#------------------------------------------------------------------------------- # Stage 2.4: 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 2699 = # 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 file 2.4_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 file 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.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) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.99539 0.781566 8097 2 96.4565 47.4908 2699 Per MPI rank memory allocation (min/avg/max) = 13.7 | 14.09 | 14.27 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 18705.812 91446.309 1.3291045 427.22241 141.31641 221.96479 0 0 27811.123 35668.162 -226.3957 -218591.6 -154749.03 7943.8987 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.7624e-06 8097 2 103.7 0.000115234 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.58931e-06 8097 2 103.7 0.000113151 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.07759e-06 8097 2 103.7 8.78321e-05 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.11622e-06 8097 2 103.7 9.49705e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.53133e-06 8097 2 103.7 0.000106017 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.37118e-06 8097 2 103.7 0.000112455 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.11516e-06 8097 2 103.7 9.132e-05 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.06837e-06 8097 2 103.7 9.64924e-05 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.17542e-06 8097 2 103.7 9.38969e-05 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.31065e-06 8097 2 103.7 9.6719e-05 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.16694e-06 8097 2 103.7 9.56972e-05 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.07831e-06 8097 2 103.7 0.0001025 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.33567e-06 8097 2 103.7 9.42541e-05 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.46961e-06 8097 2 103.7 9.63114e-05 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.12922e-06 8097 2 103.7 0.000102031 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.55516e-06 8097 2 103.7 0.000118741 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.27744e-06 8097 2 103.7 0.000119392 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.2329e-06 8097 2 103.7 0.000105486 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.25432e-06 8097 2 103.7 9.32832e-05 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.43483e-06 8097 2 103.7 0.000109411 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.24104e-06 8097 2 103.7 9.30054e-05 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.50067e-06 8097 2 103.7 8.84804e-05 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.20055e-06 8097 2 103.7 8.77327e-05 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.29681e-06 8097 2 103.7 9.21413e-05 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.27661e-06 8097 2 103.7 9.99271e-05 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.15018e-06 8097 2 103.7 0.000129081 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.1217e-06 8097 2 103.7 9.1259e-05 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.78132e-06 8097 2 103.7 0.000101585 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.26059e-06 8097 2 103.7 9.91673e-05 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.20185e-06 8097 2 103.7 9.38511e-05 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.5776e-06 8097 2 103.7 0.000107849 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.3996e-06 8097 2 103.7 0.000104767 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.03217e-06 8097 2 103.7 9.82771e-05 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.33514e-06 8097 2 103.7 9.80819e-05 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.14397e-06 8097 2 103.7 8.85281e-05 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.43005e-06 8097 2 103.7 0.000121219 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.20462e-06 8097 2 103.7 9.08922e-05 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.13682e-06 8097 2 103.7 0.000110296 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.29116e-06 8097 2 103.7 0.000102858 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.21126e-06 8097 2 103.7 0.000105808 2699 2000000 2000000 2975.0548 91446.309 1.3291045 298.73426 40.533371 71.948456 0 0 24083.729 19876.846 -226.3957 -220285.28 -176212.22 5554.7525 Loop time of 25893.2 on 16 procs for 2000000 steps with 8938 atoms Performance: 6.674 ns/day, 3.596 hours/ns, 77.240 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16180 | 16953 | 18224 | 463.4 | 65.47 Bond | 5.5051 | 8.9008 | 12.493 | 61.4 | 0.03 Kspace | 5128 | 6408.2 | 7179.2 | 756.7 | 24.75 Neigh | 1016 | 1016.7 | 1017.4 | 1.4 | 3.93 Comm | 550.55 | 559.73 | 572.59 | 26.2 | 2.16 Output | 0.01494 | 0.016636 | 0.018174 | 0.8 | 0.00 Modify | 878.89 | 885.09 | 890.22 | 13.1 | 3.42 Other | | 61.28 | | | 0.24 Nlocal: 558.625 ave 592 max 534 min Histogram: 2 1 2 3 2 2 1 2 0 1 Nghost: 8993.88 ave 9087 max 8896 min Histogram: 1 1 2 2 2 1 2 2 2 1 Neighs: 313573 ave 337214 max 296952 min Histogram: 1 3 2 2 3 3 0 0 1 1 Total # of neighbors = 5017173 Ave neighs/atom = 561.33061 Ave special neighs/atom = 1.8722309 Neighbor list builds = 97879 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.21126e-06 8097 2 103.7 0.000105808 2699 Per MPI rank memory allocation (min/avg/max) = 14.04 | 14.19 | 14.3 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 2976.1809 91446.309 1.3291045 298.73426 40.533371 71.948456 0 0 24083.729 19876.846 -226.3957 -220285.28 -176212.22 5554.7525 Loop time of 4.00031e-06 on 16 procs for 0 steps with 8938 atoms 125.0% 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 | | 4e-06 | | |100.00 Nlocal: 558.625 ave 592 max 534 min Histogram: 2 1 2 3 2 2 1 2 0 1 Nghost: 8993.88 ave 9087 max 8896 min Histogram: 1 1 2 2 2 1 2 2 2 1 Neighs: 313573 ave 337214 max 296952 min Histogram: 1 3 2 2 3 3 0 0 1 1 Total # of neighbors = 5017173 Ave neighs/atom = 561.33061 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out