#------------------------------------------------------------------------------- # 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 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 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) = 0.25187548 grid = 24 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0023982645 estimated relative force accuracy = 7.2223022e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1728 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 8.78408e-13 6000 1 103.7 7.35696e-11 2000 Per MPI rank memory allocation (min/avg/max) = 8.363 | 9.786 | 10.71 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 -300.72719 119542.27 0.50049569 293.08383 0 0 0 0 4918.1096 77548.181 -52.177571 -103665.66 -21199.37 3493.6353 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.71335e-06 6000 1 103.7 0.000125887 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.63808e-06 6000 1 103.7 0.000122945 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.75992e-06 6000 1 103.7 0.000145523 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.08456e-06 6000 1 103.7 9.16219e-05 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.26142e-06 6000 1 103.7 0.000109215 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.80642e-06 6000 1 103.7 0.000123391 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.65983e-06 6000 1 103.7 0.000128899 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.92913e-06 6000 1 103.7 0.000155 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.11383e-06 6000 1 103.7 9.06578e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.10813e-06 6000 1 103.7 0.000104761 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.57918e-06 6000 1 103.7 0.000111834 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.23825e-06 6000 1 103.7 0.000110734 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.369e-06 6000 1 103.7 0.000102161 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.14954e-06 6000 1 103.7 0.000100252 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.11977e-06 6000 1 103.7 9.17232e-05 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.25905e-06 6000 1 103.7 9.34935e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.32878e-06 6000 1 103.7 9.44791e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.17218e-06 6000 1 103.7 9.56142e-05 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.14473e-06 6000 1 103.7 0.000105351 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.26379e-06 6000 1 103.7 0.000114136 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 2.12765e-06 6000 1 103.7 0.000145253 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.2718e-06 6000 1 103.7 0.000116693 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.3352e-06 6000 1 103.7 0.000112923 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.38382e-06 6000 1 103.7 9.56582e-05 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.51993e-06 6000 1 103.7 0.000105272 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.36718e-06 6000 1 103.7 0.000101946 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.15857e-06 6000 1 103.7 9.58564e-05 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.11877e-06 6000 1 103.7 9.56816e-05 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.18832e-06 6000 1 103.7 0.000117379 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.19565e-06 6000 1 103.7 9.0391e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.1806e-06 6000 1 103.7 9.59917e-05 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.11837e-06 6000 1 103.7 9.71998e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.67066e-06 6000 1 103.7 0.00013249 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.11782e-06 6000 1 103.7 9.27585e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.21107e-06 6000 1 103.7 9.62887e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.14563e-06 6000 1 103.7 9.1982e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.2375e-06 6000 1 103.7 0.000100514 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.31912e-06 6000 1 103.7 0.000105849 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.13622e-06 6000 1 103.7 9.67591e-05 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.47032e-06 6000 1 103.7 0.000111823 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.18687e-06 6000 1 103.7 9.67721e-05 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.59969e-06 6000 1 103.7 0.000104025 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.49251e-06 6000 1 103.7 9.74267e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.2156e-06 6000 1 103.7 0.0001139 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.59295e-06 6000 1 103.7 0.000117188 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.20809e-06 6000 1 103.7 9.23851e-05 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.76824e-06 6000 1 103.7 0.000114512 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.42737e-06 6000 1 103.7 0.00010801 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.3043e-06 6000 1 103.7 9.92191e-05 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.59406e-06 6000 1 103.7 0.000113085 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.29116e-06 6000 1 103.7 8.99749e-05 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.52018e-06 6000 1 103.7 0.000111602 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.22424e-06 6000 1 103.7 9.38855e-05 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.88275e-06 6000 1 103.7 0.000121317 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.13578e-06 6000 1 103.7 9.54397e-05 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.19331e-06 6000 1 103.7 9.8253e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.38153e-06 6000 1 103.7 0.00011738 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.55918e-06 6000 1 103.7 0.000170086 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.16432e-06 6000 1 103.7 8.94805e-05 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.25492e-06 6000 1 103.7 0.000107468 2000 3000000 3000000 -125.18304 119542.27 0.50049569 294.8403 0 0 0 0 5149.9445 77243.887 -52.177571 -103664.63 -21270.8 3514.5728 Loop time of 24249.3 on 32 procs for 3000000 steps with 6000 atoms Performance: 10.689 ns/day, 2.245 hours/ns, 123.715 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5211 | 8033.4 | 17283 |8815.4 | 33.13 Bond | 2.3996 | 3.3409 | 4.9499 | 29.8 | 0.01 Kspace | 4203.9 | 13578 | 21877 |6872.8 | 55.99 Neigh | 911.09 | 923.56 | 964.76 | 55.1 | 3.81 Comm | 23.472 | 560.85 | 852.44 |1322.1 | 2.31 Output | 0.011339 | 0.012971 | 0.014364 | 0.8 | 0.00 Modify | 931.76 | 1098.3 | 1328.3 | 503.6 | 4.53 Other | | 52.19 | | | 0.22 Nlocal: 187.5 ave 383 max 0 min Histogram: 12 4 0 0 0 0 0 0 2 14 Nghost: 3941.97 ave 7838 max 0 min Histogram: 8 0 3 5 0 0 4 4 0 8 Neighs: 97597.6 ave 219220 max 0 min Histogram: 16 0 0 0 0 0 0 4 4 8 Total # of neighbors = 3123124 Ave neighs/atom = 520.52067 Ave special neighs/atom = 2 Neighbor list builds = 148559 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) = 0.25187548 grid = 24 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0023982645 estimated relative force accuracy = 7.2223022e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1728 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.25492e-06 6000 1 103.7 0.000107468 2000 Per MPI rank memory allocation (min/avg/max) = 8.362 | 9.816 | 10.71 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 -124.81114 119542.27 0.50049569 294.8403 0 0 0 0 5149.9445 77243.887 -52.177571 -103664.63 -21270.8 3514.5728 Loop time of 6.60481e-06 on 32 procs for 0 steps with 6000 atoms 133.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 6.605e-06 | | |100.00 Nlocal: 187.5 ave 383 max 0 min Histogram: 12 4 0 0 0 0 0 0 2 14 Nghost: 3941.97 ave 7838 max 0 min Histogram: 8 0 3 5 0 0 4 4 0 8 Neighs: 97597.6 ave 219220 max 0 min Histogram: 16 0 0 0 0 0 0 4 4 8 Total # of neighbors = 3123124 Ave neighs/atom = 520.52067 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 17:57:55