#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 1 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 100000 100000 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 2.5_averages.txt off 1 fix 3 movable ave/time 100 1 100 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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.5.restart dump sci all custom 100000 2.5.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.47027e-12 8304 2 103.7 1.4299e-10 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.19 | 14.79 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-06 114.92463 140505.98 1.42352 299.67324 56.758096 63.551762 0 0 34600.5 -51036.673 -315.99625 -291945.2 -308261.06 6813.8559 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.7226e-06 8304 2 103.7 0.000102527 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.53905e-06 8304 2 103.7 0.00012015 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.15708e-06 8304 2 103.7 9.46778e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.34097e-06 8304 2 103.7 0.000103188 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.40529e-06 8304 2 103.7 9.73974e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.18373e-06 8304 2 103.7 8.92356e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.50942e-06 8304 2 103.7 0.000105977 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.47126e-06 8304 2 103.7 0.00010062 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.42999e-06 8304 2 103.7 9.87894e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.27932e-06 8304 2 103.7 9.50307e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.11616e-06 8304 2 103.7 9.10419e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.23303e-06 8304 2 103.7 0.000102441 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.13466e-06 8304 2 103.7 0.00010251 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.13153e-06 8304 2 103.7 0.00010154 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.14851e-06 8304 2 103.7 0.000110072 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.42935e-06 8304 2 103.7 0.000107324 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.32884e-06 8304 2 103.7 9.1503e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.01897e-06 8304 2 103.7 0.000100157 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.20042e-06 8304 2 103.7 8.78245e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.35974e-06 8304 2 103.7 9.814e-05 2768 1000000 1000000 -88.604834 140505.98 1.42352 294.82895 44.402032 63.926864 0 0 34549.961 -51005.426 -315.99625 -291946.8 -308293.94 6703.7084 Loop time of 14133.5 on 16 procs for 1000000 steps with 10721 atoms Performance: 6.113 ns/day, 3.926 hours/ns, 70.754 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2252.4 | 8085.8 | 10888 |3703.5 | 57.21 Bond | 1.0876 | 3.5021 | 6.2038 | 89.2 | 0.02 Kspace | 1976.4 | 4779.3 | 10621 |4823.8 | 33.82 Neigh | 560.33 | 561.48 | 562.83 | 3.3 | 3.97 Comm | 246.85 | 295.25 | 318.1 | 160.0 | 2.09 Output | 0.016336 | 0.018262 | 0.020015 | 0.9 | 0.00 Modify | 369.34 | 387.1 | 428.47 | 121.0 | 2.74 Other | | 21.02 | | | 0.15 Nlocal: 670.062 ave 822 max 352 min Histogram: 4 0 0 0 0 0 0 1 5 6 Nghost: 8252.5 ave 9757 max 6992 min Histogram: 4 0 0 2 6 0 0 0 0 4 Neighs: 313252 ave 424374 max 88560 min Histogram: 4 0 0 0 0 0 0 1 5 6 Total # of neighbors = 5012038 Ave neighs/atom = 467.49725 Ave special neighs/atom = 1.6069397 Neighbor list builds = 49579 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.35974e-06 8304 2 103.7 9.814e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.21 | 14.79 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 1000000 1000000 -87.96258 140505.98 1.42352 294.82895 44.402032 63.926864 0 0 34549.961 -51005.426 -315.99625 -291946.8 -308293.94 6703.7084 Loop time of 9.38763e-06 on 16 procs for 0 steps with 10721 atoms 113.2% CPU use with 16 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 | | 9.388e-06 | | |100.00 Nlocal: 670.062 ave 822 max 352 min Histogram: 4 0 0 0 0 0 0 1 5 6 Nghost: 8252.5 ave 9757 max 6992 min Histogram: 4 0 0 2 6 0 0 0 0 4 Neighs: 313252 ave 424374 max 88560 min Histogram: 4 0 0 0 0 0 0 1 5 6 Total # of neighbors = 5012038 Ave neighs/atom = 467.49725 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out