#------------------------------------------------------------------------------- # 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 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 file 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.47027e-12 8304 2 103.7 1.4299e-10 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.19 | 14.79 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-06 114.92463 140505.98 1.42352 299.67324 56.758096 63.551762 0 0 34600.5 -51036.673 -315.99625 -291945.2 -308261.06 6813.8559 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.7226e-06 8304 2 103.7 0.000102527 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.53905e-06 8304 2 103.7 0.00012015 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.15708e-06 8304 2 103.7 9.46778e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.34097e-06 8304 2 103.7 0.000103188 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.40529e-06 8304 2 103.7 9.73974e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.18373e-06 8304 2 103.7 8.92356e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.50942e-06 8304 2 103.7 0.000105977 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.47126e-06 8304 2 103.7 0.00010062 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.42999e-06 8304 2 103.7 9.87894e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.27932e-06 8304 2 103.7 9.50307e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.11616e-06 8304 2 103.7 9.10419e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.23303e-06 8304 2 103.7 0.000102441 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.13466e-06 8304 2 103.7 0.00010251 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.13153e-06 8304 2 103.7 0.00010154 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.14851e-06 8304 2 103.7 0.000110072 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.42935e-06 8304 2 103.7 0.000107324 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.32884e-06 8304 2 103.7 9.1503e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.01897e-06 8304 2 103.7 0.000100157 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.20042e-06 8304 2 103.7 8.78245e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.35974e-06 8304 2 103.7 9.814e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.08753e-06 8304 2 103.7 9.03948e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.16175e-06 8304 2 103.7 0.000102089 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.15215e-06 8304 2 103.7 0.000106516 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.16417e-06 8304 2 103.7 9.89926e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.56669e-06 8304 2 103.7 9.35136e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.82873e-06 8304 2 103.7 0.00011859 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.49316e-06 8304 2 103.7 0.000104159 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 2.03044e-06 8304 2 103.7 0.000161998 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.3695e-06 8304 2 103.7 0.000110965 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.43505e-06 8304 2 103.7 9.3398e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.24493e-06 8304 2 103.7 9.53067e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.17077e-06 8304 2 103.7 9.52282e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.79717e-06 8304 2 103.7 0.000113314 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.26089e-06 8304 2 103.7 9.58417e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.21434e-06 8304 2 103.7 8.83425e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.20997e-06 8304 2 103.7 9.32432e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.27014e-06 8304 2 103.7 9.98515e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.53989e-06 8304 2 103.7 9.99585e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.26354e-06 8304 2 103.7 0.00010222 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.46046e-06 8304 2 103.7 0.000102917 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.24037e-06 8304 2 103.7 9.7096e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.20572e-06 8304 2 103.7 0.000102356 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.16729e-06 8304 2 103.7 9.40828e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.19412e-06 8304 2 103.7 0.000109825 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.23467e-06 8304 2 103.7 0.000105987 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.28429e-06 8304 2 103.7 0.00011296 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.78151e-06 8304 2 103.7 0.000105724 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.13139e-06 8304 2 103.7 9.41185e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.27595e-06 8304 2 103.7 9.45372e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.07603e-06 8304 2 103.7 8.7206e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.48115e-06 8304 2 103.7 0.000122242 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.11011e-06 8304 2 103.7 9.65366e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.36139e-06 8304 2 103.7 0.00011509 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.53188e-06 8304 2 103.7 0.000102879 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.23563e-06 8304 2 103.7 9.11601e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.11089e-06 8304 2 103.7 9.33262e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.08335e-06 8304 2 103.7 9.16414e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.55754e-06 8304 2 103.7 0.000127593 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.35668e-06 8304 2 103.7 9.38776e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.38232e-06 8304 2 103.7 0.000102125 2768 3000000 3000000 -137.04609 140505.98 1.42352 298.9956 41.84719 57.609575 0 0 34454.721 -50900.861 -315.99625 -291943.15 -308289.84 6798.4481 Loop time of 38702.2 on 16 procs for 3000000 steps with 10721 atoms Performance: 6.697 ns/day, 3.584 hours/ns, 77.515 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6078.9 | 21495 | 29436 |6033.2 | 55.54 Bond | 3.1659 | 9.4387 | 16.714 | 144.1 | 0.02 Kspace | 5795.2 | 13748 | 29188 |7554.2 | 35.52 Neigh | 1529.6 | 1532.6 | 1535.9 | 5.3 | 3.96 Comm | 686.69 | 814.03 | 878.76 | 256.9 | 2.10 Output | 0.015604 | 0.017499 | 0.019209 | 0.9 | 0.00 Modify | 995.54 | 1045 | 1152.9 | 194.1 | 2.70 Other | | 57.46 | | | 0.15 Nlocal: 670.062 ave 821 max 355 min Histogram: 4 0 0 0 0 0 0 0 8 4 Nghost: 8233.44 ave 9784 max 7005 min Histogram: 4 0 0 5 3 0 0 0 0 4 Neighs: 312964 ave 424480 max 88045 min Histogram: 4 0 0 0 0 0 0 1 6 5 Total # of neighbors = 5007428 Ave neighs/atom = 467.06725 Ave special neighs/atom = 1.6069397 Neighbor list builds = 148771 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.38232e-06 8304 2 103.7 0.000102125 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.21 | 14.79 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 -136.51904 140505.98 1.42352 298.9956 41.84719 57.609575 0 0 34454.721 -50900.861 -315.99625 -291943.15 -308289.84 6798.4481 Loop time of 3.80269e-06 on 16 procs for 0 steps with 10721 atoms 129.8% CPU use with 16 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 | | 3.803e-06 | | |100.00 Nlocal: 670.062 ave 821 max 355 min Histogram: 4 0 0 0 0 0 0 0 8 4 Nghost: 8233.44 ave 9784 max 7005 min Histogram: 4 0 0 5 3 0 0 0 0 4 Neighs: 312964 ave 424480 max 88045 min Histogram: 4 0 0 0 0 0 0 1 6 5 Total # of neighbors = 5007428 Ave neighs/atom = 467.06725 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out