#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3659 = # 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 8.51652e-13 10977 2 103.7 7.51328e-11 3659 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.1 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 338263.69 142807.9 1.3823791 300.48363 270.8173 390.18985 0 0 273407.92 -65423.452 -383.2647 -382454.94 -173809.46 8166.8523 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.357e-06 10977 2 103.7 0.0001152 3659 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.18965e-06 10977 2 103.7 9.45346e-05 3659 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.18287e-06 10977 2 103.7 9.95771e-05 3659 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.15264e-06 10977 2 103.7 9.21084e-05 3659 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.50643e-06 10977 2 103.7 9.88826e-05 3659 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.51984e-06 10977 2 103.7 0.000116853 3659 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.43972e-06 10977 2 103.7 9.54029e-05 3659 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.52474e-06 10977 2 103.7 0.000108997 3659 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.19939e-06 10977 2 103.7 9.45696e-05 3659 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.17925e-06 10977 2 103.7 9.09049e-05 3659 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.53697e-06 10977 2 103.7 0.000101859 3659 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.45658e-06 10977 2 103.7 9.72016e-05 3659 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.16854e-06 10977 2 103.7 0.000102728 3659 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.80046e-06 10977 2 103.7 0.000105235 3659 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.19135e-06 10977 2 103.7 9.51788e-05 3659 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.27502e-06 10977 2 103.7 9.44782e-05 3659 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.57837e-06 10977 2 103.7 0.000105649 3659 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.41337e-06 10977 2 103.7 0.000123031 3659 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.24506e-06 10977 2 103.7 9.9692e-05 3659 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.20841e-06 10977 2 103.7 8.86468e-05 3659 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.14936e-06 10977 2 103.7 9.24854e-05 3659 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.44931e-06 10977 2 103.7 9.09673e-05 3659 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.1615e-06 10977 2 103.7 9.24645e-05 3659 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.27876e-06 10977 2 103.7 9.77852e-05 3659 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.21499e-06 10977 2 103.7 0.000111541 3659 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.16681e-06 10977 2 103.7 0.000121794 3659 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.81482e-06 10977 2 103.7 0.000112659 3659 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.28326e-06 10977 2 103.7 9.49428e-05 3659 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.20732e-06 10977 2 103.7 9.68784e-05 3659 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.47982e-06 10977 2 103.7 0.000108488 3659 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.14112e-06 10977 2 103.7 0.000109246 3659 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.17019e-06 10977 2 103.7 9.72059e-05 3659 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.4337e-06 10977 2 103.7 9.65819e-05 3659 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.11611e-06 10977 2 103.7 9.77426e-05 3659 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.2597e-06 10977 2 103.7 9.63213e-05 3659 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.15727e-06 10977 2 103.7 8.76737e-05 3659 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.26386e-06 10977 2 103.7 0.000100728 3659 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.37285e-06 10977 2 103.7 0.000104761 3659 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.8815e-06 10977 2 103.7 0.0001149 3659 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.17588e-06 10977 2 103.7 9.91307e-05 3659 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.34098e-06 10977 2 103.7 9.37905e-05 3659 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.41612e-06 10977 2 103.7 8.97976e-05 3659 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.11371e-06 10977 2 103.7 9.11296e-05 3659 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.31218e-06 10977 2 103.7 0.000110033 3659 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.4305e-06 10977 2 103.7 9.82337e-05 3659 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.02207e-06 10977 2 103.7 0.000112688 3659 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.30706e-06 10977 2 103.7 0.00010302 3659 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.37513e-06 10977 2 103.7 0.0001009 3659 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.42345e-06 10977 2 103.7 0.000102119 3659 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.30494e-06 10977 2 103.7 9.17976e-05 3659 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.2257e-06 10977 2 103.7 9.82138e-05 3659 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.19784e-06 10977 2 103.7 9.35952e-05 3659 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.2865e-06 10977 2 103.7 9.56013e-05 3659 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.2553e-06 10977 2 103.7 8.99612e-05 3659 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.25267e-06 10977 2 103.7 9.35719e-05 3659 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.16182e-06 10977 2 103.7 0.000105217 3659 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.61291e-06 10977 2 103.7 0.000118412 3659 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.59914e-06 10977 2 103.7 0.000111675 3659 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.30794e-06 10977 2 103.7 8.9048e-05 3659 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.35074e-06 10977 2 103.7 9.51867e-05 3659 3000000 3000000 337416.45 142807.9 1.3823791 298.83387 262.99263 404.00113 0 0 272802.73 -64746.773 -383.2647 -382436.88 -173713.93 8122.0134 Loop time of 38329.6 on 32 procs for 3000000 steps with 13738 atoms Performance: 6.762 ns/day, 3.549 hours/ns, 78.268 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15111 | 19409 | 27318 |3018.4 | 50.64 Bond | 4.5259 | 21.404 | 54.001 | 371.6 | 0.06 Kspace | 5858.6 | 13825 | 18186 |3604.1 | 36.07 Neigh | 1411.4 | 1415 | 1419 | 6.1 | 3.69 Comm | 1522.2 | 1649.5 | 1789.1 | 209.0 | 4.30 Output | 0.01472 | 0.017608 | 0.020327 | 1.3 | 0.00 Modify | 1812.5 | 1921.6 | 2000.5 | 141.1 | 5.01 Other | | 88.09 | | | 0.23 Nlocal: 429.312 ave 522 max 368 min Histogram: 4 5 8 7 0 0 0 0 2 6 Nghost: 8150.66 ave 8718 max 7327 min Histogram: 8 0 0 0 0 2 7 7 0 8 Neighs: 240215 ave 345278 max 183267 min Histogram: 5 12 6 1 0 0 0 0 3 5 Total # of neighbors = 7686868 Ave neighs/atom = 559.53327 Ave special neighs/atom = 1.8702868 Neighbor list builds = 149728 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.35074e-06 10977 2 103.7 9.51867e-05 3659 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.1 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 337417.42 142807.9 1.3823791 298.83387 262.99263 404.00113 0 0 272802.73 -64746.773 -383.2647 -382436.88 -173713.93 8122.0134 Loop time of 7.82163e-06 on 32 procs for 0 steps with 13738 atoms 115.9% 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 | | 7.822e-06 | | |100.00 Nlocal: 429.312 ave 522 max 368 min Histogram: 4 5 8 7 0 0 0 0 2 6 Nghost: 8150.66 ave 8718 max 7327 min Histogram: 8 0 0 0 0 2 7 7 0 8 Neighs: 240215 ave 345278 max 183267 min Histogram: 5 12 6 1 0 0 0 0 3 5 Total # of neighbors = 7686868 Ave neighs/atom = 559.53327 Ave special neighs/atom = 1.8702868 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out