#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 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 200000 200000 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 200 1 200 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.20127118 grid = 18 18 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0030938427 estimated relative force accuracy = 9.3170153e-06 using double precision KISS FFT 3d grid and FFT values/proc = 2304 324 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999135 0.0538681 6000 1 98.0059 9.08631 2000 Per MPI rank memory allocation (min/avg/max) = 9.877 | 10.18 | 10.28 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 1899.8676 59830.193 1.0000033 447.33728 0 0 0 0 8686.2956 43267.023 -53.651864 -82873.422 -30920.104 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.34945e-06 6000 1 103.7 0.000107626 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.21132e-06 6000 1 103.7 9.09702e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.46681e-06 6000 1 103.7 9.48588e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.15989e-06 6000 1 103.7 9.40752e-05 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.40958e-06 6000 1 103.7 0.000100835 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.24268e-06 6000 1 103.7 0.000110149 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.27383e-06 6000 1 103.7 9.98985e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.24247e-06 6000 1 103.7 9.96832e-05 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.07945e-06 6000 1 103.7 9.6307e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.19695e-06 6000 1 103.7 0.000106327 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.22215e-06 6000 1 103.7 0.000102744 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.24079e-06 6000 1 103.7 9.03689e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.27561e-06 6000 1 103.7 9.38084e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.44299e-06 6000 1 103.7 0.000114928 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.19933e-06 6000 1 103.7 9.58095e-05 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.11415e-06 6000 1 103.7 8.93216e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.1517e-06 6000 1 103.7 9.70849e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.46449e-06 6000 1 103.7 0.00012536 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.35413e-06 6000 1 103.7 0.000107301 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.11956e-06 6000 1 103.7 9.32399e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.20011e-06 6000 1 103.7 9.28158e-05 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.33253e-06 6000 1 103.7 0.00010558 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.17058e-06 6000 1 103.7 9.28675e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.3925e-06 6000 1 103.7 0.000100435 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.75975e-06 6000 1 103.7 0.000136251 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.25279e-06 6000 1 103.7 0.000101328 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.51915e-06 6000 1 103.7 0.000116009 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.21476e-06 6000 1 103.7 0.000105842 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.13299e-06 6000 1 103.7 0.000103257 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.25415e-06 6000 1 103.7 9.77395e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.64162e-06 6000 1 103.7 0.000115531 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.67826e-06 6000 1 103.7 0.000142485 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.35451e-06 6000 1 103.7 0.000118753 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.61001e-06 6000 1 103.7 9.67937e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.09134e-06 6000 1 103.7 0.000103548 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.1523e-06 6000 1 103.7 0.000102572 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.36131e-06 6000 1 103.7 0.000104315 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.15063e-06 6000 1 103.7 0.000112662 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.09427e-06 6000 1 103.7 0.00011063 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.32496e-06 6000 1 103.7 0.000119518 2000 2000000 2000000 -385.40093 59830.193 1.0000033 304.23151 0 0 0 0 4992.6662 56268.339 -53.651864 -82863.385 -21602.38 3626.5185 Loop time of 17478 on 32 procs for 2000000 steps with 6000 atoms Performance: 9.887 ns/day, 2.427 hours/ns, 114.430 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10590 | 11636 | 12668 | 429.9 | 66.57 Bond | 2.1054 | 2.5119 | 3.939 | 19.5 | 0.01 Kspace | 1633.4 | 2669.2 | 3717.1 | 898.9 | 15.27 Neigh | 593.79 | 594.41 | 594.93 | 1.1 | 3.40 Comm | 1328.5 | 1347 | 1368.9 | 29.1 | 7.71 Output | 0.009163 | 0.010992 | 0.012719 | 1.0 | 0.00 Modify | 1161.2 | 1177.9 | 1192.7 | 26.3 | 6.74 Other | | 51.49 | | | 0.29 Nlocal: 187.5 ave 199 max 175 min Histogram: 3 1 5 1 4 3 7 2 4 2 Nghost: 9987.69 ave 10076 max 9885 min Histogram: 3 1 1 2 5 6 7 1 2 4 Neighs: 193374 ave 220410 max 171856 min Histogram: 3 0 5 7 5 6 2 1 2 1 Total # of neighbors = 6187983 Ave neighs/atom = 1031.3305 Ave special neighs/atom = 2 Neighbor list builds = 98415 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.20127118 grid = 18 18 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0030938427 estimated relative force accuracy = 9.3170153e-06 using double precision KISS FFT 3d grid and FFT values/proc = 2304 324 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.32496e-06 6000 1 103.7 0.000119518 2000 Per MPI rank memory allocation (min/avg/max) = 10.25 | 10.27 | 10.28 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 2000000 2000000 -384.90398 59830.193 1.0000033 304.23151 0 0 0 0 4992.6662 56268.339 -53.651864 -82863.385 -21602.38 3626.5185 Loop time of 1.45729e-05 on 32 procs for 0 steps with 6000 atoms 110.4% 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 | | 1.457e-05 | | |100.00 Nlocal: 187.5 ave 199 max 175 min Histogram: 3 1 5 1 4 3 7 2 4 2 Nghost: 9987.69 ave 10076 max 9885 min Histogram: 3 1 1 2 5 6 7 1 2 4 Neighs: 193374 ave 220410 max 171856 min Histogram: 3 0 5 7 5 6 2 1 2 1 Total # of neighbors = 6187983 Ave neighs/atom = 1031.3305 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_NPT.out