#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 4 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 400000 400000 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 2.5_averages.txt off 1 fix 3 movable ave/time 400 1 400 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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 4000000 2.5.restart dump sci all custom 400000 2.5.xyz id mol type q xs ys zs timestep 1 run 4000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.07847e-13 8304 2 103.7 7.48628e-11 2768 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.28 | 17.25 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 -233.58634 140505.98 1.42352 299.70713 41.848576 69.21725 0 0 34444.48 -50954.863 -315.99625 -291936.32 -308335.64 6814.6266 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.24342e-06 8304 2 103.7 9.98071e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.31579e-06 8304 2 103.7 9.71793e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.23031e-06 8304 2 103.7 9.34821e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25934e-06 8304 2 103.7 9.11901e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.16414e-06 8304 2 103.7 9.69398e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.61231e-06 8304 2 103.7 0.000129489 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.04006e-06 8304 2 103.7 9.51968e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.10116e-06 8304 2 103.7 9.29314e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.12466e-06 8304 2 103.7 0.000113726 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.66614e-06 8304 2 103.7 0.000114996 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.42539e-06 8304 2 103.7 9.31907e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.86486e-06 8304 2 103.7 0.000119448 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.23804e-06 8304 2 103.7 9.59166e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.3962e-06 8304 2 103.7 9.12294e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.0417e-06 8304 2 103.7 0.000102055 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.20128e-06 8304 2 103.7 9.27323e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.12556e-06 8304 2 103.7 9.54833e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.47499e-06 8304 2 103.7 9.35099e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.52855e-06 8304 2 103.7 0.000101859 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.25034e-06 8304 2 103.7 0.000100154 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.24208e-06 8304 2 103.7 8.96671e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.17835e-06 8304 2 103.7 9.39025e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.20667e-06 8304 2 103.7 9.06246e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.28491e-06 8304 2 103.7 9.22519e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.27683e-06 8304 2 103.7 9.19331e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.62519e-06 8304 2 103.7 0.000114475 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.31192e-06 8304 2 103.7 9.21725e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.13155e-06 8304 2 103.7 9.85834e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.21804e-06 8304 2 103.7 0.000101782 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.10497e-06 8304 2 103.7 9.73353e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.23424e-06 8304 2 103.7 0.00010546 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.15907e-06 8304 2 103.7 9.49925e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.35979e-06 8304 2 103.7 8.822e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.12542e-06 8304 2 103.7 9.6759e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.42563e-06 8304 2 103.7 0.000114798 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.27548e-06 8304 2 103.7 9.48047e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.20928e-06 8304 2 103.7 0.000100841 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.89986e-06 8304 2 103.7 0.000110991 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.26743e-06 8304 2 103.7 9.37269e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.35979e-06 8304 2 103.7 0.00013107 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.33763e-06 8304 2 103.7 0.000102376 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.30291e-06 8304 2 103.7 9.92738e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.13036e-06 8304 2 103.7 9.72317e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.20642e-06 8304 2 103.7 0.000101197 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.08719e-06 8304 2 103.7 8.54029e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.35572e-06 8304 2 103.7 9.13985e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.20548e-06 8304 2 103.7 9.39765e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.21105e-06 8304 2 103.7 0.000105722 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.45394e-06 8304 2 103.7 0.000108478 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.45116e-06 8304 2 103.7 0.000111641 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.06987e-06 8304 2 103.7 9.90817e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.33689e-06 8304 2 103.7 0.000106883 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.07216e-06 8304 2 103.7 8.72182e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.15109e-06 8304 2 103.7 9.26336e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.14316e-06 8304 2 103.7 9.27333e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.84403e-06 8304 2 103.7 0.000110113 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.17382e-06 8304 2 103.7 0.000108963 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.3469e-06 8304 2 103.7 9.06441e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.19146e-06 8304 2 103.7 9.10914e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.40102e-06 8304 2 103.7 9.5857e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.42355e-06 8304 2 103.7 0.000125249 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.52731e-06 8304 2 103.7 9.96988e-05 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.51727e-06 8304 2 103.7 9.76246e-05 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.39535e-06 8304 2 103.7 9.81208e-05 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.11504e-06 8304 2 103.7 9.53406e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.62829e-06 8304 2 103.7 0.00012005 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.36241e-06 8304 2 103.7 0.000100922 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.26795e-06 8304 2 103.7 0.000100228 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.76541e-06 8304 2 103.7 0.000131444 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.3741e-06 8304 2 103.7 0.000100832 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.45878e-06 8304 2 103.7 0.000106245 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.40097e-06 8304 2 103.7 0.000108554 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.35541e-06 8304 2 103.7 9.96111e-05 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.31377e-06 8304 2 103.7 9.51423e-05 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.02439e-06 8304 2 103.7 9.36398e-05 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.49995e-06 8304 2 103.7 0.000101703 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.87933e-06 8304 2 103.7 0.000121038 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.11384e-06 8304 2 103.7 9.72543e-05 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.18898e-06 8304 2 103.7 9.28727e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.03981e-06 8304 2 103.7 9.25576e-05 2768 4000000 4000000 -295.72495 140505.98 1.42352 299.22493 45.63275 76.46349 0 0 34482.165 -51089.543 -315.99625 -291932.23 -308417.51 6803.6624 Loop time of 94214.9 on 8 procs for 4000000 steps with 10721 atoms Performance: 3.668 ns/day, 6.543 hours/ns, 42.456 timesteps/s 98.7% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15945 | 56488 | 74497 |9838.9 | 59.96 Bond | 5.0354 | 21.753 | 32.193 | 229.0 | 0.02 Kspace | 12695 | 30730 | 71312 |13353.0 | 32.62 Neigh | 3929 | 3934.1 | 3940.9 | 6.1 | 4.18 Comm | 984.19 | 1118.3 | 1204.5 | 246.0 | 1.19 Output | 0.025195 | 0.02812 | 0.03081 | 1.1 | 0.00 Modify | 1743.7 | 1808.9 | 1905.4 | 143.7 | 1.92 Other | | 113.6 | | | 0.12 Nlocal: 1340.12 ave 1597 max 707 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11110.1 ave 13085 max 9593 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 625992 ave 821123 max 177125 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5007934 Ave neighs/atom = 467.11445 Ave special neighs/atom = 1.6069397 Neighbor list builds = 198492 Dangerous builds = 0 undump sci restart 0 dump sci all custom 4000000 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.03981e-06 8304 2 103.7 9.25576e-05 2768 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.3 | 17.25 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 4000000 4000000 -295.13085 140505.98 1.42352 299.22493 45.63275 76.46349 0 0 34482.165 -51089.543 -315.99625 -291932.23 -308417.51 6803.6624 Loop time of 3.06863e-06 on 8 procs for 0 steps with 10721 atoms 122.2% CPU use with 8 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 | | 3.069e-06 | | |100.00 Nlocal: 1340.12 ave 1597 max 707 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11110.1 ave 13085 max 9593 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 625992 ave 821123 max 177125 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5007934 Ave neighs/atom = 467.11445 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out