#------------------------------------------------------------------------------- # Stage 2.6: 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 4018 = # 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 v_surfacetension file 2.6_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 v_surfacetension file 2.6_instantaneous.txt restart 2000000 2.6.restart dump sci all custom 200000 2.6.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) = 0.31988 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.003651357 estimated relative force accuracy = 1.0995953e-05 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.0044e-13 12054 2 103.7 7.50049e-11 4018 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.66 | 14.4 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 -396.86794 193007.11 0.88902312 295.15381 63.073576 87.082501 0 0 26490.42 142104.32 -435.22696 -368638.74 -199893.84 8012.3154 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.13788e-06 12054 2 103.7 0.000106519 4018 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.47348e-06 12054 2 103.7 0.000102893 4018 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.212e-06 12054 2 103.7 9.70395e-05 4018 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.14961e-06 12054 2 103.7 9.64859e-05 4018 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.41664e-06 12054 2 103.7 0.000112635 4018 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.50462e-06 12054 2 103.7 0.000135412 4018 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.51265e-06 12054 2 103.7 0.000100798 4018 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.36512e-06 12054 2 103.7 9.07116e-05 4018 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.40475e-06 12054 2 103.7 9.87115e-05 4018 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.5068e-06 12054 2 103.7 0.000115331 4018 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.46411e-06 12054 2 103.7 0.00010361 4018 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.77485e-06 12054 2 103.7 0.000113428 4018 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.22782e-06 12054 2 103.7 9.43516e-05 4018 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.41113e-06 12054 2 103.7 0.000150531 4018 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.25086e-06 12054 2 103.7 9.9117e-05 4018 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.25573e-06 12054 2 103.7 9.48805e-05 4018 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.34167e-06 12054 2 103.7 9.65551e-05 4018 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.34354e-06 12054 2 103.7 9.26148e-05 4018 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.05301e-06 12054 2 103.7 0.000107041 4018 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.14412e-06 12054 2 103.7 0.000100216 4018 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.40992e-06 12054 2 103.7 0.000104415 4018 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.43654e-06 12054 2 103.7 9.31895e-05 4018 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.12808e-06 12054 2 103.7 9.84054e-05 4018 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.51455e-06 12054 2 103.7 0.000104147 4018 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.25465e-06 12054 2 103.7 0.000106926 4018 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.10791e-06 12054 2 103.7 9.68435e-05 4018 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.5506e-06 12054 2 103.7 0.000134724 4018 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.32856e-06 12054 2 103.7 0.000111901 4018 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.12654e-06 12054 2 103.7 9.50737e-05 4018 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.22655e-06 12054 2 103.7 9.20603e-05 4018 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.47619e-06 12054 2 103.7 0.000111096 4018 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.16796e-06 12054 2 103.7 9.41066e-05 4018 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.31584e-06 12054 2 103.7 0.000101269 4018 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.56175e-06 12054 2 103.7 9.49286e-05 4018 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.53322e-06 12054 2 103.7 0.000100831 4018 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.24149e-06 12054 2 103.7 8.93561e-05 4018 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.1144e-06 12054 2 103.7 9.32863e-05 4018 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.29013e-06 12054 2 103.7 0.000107405 4018 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.2956e-06 12054 2 103.7 9.78027e-05 4018 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.40241e-06 12054 2 103.7 9.49887e-05 4018 2000000 2000000 -197.40002 193007.11 0.88902312 296.84123 61.565146 87.131442 0 0 26652.256 141967.16 -435.22696 -368647.77 -199879.65 8058.1225 Loop time of 17690.3 on 32 procs for 2000000 steps with 13126 atoms Performance: 9.768 ns/day, 2.457 hours/ns, 113.056 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 881.15 | 5796.6 | 8841.1 |3899.5 | 32.77 Bond | 2.1957 | 6.0934 | 15.562 | 142.8 | 0.03 Kspace | 6531.9 | 9601.9 | 14550 |3044.0 | 54.28 Neigh | 517.57 | 520.89 | 525.04 | 10.2 | 2.94 Comm | 520.52 | 703.51 | 785.26 | 382.0 | 3.98 Output | 0.014643 | 0.017439 | 0.020165 | 1.3 | 0.00 Modify | 952.39 | 1010.5 | 1159.9 | 267.7 | 5.71 Other | | 50.79 | | | 0.29 Nlocal: 410.188 ave 581 max 25 min Histogram: 8 0 0 0 0 0 0 2 6 16 Nghost: 4509.16 ave 6138 max 3272 min Histogram: 8 0 8 0 8 0 0 0 0 8 Neighs: 111270 ave 177208 max 6424 min Histogram: 8 0 0 0 0 6 2 0 6 10 Total # of neighbors = 3560633 Ave neighs/atom = 271.26566 Ave special neighs/atom = 1.9037026 Neighbor list builds = 102957 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.6.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) = 0.31988 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.003651357 estimated relative force accuracy = 1.0995953e-05 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.40241e-06 12054 2 103.7 9.49887e-05 4018 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.66 | 14.4 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 -196.82101 193007.11 0.88902312 296.84123 61.565146 87.131442 0 0 26652.256 141967.16 -435.22696 -368647.77 -199879.65 8058.1225 Loop time of 8.16362e-06 on 32 procs for 0 steps with 13126 atoms 118.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.164e-06 | | |100.00 Nlocal: 410.188 ave 581 max 25 min Histogram: 8 0 0 0 0 0 0 2 6 16 Nghost: 4509.16 ave 6138 max 3272 min Histogram: 8 0 8 0 8 0 0 0 0 8 Neighs: 111270 ave 177208 max 6424 min Histogram: 8 0 0 0 0 6 2 0 6 10 Total # of neighbors = 3560633 Ave neighs/atom = 271.26566 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 17:11:33