#------------------------------------------------------------------------------- # 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 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 2.4_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 fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00088 0.0704157 8304 2 97.6595 9.8462 2768 Per MPI rank memory allocation (min/avg/max) = 12.42 | 13.2 | 13.76 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 -2989.9456 143908.11 1.3942094 410.14353 6.7571064 28.334897 0 0 32424.626 -37472.532 -320.88394 -277806.09 -282818.91 8993.151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.59658e-06 8304 2 103.7 0.000123927 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.13393e-06 8304 2 103.7 8.71874e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.14764e-06 8304 2 103.7 0.000123231 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.11727e-06 8304 2 103.7 9.36909e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.63078e-06 8304 2 103.7 0.000119973 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.39024e-06 8304 2 103.7 9.6286e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.22954e-06 8304 2 103.7 9.19944e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1324e-06 8304 2 103.7 9.45212e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.16014e-06 8304 2 103.7 9.77075e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.39145e-06 8304 2 103.7 0.000117193 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.12756e-06 8304 2 103.7 9.1904e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.57353e-06 8304 2 103.7 9.66499e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.46323e-06 8304 2 103.7 0.000100931 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.29673e-06 8304 2 103.7 9.07544e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.28576e-06 8304 2 103.7 9.66937e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.15029e-06 8304 2 103.7 9.39539e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.13844e-06 8304 2 103.7 0.000102239 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.10983e-06 8304 2 103.7 9.29646e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.36119e-06 8304 2 103.7 9.81763e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.34306e-06 8304 2 103.7 0.000112888 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.18462e-06 8304 2 103.7 9.42323e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.48787e-06 8304 2 103.7 0.000103172 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.28101e-06 8304 2 103.7 9.48361e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.5939e-06 8304 2 103.7 9.88963e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.12522e-06 8304 2 103.7 8.89974e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.20804e-06 8304 2 103.7 9.56889e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.36351e-06 8304 2 103.7 0.000103833 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.39818e-06 8304 2 103.7 0.000109903 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.32784e-06 8304 2 103.7 0.000115551 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.3501e-06 8304 2 103.7 9.43323e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.13382e-06 8304 2 103.7 9.01116e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.3281e-06 8304 2 103.7 0.000110613 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.18762e-06 8304 2 103.7 9.26864e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.06796e-06 8304 2 103.7 8.88607e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.1114e-06 8304 2 103.7 0.000102671 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.14198e-06 8304 2 103.7 9.42491e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.35251e-06 8304 2 103.7 9.02864e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.2041e-06 8304 2 103.7 9.70043e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.12807e-06 8304 2 103.7 0.000108913 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.28479e-06 8304 2 103.7 0.000116439 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.2968e-06 8304 2 103.7 0.000101975 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.62046e-06 8304 2 103.7 0.000110776 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.34553e-06 8304 2 103.7 8.92335e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.70885e-06 8304 2 103.7 0.000128739 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.25648e-06 8304 2 103.7 8.80303e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.21221e-06 8304 2 103.7 0.000114371 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.54725e-06 8304 2 103.7 0.00011546 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.30165e-06 8304 2 103.7 9.4223e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.25155e-06 8304 2 103.7 0.000108975 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.20724e-06 8304 2 103.7 9.14884e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.5982e-06 8304 2 103.7 9.59912e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.39087e-06 8304 2 103.7 0.000103093 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.16153e-06 8304 2 103.7 9.15191e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.75478e-06 8304 2 103.7 0.00012736 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.15051e-06 8304 2 103.7 9.22997e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.18477e-06 8304 2 103.7 9.53044e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.90822e-06 8304 2 103.7 0.000128696 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.22233e-06 8304 2 103.7 0.000116072 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.35366e-06 8304 2 103.7 9.84589e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.52823e-06 8304 2 103.7 9.67474e-05 2768 3000000 3000000 -940.26041 143908.11 1.3942094 297.08169 37.376139 64.399102 0 0 29236.785 -19798.015 -320.88394 -277697.19 -268156.64 6514.0622 Loop time of 28696.8 on 32 procs for 3000000 steps with 10381 atoms Performance: 9.032 ns/day, 2.657 hours/ns, 104.541 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2700 | 12628 | 18346 |5335.9 | 44.01 Bond | 2.7634 | 7.7327 | 13.283 | 130.1 | 0.03 Kspace | 6133.4 | 11876 | 21825 |5523.1 | 41.38 Neigh | 1291.4 | 1293.7 | 1296.5 | 4.6 | 4.51 Comm | 911.44 | 1279.2 | 1428.7 | 469.6 | 4.46 Output | 0.014761 | 0.017176 | 0.019521 | 1.1 | 0.00 Modify | 1421.3 | 1548 | 1856.7 | 371.5 | 5.39 Other | | 63.84 | | | 0.22 Nlocal: 324.406 ave 425 max 128 min Histogram: 8 0 0 0 0 0 1 5 8 10 Nghost: 6029.09 ave 7549 max 3915 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 148405 ave 223375 max 26764 min Histogram: 8 0 0 0 0 3 2 3 9 7 Total # of neighbors = 4748961 Ave neighs/atom = 457.46662 Ave special neighs/atom = 1.6595704 Neighbor list builds = 148929 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.52823e-06 8304 2 103.7 9.67474e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.43 | 13.24 | 13.76 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 -939.68367 143908.11 1.3942094 297.08169 37.376139 64.399102 0 0 29236.785 -19798.015 -320.88394 -277697.19 -268156.64 6514.0622 Loop time of 1.44637e-05 on 32 procs for 0 steps with 10381 atoms 116.7% 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 | | 1.446e-05 | | |100.00 Nlocal: 324.406 ave 425 max 128 min Histogram: 8 0 0 0 0 0 1 5 8 10 Nghost: 6029.09 ave 7549 max 3915 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 148405 ave 223375 max 26764 min Histogram: 8 0 0 0 0 3 2 3 9 7 Total # of neighbors = 4748961 Ave neighs/atom = 457.46662 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_Custom.out