#------------------------------------------------------------------------------- # 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 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) = 0.31995351 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031543348 estimated relative force accuracy = 9.4991856e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.0921e-13 8304 2 103.7 8.03624e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.74 | 13.14 | 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 -40.405344 194899.49 0.62291099 296.25435 37.945843 68.347664 0 0 21189.07 86071.117 -213.64394 -267712.73 -160346.25 5591.6496 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.40571e-06 8304 2 103.7 9.55072e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.2974e-06 8304 2 103.7 9.37594e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.19864e-06 8304 2 103.7 0.0001096 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.05681e-06 8304 2 103.7 8.58154e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.20893e-06 8304 2 103.7 0.000106481 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.29207e-06 8304 2 103.7 9.48608e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.39536e-06 8304 2 103.7 9.51069e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.14725e-06 8304 2 103.7 9.77767e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.8164e-06 8304 2 103.7 0.0001126 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.61727e-06 8304 2 103.7 0.000122143 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 2.06272e-06 8304 2 103.7 0.000161382 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.20463e-06 8304 2 103.7 9.25884e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.20368e-06 8304 2 103.7 0.000106957 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.71562e-06 8304 2 103.7 0.000139479 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.18543e-06 8304 2 103.7 9.05538e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.45891e-06 8304 2 103.7 0.000122859 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21296e-06 8304 2 103.7 8.91477e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.09433e-06 8304 2 103.7 8.90517e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.12105e-06 8304 2 103.7 8.95298e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.5758e-06 8304 2 103.7 0.000100737 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.4026e-06 8304 2 103.7 0.000107649 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.20001e-06 8304 2 103.7 0.000101077 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.07937e-06 8304 2 103.7 0.000104056 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.35813e-06 8304 2 103.7 9.74599e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.67751e-06 8304 2 103.7 0.000112008 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.07839e-06 8304 2 103.7 0.000110824 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.13638e-06 8304 2 103.7 9.05004e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.30537e-06 8304 2 103.7 0.00010242 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.59691e-06 8304 2 103.7 9.87127e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.2784e-06 8304 2 103.7 9.08502e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.18282e-06 8304 2 103.7 9.35933e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.46469e-06 8304 2 103.7 0.000108719 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.41871e-06 8304 2 103.7 0.000116211 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.12968e-06 8304 2 103.7 0.000102057 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.23665e-06 8304 2 103.7 8.97228e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.26304e-06 8304 2 103.7 9.58418e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.55201e-06 8304 2 103.7 0.000131882 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.25004e-06 8304 2 103.7 0.000101777 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.25929e-06 8304 2 103.7 9.5537e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.45493e-06 8304 2 103.7 9.46468e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.17156e-06 8304 2 103.7 9.77195e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.42337e-06 8304 2 103.7 0.000105188 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.20844e-06 8304 2 103.7 8.8806e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.21347e-06 8304 2 103.7 0.000102377 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.43589e-06 8304 2 103.7 0.000103663 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.25566e-06 8304 2 103.7 0.000108844 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.13889e-06 8304 2 103.7 9.43061e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.56024e-06 8304 2 103.7 0.00011332 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.19029e-06 8304 2 103.7 9.29099e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.18987e-06 8304 2 103.7 9.21638e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.19377e-06 8304 2 103.7 9.26493e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.39398e-06 8304 2 103.7 8.74754e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.109e-06 8304 2 103.7 8.94586e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.3701e-06 8304 2 103.7 0.000103179 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.23656e-06 8304 2 103.7 9.5261e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.35849e-06 8304 2 103.7 0.000110102 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.35385e-06 8304 2 103.7 9.67697e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.30477e-06 8304 2 103.7 0.00010182 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.41821e-06 8304 2 103.7 0.000104109 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.46871e-06 8304 2 103.7 0.000117342 2768 3000000 3000000 -76.601798 194899.49 0.62291099 295.08939 53.973299 65.785438 0 0 21136.629 86152.475 -213.64394 -267725.99 -160317.13 5569.6615 Loop time of 24657.3 on 32 procs for 3000000 steps with 9101 atoms Performance: 10.512 ns/day, 2.283 hours/ns, 121.668 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 | 241.05 | 5811.2 | 12399 |7207.5 | 23.57 Bond | 3.0274 | 7.6945 | 18.345 | 181.4 | 0.03 Kspace | 9599.6 | 16210 | 21825 |4339.8 | 65.74 Neigh | 678.99 | 684.52 | 693.41 | 20.2 | 2.78 Comm | 391.92 | 649.96 | 823.17 | 623.4 | 2.64 Output | 0.014089 | 0.016067 | 0.01796 | 0.9 | 0.00 Modify | 1115.3 | 1231.7 | 1401.9 | 332.8 | 5.00 Other | | 62.01 | | | 0.25 Nlocal: 284.406 ave 567 max 0 min Histogram: 14 2 0 0 0 0 0 0 1 15 Nghost: 3125.78 ave 4723 max 1528 min Histogram: 11 5 0 0 0 0 0 0 4 12 Neighs: 74653.5 ave 169489 max 0 min Histogram: 16 0 0 0 0 0 0 2 8 6 Total # of neighbors = 2388913 Ave neighs/atom = 262.48907 Ave special neighs/atom = 1.8929788 Neighbor list builds = 150008 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) = 0.31995351 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031543348 estimated relative force accuracy = 9.4991856e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.46871e-06 8304 2 103.7 0.000117342 2768 Per MPI rank memory allocation (min/avg/max) = 11.91 | 13.11 | 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 -76.247335 194899.49 0.62291099 295.08939 53.973299 65.785438 0 0 21136.629 86152.475 -213.64394 -267725.99 -160317.13 5569.6615 Loop time of 1.07802e-05 on 32 procs for 0 steps with 9101 atoms 106.1% 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 | | 1.078e-05 | | |100.00 Nlocal: 284.406 ave 567 max 0 min Histogram: 14 2 0 0 0 0 0 0 1 15 Nghost: 3125.78 ave 4723 max 1528 min Histogram: 11 5 0 0 0 0 0 0 4 12 Neighs: 74653.5 ave 169489 max 0 min Histogram: 16 0 0 0 0 0 0 2 8 6 Total # of neighbors = 2388913 Ave neighs/atom = 262.48907 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: 18:18:22