#------------------------------------------------------------------------------- # 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 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 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) = 0.24710655 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033650847 estimated relative force accuracy = 1.0133853e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00018 0.0551733 6000 1 97.8333 10.1198 2000 Per MPI rank memory allocation (min/avg/max) = 8.266 | 9.507 | 10.6 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-06 611.20039 120435.32 0.49678445 447.33728 0 0 0 0 9760.4305 60854.776 -51.790667 -101716.07 -31100.862 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.36753e-06 6000 1 103.7 9.23876e-05 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.2802e-06 6000 1 103.7 0.000111038 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.09877e-06 6000 1 103.7 9.93949e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.30493e-06 6000 1 103.7 0.000111055 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.22341e-06 6000 1 103.7 0.000103451 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.25467e-06 6000 1 103.7 9.47471e-05 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.17634e-06 6000 1 103.7 8.85552e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.36134e-06 6000 1 103.7 9.67954e-05 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.23104e-06 6000 1 103.7 0.000100928 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.23499e-06 6000 1 103.7 9.08115e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.4505e-06 6000 1 103.7 0.000107941 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.30974e-06 6000 1 103.7 9.67637e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 2.02402e-06 6000 1 103.7 0.000134817 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.24296e-06 6000 1 103.7 9.30312e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.15639e-06 6000 1 103.7 9.25493e-05 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.12882e-06 6000 1 103.7 9.255e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.24275e-06 6000 1 103.7 9.42178e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.61426e-06 6000 1 103.7 0.00011389 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.48344e-06 6000 1 103.7 0.000118602 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.32776e-06 6000 1 103.7 0.000121023 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.30034e-06 6000 1 103.7 8.96717e-05 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.13867e-06 6000 1 103.7 9.67207e-05 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.50765e-06 6000 1 103.7 0.000105316 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.18812e-06 6000 1 103.7 9.30922e-05 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.27702e-06 6000 1 103.7 0.000121302 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.22595e-06 6000 1 103.7 0.000100178 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.56895e-06 6000 1 103.7 0.000100824 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.30289e-06 6000 1 103.7 0.000100343 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.25871e-06 6000 1 103.7 0.000104198 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.6704e-06 6000 1 103.7 0.000140203 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.67998e-06 6000 1 103.7 0.000108517 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.10022e-06 6000 1 103.7 9.13233e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.26745e-06 6000 1 103.7 9.50173e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.42864e-06 6000 1 103.7 0.000156771 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.06607e-06 6000 1 103.7 9.0665e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.19724e-06 6000 1 103.7 9.38379e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.60888e-06 6000 1 103.7 0.000113354 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.7599e-06 6000 1 103.7 0.000124835 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.35811e-06 6000 1 103.7 0.000102978 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.90464e-06 6000 1 103.7 0.000136598 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.20691e-06 6000 1 103.7 9.61072e-05 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.41177e-06 6000 1 103.7 9.84091e-05 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.2558e-06 6000 1 103.7 0.000125018 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.5462e-06 6000 1 103.7 0.000102717 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.15196e-06 6000 1 103.7 9.14472e-05 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.11937e-06 6000 1 103.7 9.61648e-05 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.44504e-06 6000 1 103.7 9.14054e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.50435e-06 6000 1 103.7 0.000110572 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.49581e-06 6000 1 103.7 0.000104125 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.14116e-06 6000 1 103.7 9.033e-05 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.31282e-06 6000 1 103.7 0.000140842 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.29377e-06 6000 1 103.7 9.43932e-05 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.29293e-06 6000 1 103.7 0.000100634 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.72035e-06 6000 1 103.7 0.000112668 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.22588e-06 6000 1 103.7 9.45076e-05 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.40741e-06 6000 1 103.7 9.94808e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.22111e-06 6000 1 103.7 0.000101401 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.57181e-06 6000 1 103.7 0.000113669 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.40018e-06 6000 1 103.7 0.000123856 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.3754e-06 6000 1 103.7 0.000112384 2000 3000000 3000000 -236.73851 120435.32 0.49678445 299.8936 0 0 0 0 5047.8969 75576.694 -51.790667 -101689.99 -21065.399 3574.8095 Loop time of 24891.6 on 32 procs for 3000000 steps with 6000 atoms Performance: 10.413 ns/day, 2.305 hours/ns, 120.523 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.471 | 7757.1 | 18451 |8679.4 | 31.16 Bond | 2.4305 | 3.5621 | 8.2017 | 60.4 | 0.01 Kspace | 3505.2 | 14262 | 22127 |6437.6 | 57.30 Neigh | 1122.6 | 1130 | 1141.1 | 17.8 | 4.54 Comm | 299.99 | 664.49 | 883.43 | 817.3 | 2.67 Output | 0.012306 | 0.014054 | 0.015646 | 0.8 | 0.00 Modify | 871.16 | 1030.1 | 1266.7 | 479.4 | 4.14 Other | | 44.26 | | | 0.18 Nlocal: 187.5 ave 382 max 0 min Histogram: 12 2 2 0 0 0 1 1 2 12 Nghost: 4100 ave 7684 max 538 min Histogram: 4 4 0 4 4 4 4 0 4 4 Neighs: 91733.9 ave 226935 max 0 min Histogram: 16 0 0 0 0 1 5 1 5 4 Total # of neighbors = 2935484 Ave neighs/atom = 489.24733 Ave special neighs/atom = 2 Neighbor list builds = 148997 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) = 0.24710655 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033650847 estimated relative force accuracy = 1.0133853e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.3754e-06 6000 1 103.7 0.000112384 2000 Per MPI rank memory allocation (min/avg/max) = 8.301 | 9.725 | 10.6 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 -236.43533 120435.32 0.49678445 299.8936 0 0 0 0 5047.8969 75576.694 -51.790667 -101689.99 -21065.399 3574.8095 Loop time of 1.21114e-05 on 32 procs for 0 steps with 6000 atoms 101.4% 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 | | 1.211e-05 | | |100.00 Nlocal: 187.5 ave 382 max 0 min Histogram: 12 2 2 0 0 0 1 1 2 12 Nghost: 4100 ave 7684 max 538 min Histogram: 4 4 0 4 4 4 4 0 4 4 Neighs: 91733.9 ave 226935 max 0 min Histogram: 16 0 0 0 0 1 5 1 5 4 Total # of neighbors = 2935484 Ave neighs/atom = 489.24733 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out