#------------------------------------------------------------------------------- # 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 1928 = # 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) = 0.2507789 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0034789377 estimated relative force accuracy = 1.0476718e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00173 0.0648551 5784 2 97.4964 9.68719 1928 Per MPI rank memory allocation (min/avg/max) = 10.94 | 12.28 | 13.54 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-06 788.52042 137108.63 0.6335873 427.16581 5.4783809 16.869476 0 0 19722.755 -2024.9545 -77.153063 -152579.23 -134859.08 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.81425e-06 5784 2 103.7 0.000115733 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.24587e-06 5784 2 103.7 0.000100307 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.54495e-06 5784 2 103.7 0.000125784 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.26174e-06 5784 2 103.7 9.82189e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.15408e-06 5784 2 103.7 8.59031e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.36982e-06 5784 2 103.7 0.000104613 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.28229e-06 5784 2 103.7 0.000135444 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.33418e-06 5784 2 103.7 9.49676e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.57626e-06 5784 2 103.7 0.000115705 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.06476e-06 5784 2 103.7 9.70673e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.07451e-06 5784 2 103.7 9.2351e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.28169e-06 5784 2 103.7 8.79054e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.2479e-06 5784 2 103.7 9.30288e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.06741e-06 5784 2 103.7 9.66931e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.36763e-06 5784 2 103.7 9.43894e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.10993e-06 5784 2 103.7 8.65406e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.1557e-06 5784 2 103.7 9.91488e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.07341e-06 5784 2 103.7 9.30667e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.20826e-06 5784 2 103.7 9.09584e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17813e-06 5784 2 103.7 8.98634e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.2008e-06 5784 2 103.7 9.15771e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.2808e-06 5784 2 103.7 9.39372e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.06285e-06 5784 2 103.7 9.05319e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.26145e-06 5784 2 103.7 9.34345e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.2282e-06 5784 2 103.7 9.53073e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 9.32827e-07 5784 2 103.7 9.06348e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.45423e-06 5784 2 103.7 0.00012331 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.1107e-06 5784 2 103.7 8.83682e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.31778e-06 5784 2 103.7 0.000108697 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.57376e-06 5784 2 103.7 0.00012011 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.09866e-06 5784 2 103.7 9.36187e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.25953e-06 5784 2 103.7 9.86186e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.05177e-06 5784 2 103.7 9.22616e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.26357e-06 5784 2 103.7 0.000103606 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.22356e-06 5784 2 103.7 9.35106e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.06477e-06 5784 2 103.7 8.98763e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.91872e-06 5784 2 103.7 0.000118513 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.30196e-06 5784 2 103.7 0.000102558 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.24656e-06 5784 2 103.7 9.74257e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.10897e-06 5784 2 103.7 0.000106607 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.10091e-06 5784 2 103.7 9.80389e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.51976e-06 5784 2 103.7 0.000125736 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.23246e-06 5784 2 103.7 9.11277e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.10088e-06 5784 2 103.7 8.84886e-05 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.20856e-06 5784 2 103.7 9.62491e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.24655e-06 5784 2 103.7 9.99888e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.73203e-06 5784 2 103.7 0.000128582 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.13159e-06 5784 2 103.7 9.26303e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.13505e-06 5784 2 103.7 9.07729e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.34508e-06 5784 2 103.7 9.86789e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.63769e-06 5784 2 103.7 0.000111658 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.3139e-06 5784 2 103.7 0.000131743 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.10054e-06 5784 2 103.7 0.000100946 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.26837e-06 5784 2 103.7 8.9174e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.23226e-06 5784 2 103.7 9.68652e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.56609e-06 5784 2 103.7 0.000149016 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.05372e-06 5784 2 103.7 9.70499e-05 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.13686e-06 5784 2 103.7 9.3311e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.27746e-06 5784 2 103.7 9.39275e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.16048e-06 5784 2 103.7 9.74161e-05 1928 3000000 3000000 1.2980044 137108.63 0.6335873 297.71395 31.286651 34.737045 0 0 16376.286 11283.155 -77.153063 -152642.1 -124916.64 3956.1573 Loop time of 25560.5 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.141 ns/day, 2.367 hours/ns, 117.369 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 | 4.8477 | 7706.9 | 18614 |8526.6 | 30.15 Bond | 2.5984 | 5.459 | 12.763 | 137.9 | 0.02 Kspace | 3948.6 | 14907 | 22759 |6171.9 | 58.32 Neigh | 1147.2 | 1153.9 | 1164.2 | 16.4 | 4.51 Comm | 253.03 | 650.52 | 891.86 | 895.3 | 2.55 Output | 0.010509 | 0.012374 | 0.014045 | 0.9 | 0.00 Modify | 915.61 | 1092.3 | 1335.9 | 503.9 | 4.27 Other | | 44.76 | | | 0.18 Nlocal: 199.594 ave 425 max 0 min Histogram: 12 0 1 3 0 0 4 0 3 9 Nghost: 3956.09 ave 7726 max 139 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 91447.6 ave 222313 max 0 min Histogram: 16 0 0 0 0 2 2 2 5 5 Total # of neighbors = 2926323 Ave neighs/atom = 458.16862 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145259 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) = 0.2507789 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0034789377 estimated relative force accuracy = 1.0476718e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.16048e-06 5784 2 103.7 9.74161e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.08 | 12.42 | 13.54 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 1.7380883 137108.63 0.6335873 297.71395 31.286651 34.737045 0 0 16376.286 11283.155 -77.153063 -152642.1 -124916.64 3956.1573 Loop time of 6.91228e-06 on 32 procs for 0 steps with 6387 atoms 113.9% 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 | | 6.912e-06 | | |100.00 Nlocal: 199.594 ave 425 max 0 min Histogram: 12 0 1 3 0 0 4 0 3 9 Nghost: 3956.09 ave 7726 max 139 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 91447.6 ave 222313 max 0 min Histogram: 16 0 0 0 0 2 2 2 5 5 Total # of neighbors = 2926323 Ave neighs/atom = 458.16862 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out