#------------------------------------------------------------------------------- # 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 2009 = # 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 v_surfacetension 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 v_surfacetension file 2.5_instantaneous.txt 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) = 0.25044719 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033056861 estimated relative force accuracy = 9.9549755e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.37299e-13 6027 2 103.7 8.20819e-11 2009 Per MPI rank memory allocation (min/avg/max) = 11.07 | 12.54 | 13.52 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 -211.08509 139673.96 0.614244 301.54156 36.950061 47.71411 0 0 13231.123 31626.802 -75.627082 -144720.2 -99777.606 4092.4099 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.22271e-06 6027 2 103.7 9.30923e-05 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.07161e-06 6027 2 103.7 9.33353e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.26452e-06 6027 2 103.7 9.174e-05 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25539e-06 6027 2 103.7 9.6464e-05 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.23706e-06 6027 2 103.7 0.000103887 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.10553e-06 6027 2 103.7 9.39034e-05 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.42325e-06 6027 2 103.7 8.91911e-05 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.21959e-06 6027 2 103.7 9.17738e-05 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.21493e-06 6027 2 103.7 0.000108442 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.10082e-06 6027 2 103.7 8.6995e-05 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.44514e-06 6027 2 103.7 0.000112162 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.31058e-06 6027 2 103.7 0.000100791 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.08118e-06 6027 2 103.7 0.000104639 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.23978e-06 6027 2 103.7 9.31172e-05 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.25824e-06 6027 2 103.7 9.4057e-05 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.41945e-06 6027 2 103.7 0.000114588 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.10453e-06 6027 2 103.7 9.16371e-05 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.3283e-06 6027 2 103.7 9.32335e-05 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.21367e-06 6027 2 103.7 9.1158e-05 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.32411e-06 6027 2 103.7 8.18414e-05 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.21822e-06 6027 2 103.7 0.000100842 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.51197e-06 6027 2 103.7 0.000121319 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.15587e-06 6027 2 103.7 0.000100903 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20133e-06 6027 2 103.7 0.000113101 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.0869e-06 6027 2 103.7 9.22155e-05 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.30872e-06 6027 2 103.7 9.85867e-05 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.57179e-06 6027 2 103.7 0.000111532 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.33959e-06 6027 2 103.7 0.000108645 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.20072e-06 6027 2 103.7 0.000103568 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.14794e-06 6027 2 103.7 8.61517e-05 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.14487e-06 6027 2 103.7 9.34424e-05 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.28444e-06 6027 2 103.7 0.000115176 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.16907e-06 6027 2 103.7 0.000105021 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.24195e-06 6027 2 103.7 9.37809e-05 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.05809e-06 6027 2 103.7 0.000101956 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.23771e-06 6027 2 103.7 9.22277e-05 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.27439e-06 6027 2 103.7 9.94444e-05 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.097e-06 6027 2 103.7 8.23081e-05 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.19068e-06 6027 2 103.7 0.000100412 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.21003e-06 6027 2 103.7 0.000101972 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.47048e-06 6027 2 103.7 0.000114011 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.26682e-06 6027 2 103.7 9.39713e-05 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.41804e-06 6027 2 103.7 0.000113518 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.29814e-06 6027 2 103.7 0.000122375 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.1803e-06 6027 2 103.7 0.000135887 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.34485e-06 6027 2 103.7 0.000101583 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.73385e-06 6027 2 103.7 0.000113529 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.48794e-06 6027 2 103.7 0.000130744 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.40593e-06 6027 2 103.7 0.000115606 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.66457e-06 6027 2 103.7 0.000128898 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.11785e-06 6027 2 103.7 9.68876e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.33388e-06 6027 2 103.7 9.74699e-05 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.35394e-06 6027 2 103.7 0.000103872 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.20051e-06 6027 2 103.7 0.000104082 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.1845e-06 6027 2 103.7 9.25816e-05 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.18606e-06 6027 2 103.7 0.000107802 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.56651e-06 6027 2 103.7 0.000128662 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.23158e-06 6027 2 103.7 0.000107941 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.53732e-06 6027 2 103.7 0.000118156 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.09329e-06 6027 2 103.7 9.79579e-05 2009 3000000 3000000 338.48263 139673.96 0.614244 305.26448 37.134152 50.157998 0 0 13435.423 31445.338 -75.627082 -144738.78 -99770.729 4142.9361 Loop time of 26291.4 on 32 procs for 3000000 steps with 6563 atoms Performance: 9.859 ns/day, 2.434 hours/ns, 114.106 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.985 | 8013.6 | 18843 |8864.2 | 30.48 Bond | 2.6303 | 6.0494 | 16.864 | 156.4 | 0.02 Kspace | 4211.3 | 15087 | 23202 |6497.0 | 57.38 Neigh | 1215.6 | 1223.1 | 1234.5 | 16.4 | 4.65 Comm | 328.8 | 700.71 | 935.31 | 825.6 | 2.67 Output | 0.010683 | 0.012408 | 0.013869 | 0.9 | 0.00 Modify | 1036.4 | 1201.7 | 1447.7 | 467.6 | 4.57 Other | | 58.94 | | | 0.22 Nlocal: 205.094 ave 420 max 0 min Histogram: 14 0 2 0 0 0 0 0 4 12 Nghost: 4019.72 ave 7590 max 451 min Histogram: 8 0 0 6 2 2 6 0 0 8 Neighs: 95667.2 ave 234604 max 0 min Histogram: 16 0 0 0 0 1 3 4 2 6 Total # of neighbors = 3061350 Ave neighs/atom = 466.45589 Ave special neighs/atom = 1.9037026 Neighbor list builds = 146349 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) = 0.25044719 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033056861 estimated relative force accuracy = 9.9549755e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.09329e-06 6027 2 103.7 9.79579e-05 2009 Per MPI rank memory allocation (min/avg/max) = 11.07 | 12.54 | 13.52 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 338.90575 139673.96 0.614244 305.26448 37.134152 50.157998 0 0 13435.423 31445.338 -75.627082 -144738.78 -99770.729 4142.9361 Loop time of 1.27256e-05 on 32 procs for 0 steps with 6563 atoms 101.4% 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 | | 1.273e-05 | | |100.00 Nlocal: 205.094 ave 420 max 0 min Histogram: 14 0 2 0 0 0 0 0 4 12 Nghost: 4019.72 ave 7590 max 451 min Histogram: 8 0 0 6 2 2 6 0 0 8 Neighs: 95667.2 ave 234604 max 0 min Histogram: 16 0 0 0 0 1 3 4 2 6 Total # of neighbors = 3061350 Ave neighs/atom = 466.45589 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: 19:24:06