#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.56586e-13 6000 1 103.7 7.58718e-11 2000 Per MPI rank memory allocation (min/avg/max) = 8.438 | 9.649 | 10.26 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 -46.346677 119078.03 0.50244692 301.41176 0 0 0 0 5165.8663 95901.211 -89.819258 -122205.24 -21138.162 3592.9064 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.73015e-06 6000 1 103.7 0.000118999 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.86627e-06 6000 1 103.7 0.000121751 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.24541e-06 6000 1 103.7 9.9249e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.9072e-06 6000 1 103.7 0.000123172 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.2686e-06 6000 1 103.7 9.49413e-05 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.21066e-06 6000 1 103.7 9.40001e-05 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.11945e-06 6000 1 103.7 9.17315e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.25446e-06 6000 1 103.7 0.000104272 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 2.08547e-06 6000 1 103.7 0.000162962 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.02949e-06 6000 1 103.7 9.92106e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.45836e-06 6000 1 103.7 0.000101548 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.28002e-06 6000 1 103.7 0.000104754 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.08319e-06 6000 1 103.7 0.000118806 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.71834e-06 6000 1 103.7 0.00011739 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.14257e-06 6000 1 103.7 9.36405e-05 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.89192e-06 6000 1 103.7 0.000132007 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.16709e-06 6000 1 103.7 0.000100637 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.39458e-06 6000 1 103.7 0.000126555 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.41189e-06 6000 1 103.7 9.3555e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.64777e-06 6000 1 103.7 0.000108852 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.1667e-06 6000 1 103.7 9.83463e-05 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.16963e-06 6000 1 103.7 0.000106075 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.16652e-06 6000 1 103.7 9.91433e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.49574e-06 6000 1 103.7 0.000110305 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.63807e-06 6000 1 103.7 9.82329e-05 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.43243e-06 6000 1 103.7 9.57171e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.31683e-06 6000 1 103.7 9.65609e-05 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.95914e-06 6000 1 103.7 0.000113545 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.17407e-06 6000 1 103.7 9.24957e-05 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.11591e-06 6000 1 103.7 9.33903e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.97974e-06 6000 1 103.7 0.00013863 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.27674e-06 6000 1 103.7 0.000114706 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.12801e-06 6000 1 103.7 9.4793e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.16151e-06 6000 1 103.7 9.14967e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.71517e-06 6000 1 103.7 0.000142032 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.00928e-06 6000 1 103.7 9.10024e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.66254e-06 6000 1 103.7 0.000117614 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.51947e-06 6000 1 103.7 0.000118095 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.30459e-06 6000 1 103.7 9.94858e-05 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.39419e-06 6000 1 103.7 0.000135925 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.32894e-06 6000 1 103.7 0.00013557 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.50713e-06 6000 1 103.7 0.00010285 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.27939e-06 6000 1 103.7 9.57145e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.31363e-06 6000 1 103.7 8.90434e-05 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.09882e-06 6000 1 103.7 0.000106398 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.30519e-06 6000 1 103.7 0.000100671 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.2784e-06 6000 1 103.7 8.57646e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.43132e-06 6000 1 103.7 0.000104459 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.63772e-06 6000 1 103.7 0.000133043 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.60831e-06 6000 1 103.7 0.000121762 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.20488e-06 6000 1 103.7 9.43684e-05 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.469e-06 6000 1 103.7 9.46339e-05 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.15289e-06 6000 1 103.7 9.55252e-05 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.08834e-06 6000 1 103.7 9.23289e-05 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.19529e-06 6000 1 103.7 8.90816e-05 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.22596e-06 6000 1 103.7 9.32933e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.35726e-06 6000 1 103.7 0.0001026 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.55691e-06 6000 1 103.7 0.000100494 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.49872e-06 6000 1 103.7 9.3201e-05 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.19791e-06 6000 1 103.7 0.000110152 2000 3000000 3000000 -315.50423 119078.03 0.50244692 296.3068 0 0 0 0 4966.8992 96134.239 -89.819258 -122186.76 -21085.617 3532.0539 Loop time of 17157.7 on 32 procs for 3000000 steps with 6000 atoms Performance: 15.107 ns/day, 1.589 hours/ns, 174.849 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5507 | 4925 | 10440 |6812.7 | 28.70 Bond | 2.3719 | 3.1106 | 4.3585 | 23.1 | 0.02 Kspace | 4651 | 10256 | 15386 |4799.1 | 59.78 Neigh | 555.93 | 565.98 | 599.48 | 57.8 | 3.30 Comm | 16.279 | 430 | 649.59 |1149.7 | 2.51 Output | 0.010071 | 0.011702 | 0.013111 | 0.9 | 0.00 Modify | 803.02 | 927.38 | 1105.5 | 408.3 | 5.41 Other | | 49.91 | | | 0.29 Nlocal: 187.5 ave 380 max 0 min Histogram: 13 2 1 0 0 0 0 0 2 14 Nghost: 2913.75 ave 5720 max 0 min Histogram: 8 0 2 6 0 0 4 4 0 8 Neighs: 61758.4 ave 138925 max 0 min Histogram: 16 0 0 0 0 0 0 1 8 7 Total # of neighbors = 1976269 Ave neighs/atom = 329.37817 Ave special neighs/atom = 2 Neighbor list builds = 148587 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) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.19791e-06 6000 1 103.7 0.000110152 2000 Per MPI rank memory allocation (min/avg/max) = 8.437 | 9.649 | 10.26 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 -315.20051 119078.03 0.50244692 296.3068 0 0 0 0 4966.8992 96134.239 -89.819258 -122186.76 -21085.617 3532.0539 Loop time of 7.94237e-06 on 32 procs for 0 steps with 6000 atoms 106.2% 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 | | 7.942e-06 | | |100.00 Nlocal: 187.5 ave 380 max 0 min Histogram: 13 2 1 0 0 0 0 0 2 14 Nghost: 2913.75 ave 5720 max 0 min Histogram: 8 0 2 6 0 0 4 4 0 8 Neighs: 61758.4 ave 138925 max 0 min Histogram: 16 0 0 0 0 0 0 1 8 7 Total # of neighbors = 1976269 Ave neighs/atom = 329.37817 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 12:41:27