#------------------------------------------------------------------------------- # 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 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 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 2.5_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 file 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25549962 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 3000000 3000000 -446.93445 140505.98 1.42352 297.11558 40.355609 49.262374 0 0 34367.862 -50915.295 -315.99625 -291941.23 -308399.05 6755.7009 Loop time of 71127 on 8 procs for 3000000 steps with 10721 atoms Performance: 3.644 ns/day, 6.586 hours/ns, 42.178 timesteps/s 98.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12474 | 43482 | 55949 |8601.3 | 61.13 Bond | 3.5841 | 16.319 | 27.154 | 210.0 | 0.02 Kspace | 9890.9 | 22366 | 53401 |12004.9 | 31.45 Neigh | 2942.8 | 2946.6 | 2951.5 | 5.4 | 4.14 Comm | 771.38 | 855.52 | 917.83 | 178.0 | 1.20 Output | 0.024242 | 0.027381 | 0.030231 | 1.2 | 0.00 Modify | 1321.2 | 1372 | 1425.3 | 97.7 | 1.93 Other | | 88.65 | | | 0.12 Nlocal: 1340.12 ave 1582 max 708 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11113.8 ave 13116 max 9621 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 625555 ave 822453 max 175177 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5004440 Ave neighs/atom = 466.78855 Ave special neighs/atom = 1.6069397 Neighbor list builds = 148866 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) = 0.25549962 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 3000000 2 0.97 1.40102e-06 8304 2 103.7 9.5857e-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 3000000 3000000 -446.31993 140505.98 1.42352 297.11558 40.355609 49.262374 0 0 34367.862 -50915.295 -315.99625 -291941.23 -308399.05 6755.7009 Loop time of 1.1186e-05 on 8 procs for 0 steps with 10721 atoms 115.1% 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 | | 1.119e-05 | | |100.00 Nlocal: 1340.12 ave 1582 max 708 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11113.8 ave 13116 max 9621 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 625555 ave 822453 max 175177 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5004440 Ave neighs/atom = 466.78855 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