#------------------------------------------------------------------------------- # Stage 2.5: 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.32678321 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029937681 estimated relative force accuracy = 9.0156437e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.15863e-12 8304 2 103.7 9.02958e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.62 | 13.13 | 13.28 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-06 220.2377 97415.051 1.2462657 300.72356 47.417171 52.849898 0 0 21529.936 90038.518 -427.44005 -273251.75 -161583.03 5676.0035 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.05775e-06 8304 2 103.7 9.6486e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.19993e-06 8304 2 103.7 9.72854e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.16691e-06 8304 2 103.7 9.2908e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.6189e-06 8304 2 103.7 0.000117273 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.25165e-06 8304 2 103.7 8.71176e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.16476e-06 8304 2 103.7 0.000104595 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.25702e-06 8304 2 103.7 0.000107837 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.45285e-06 8304 2 103.7 0.000108385 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.36423e-06 8304 2 103.7 0.00010203 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15441e-06 8304 2 103.7 9.47886e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.21626e-06 8304 2 103.7 9.41597e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21434e-06 8304 2 103.7 9.61408e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.54894e-06 8304 2 103.7 9.74986e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.2347e-06 8304 2 103.7 9.76814e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.15857e-06 8304 2 103.7 9.9654e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.08222e-06 8304 2 103.7 9.71116e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.24602e-06 8304 2 103.7 9.47175e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.45564e-06 8304 2 103.7 0.000109232 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.32549e-06 8304 2 103.7 0.000116203 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.24057e-06 8304 2 103.7 0.000108191 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.33579e-06 8304 2 103.7 0.000106156 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.17471e-06 8304 2 103.7 9.67782e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.77875e-06 8304 2 103.7 0.000108936 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.23639e-06 8304 2 103.7 9.16241e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.14996e-06 8304 2 103.7 9.68483e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.23455e-06 8304 2 103.7 9.5771e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.33126e-06 8304 2 103.7 9.98564e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.29641e-06 8304 2 103.7 0.000113245 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.18855e-06 8304 2 103.7 0.000104611 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.23634e-06 8304 2 103.7 0.000105728 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.29143e-06 8304 2 103.7 9.07301e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.60747e-06 8304 2 103.7 9.69311e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.01806e-06 8304 2 103.7 8.8243e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.45661e-06 8304 2 103.7 0.000103608 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.17097e-06 8304 2 103.7 8.72146e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.31136e-06 8304 2 103.7 9.27204e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.07843e-06 8304 2 103.7 8.63076e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.05162e-06 8304 2 103.7 9.07842e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.20631e-06 8304 2 103.7 9.194e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.44781e-06 8304 2 103.7 0.000100972 2768 2000000 2000000 103.20541 97415.051 1.2462657 295.87067 52.644216 67.464711 0 0 21425.368 90195.957 -427.44005 -273267.77 -161526.34 5584.4077 Loop time of 10904.7 on 32 procs for 2000000 steps with 9101 atoms Performance: 15.846 ns/day, 1.515 hours/ns, 183.408 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4250.6 | 4467.7 | 4863.9 | 225.9 | 40.97 Bond | 2.0809 | 5.3129 | 10.311 | 105.9 | 0.05 Kspace | 4252.3 | 4656.3 | 4870.4 | 222.4 | 42.70 Neigh | 274.8 | 275.17 | 275.54 | 1.4 | 2.52 Comm | 694.41 | 707.29 | 719.33 | 21.5 | 6.49 Output | 0.008864 | 0.011215 | 0.013354 | 1.3 | 0.00 Modify | 747.3 | 756.5 | 764.89 | 16.5 | 6.94 Other | | 36.39 | | | 0.33 Nlocal: 284.406 ave 316 max 267 min Histogram: 5 5 5 6 2 3 3 2 0 1 Nghost: 4823.91 ave 4870 max 4769 min Histogram: 1 4 7 1 0 3 4 3 3 6 Neighs: 84524.9 ave 97664 max 77324 min Histogram: 4 9 2 6 0 5 3 2 0 1 Total # of neighbors = 2704798 Ave neighs/atom = 297.19789 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98689 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.32678321 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029937681 estimated relative force accuracy = 9.0156437e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.44781e-06 8304 2 103.7 0.000100972 2768 Per MPI rank memory allocation (min/avg/max) = 12.62 | 13.14 | 13.28 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 104.03844 97415.051 1.2462657 295.87067 52.644216 67.464711 0 0 21425.368 90195.957 -427.44005 -273267.77 -161526.34 5584.4077 Loop time of 7.49997e-06 on 32 procs for 0 steps with 9101 atoms 110.0% 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 | | 7.5e-06 | | |100.00 Nlocal: 284.406 ave 316 max 267 min Histogram: 5 5 5 6 2 3 3 2 0 1 Nghost: 4823.91 ave 4870 max 4769 min Histogram: 1 4 7 1 0 3 4 3 3 6 Neighs: 84524.9 ave 97664 max 77324 min Histogram: 4 9 2 6 0 5 3 2 0 1 Total # of neighbors = 2704798 Ave neighs/atom = 297.19789 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: 9:26:03