784 2 103.7 9.80068e-05 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.10495e-06 5784 2 103.7 0.000109554 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 9.98777e-07 5784 2 103.7 8.84357e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.18997e-06 5784 2 103.7 0.000103638 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.3575e-06 5784 2 103.7 9.90944e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.13736e-06 5784 2 103.7 9.64627e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.58735e-06 5784 2 103.7 0.000101381 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.05124e-06 5784 2 103.7 8.7583e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.27903e-06 5784 2 103.7 9.71955e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.09755e-06 5784 2 103.7 9.1907e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.07427e-06 5784 2 103.7 9.26713e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.26867e-06 5784 2 103.7 9.1016e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.15154e-06 5784 2 103.7 9.84199e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.75421e-06 5784 2 103.7 0.000128448 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.23896e-06 5784 2 103.7 0.000106375 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.38506e-06 5784 2 103.7 9.2497e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.13226e-06 5784 2 103.7 9.66336e-05 1928 3000000 3000000 39.97317 138087.51 0.62909591 294.97947 24.096004 42.096931 0 0 16328.406 52814.163 -152.16399 -193988.05 -124779.29 3919.8202 Loop time of 16933.8 on 32 procs for 3000000 steps with 6387 atoms Performance: 15.307 ns/day, 1.568 hours/ns, 177.160 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 148.61 | 4111.3 | 8534.3 |6097.6 | 24.28 Bond | 2.6369 | 5.881 | 13.433 | 131.4 | 0.03 Kspace | 6405.5 | 10848 | 14841 |3774.8 | 64.06 Neigh | 467.92 | 472.55 | 480.8 | 21.6 | 2.79 Comm | 339.28 | 520.17 | 650.11 | 535.4 | 3.07 Output | 0.010777 | 0.012368 | 0.013874 | 0.9 | 0.00 Modify | 832.89 | 926.9 | 1057 | 302.9 | 5.47 Other | | 49.41 | | | 0.29 Nlocal: 199.594 ave 402 max 0 min Histogram: 14 2 0 0 0 0 0 0 2 14 Nghost: 2699.97 ave 4041 max 1364 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51269.4 ave 114315 max 0 min Histogram: 16 0 0 0 0 0 0 0 10 6 Total # of neighbors = 1640620 Ave neighs/atom = 256.86864 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145583 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) = 0.31973058 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032868617 estimated relative force accuracy = 9.8982865e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.13226e-06 5784 2 103.7 9.66336e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.51 | 12.83 | 13.23 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 40.44463 138087.51 0.62909591 294.97947 24.096004 42.096931 0 0 16328.406 52814.163 -152.16399 -193988.05 -124779.29 3919.8202 Loop time of 9.84625e-06 on 32 procs for 0 steps with 6387 atoms 109.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 9.846e-06 | | |100.00 Nlocal: 199.594 ave 402 max 0 min Histogram: 14 2 0 0 0 0 0 0 2 14 Nghost: 2699.97 ave 4041 max 1364 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51269.4 ave 114315 max 0 min Histogram: 16 0 0 0 0 0 0 0 10 6 Total # of neighbors = 1640620 Ave neighs/atom = 256.86864 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: 12:37:26