#------------------------------------------------------------------------------- # Stage 2.4: 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 2009 = # 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 2.4_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 2.4_instantaneous.txt restart 3000000 2.4.restart dump sci all custom 300000 2.4.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) = 0.25041361 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033117663 estimated relative force accuracy = 9.9732859e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00086 0.0986334 6027 2 97.6883 9.0906 2009 Per MPI rank memory allocation (min/avg/max) = 10.94 | 12.27 | 13.55 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-06 147.42996 139839.06 0.6135188 429.78001 5.3808057 19.624273 0 0 16953.067 17615.542 -75.537794 -144757.95 -110164.33 5832.8145 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.82559e-06 6027 2 103.7 0.000114603 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.12633e-06 6027 2 103.7 0.000104646 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.32627e-06 6027 2 103.7 9.91585e-05 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.07994e-06 6027 2 103.7 9.02957e-05 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.16822e-06 6027 2 103.7 9.52743e-05 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.26718e-06 6027 2 103.7 9.11919e-05 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.28364e-06 6027 2 103.7 0.000145695 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.54828e-06 6027 2 103.7 0.000133911 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.54991e-06 6027 2 103.7 0.000100042 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.73391e-06 6027 2 103.7 0.000117552 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.15628e-06 6027 2 103.7 9.62014e-05 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.32239e-06 6027 2 103.7 0.000113019 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.08734e-06 6027 2 103.7 9.74724e-05 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.27024e-06 6027 2 103.7 0.00010494 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.15584e-06 6027 2 103.7 9.17929e-05 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.94284e-06 6027 2 103.7 0.00011744 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 2.40455e-06 6027 2 103.7 0.000139891 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 9.9642e-07 6027 2 103.7 9.34295e-05 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.06484e-06 6027 2 103.7 9.39991e-05 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.22548e-06 6027 2 103.7 9.47221e-05 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.00528e-06 6027 2 103.7 9.17382e-05 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.49456e-06 6027 2 103.7 0.000124201 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.21539e-06 6027 2 103.7 9.69985e-05 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.19975e-06 6027 2 103.7 9.75674e-05 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.47647e-06 6027 2 103.7 0.000114146 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.31401e-06 6027 2 103.7 9.98427e-05 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.12372e-06 6027 2 103.7 9.10631e-05 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.46379e-06 6027 2 103.7 0.000103955 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.29281e-06 6027 2 103.7 0.000101378 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.25853e-06 6027 2 103.7 0.000110541 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.07316e-06 6027 2 103.7 9.02242e-05 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.84063e-06 6027 2 103.7 0.000106558 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.15544e-06 6027 2 103.7 0.000109301 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.18857e-06 6027 2 103.7 0.000108578 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.29612e-06 6027 2 103.7 0.000101146 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.26842e-06 6027 2 103.7 0.00010353 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.48755e-06 6027 2 103.7 0.000112527 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.35191e-06 6027 2 103.7 0.000111671 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.27362e-06 6027 2 103.7 9.93936e-05 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.07153e-06 6027 2 103.7 8.95074e-05 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.4985e-06 6027 2 103.7 0.00011396 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.29712e-06 6027 2 103.7 0.000101724 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.17616e-06 6027 2 103.7 9.76608e-05 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.55876e-06 6027 2 103.7 0.000108665 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.08281e-06 6027 2 103.7 9.01548e-05 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.35329e-06 6027 2 103.7 8.91866e-05 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.07575e-06 6027 2 103.7 9.70485e-05 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.54487e-06 6027 2 103.7 0.000100468 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.66573e-06 6027 2 103.7 0.000131934 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.10289e-06 6027 2 103.7 9.4836e-05 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.07407e-06 6027 2 103.7 9.25114e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.15331e-06 6027 2 103.7 8.58593e-05 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.57475e-06 6027 2 103.7 0.000111403 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.24271e-06 6027 2 103.7 9.36882e-05 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.60864e-06 6027 2 103.7 0.000105022 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.35896e-06 6027 2 103.7 9.45253e-05 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.10178e-06 6027 2 103.7 9.77539e-05 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.22388e-06 6027 2 103.7 0.000101598 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.05509e-06 6027 2 103.7 9.39646e-05 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.15196e-06 6027 2 103.7 9.62771e-05 2009 3000000 3000000 -379.73196 139839.06 0.6135188 300.58123 39.167194 40.152321 0 0 13085.429 31819.403 -75.537794 -144708.09 -99723.934 4079.3767 Loop time of 26238.4 on 32 procs for 3000000 steps with 6563 atoms Performance: 9.879 ns/day, 2.429 hours/ns, 114.336 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9097 | 8023 | 19257 |8756.9 | 30.58 Bond | 2.6522 | 5.7071 | 18.072 | 163.0 | 0.02 Kspace | 3971.1 | 15266 | 23439 |6389.9 | 58.18 Neigh | 1141.3 | 1147.7 | 1158.6 | 17.2 | 4.37 Comm | 262.35 | 666.63 | 910.38 | 897.5 | 2.54 Output | 0.010868 | 0.012735 | 0.014422 | 0.9 | 0.00 Modify | 907.21 | 1084.9 | 1333.7 | 510.9 | 4.13 Other | | 44.75 | | | 0.17 Nlocal: 205.094 ave 423 max 0 min Histogram: 12 0 1 3 0 0 1 3 1 11 Nghost: 4023.31 ave 7876 max 227 min Histogram: 4 4 4 0 4 4 1 3 4 4 Neighs: 94962.7 ave 234606 max 0 min Histogram: 16 0 0 0 0 0 4 4 5 3 Total # of neighbors = 3038805 Ave neighs/atom = 463.02072 Ave special neighs/atom = 1.9037026 Neighbor list builds = 146333 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 2.4.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) = 0.25041361 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033117663 estimated relative force accuracy = 9.9732859e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.15196e-06 6027 2 103.7 9.62771e-05 2009 Per MPI rank memory allocation (min/avg/max) = 10.99 | 12.4 | 13.55 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 -379.37526 139839.06 0.6135188 300.58123 39.167194 40.152321 0 0 13085.429 31819.403 -75.537794 -144708.09 -99723.934 4079.3767 Loop time of 1.46478e-05 on 32 procs for 0 steps with 6563 atoms 102.2% 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 | | 1.465e-05 | | |100.00 Nlocal: 205.094 ave 423 max 0 min Histogram: 12 0 1 3 0 0 1 3 1 11 Nghost: 4023.31 ave 7876 max 227 min Histogram: 4 4 4 0 4 4 1 3 4 4 Neighs: 94962.7 ave 234606 max 0 min Histogram: 16 0 0 0 0 0 4 4 5 3 Total # of neighbors = 3038805 Ave neighs/atom = 463.02072 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out