#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 200 ps 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 20000 20000 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 20 1 20 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 200000 2.5.restart dump sci all custom 20000 2.5.xyz id mol type q xs ys zs timestep 1 run 200000 Ewald initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.31948988 estimated absolute RMS force accuracy = 0.0038193567 estimated relative force accuracy = 1.1501879e-05 KSpace vectors: actual max1d max3d = 10160 24 58824 kxmax kymax kzmax = 24 23 6 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.88956e-13 8304 2 103.7 7.21059e-11 2768 Per MPI rank memory allocation (min/avg/max) = 55.66 | 55.96 | 56.25 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 3212.6795 92859.489 1.3074058 299.10805 43.83841 109.63999 0 0 22495.784 83067.831 -448.40969 -267354.04 -161636.95 5645.5116 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.39202e-06 8304 2 103.7 0.000103727 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.40564e-06 8304 2 103.7 9.76147e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.49282e-06 8304 2 103.7 0.000124735 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.22652e-06 8304 2 103.7 0.000101144 2768 200000 200000 3031.2106 92859.489 1.3074058 294.45712 50.689261 73.886784 0 0 22513.253 83086.629 -448.40969 -267371.66 -161647.2 5557.7278 Loop time of 6500.6 on 32 procs for 200000 steps with 9101 atoms Performance: 2.658 ns/day, 9.029 hours/ns, 30.766 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 421.75 | 472.83 | 508.71 | 85.4 | 7.27 Bond | 0.33945 | 1.0765 | 2.0599 | 48.9 | 0.02 Kspace | 4274.3 | 4463.3 | 4699 | 146.2 | 68.66 Neigh | 30.205 | 30.315 | 30.445 | 1.3 | 0.47 Comm | 664.1 | 878.52 | 1268.6 | 443.1 | 13.51 Output | 0.0083204 | 0.010586 | 0.012724 | 1.3 | 0.00 Modify | 481.17 | 650.66 | 797.26 | 366.9 | 10.01 Other | | 3.901 | | | 0.06 Nlocal: 284.406 ave 303 max 265 min Histogram: 1 2 2 2 6 7 7 3 1 1 Nghost: 4926.5 ave 5050 max 4852 min Histogram: 5 3 5 5 5 2 2 3 1 1 Neighs: 88630 ave 94954 max 81211 min Histogram: 1 2 2 3 2 10 4 4 2 2 Total # of neighbors = 2836159 Ave neighs/atom = 311.63158 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9831 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.5.xyz id mol type q xs ys zs run 0 Ewald initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.31948988 estimated absolute RMS force accuracy = 0.0038193567 estimated relative force accuracy = 1.1501879e-05 KSpace vectors: actual max1d max3d = 10160 24 58824 kxmax kymax kzmax = 24 23 6 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.22652e-06 8304 2 103.7 0.000101144 2768 Per MPI rank memory allocation (min/avg/max) = 55.66 | 55.99 | 56.25 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 200000 200000 3032.2903 92859.489 1.3074058 294.45712 50.689261 73.886784 0 0 22513.253 83086.629 -448.40969 -267371.66 -161647.2 5557.7278 Loop time of 1.66226e-05 on 32 procs for 0 steps with 9101 atoms 108.3% 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 | | 1.662e-05 | | |100.00 Nlocal: 284.406 ave 303 max 265 min Histogram: 1 2 2 2 6 7 7 3 1 1 Nghost: 4926.5 ave 5050 max 4852 min Histogram: 5 3 5 5 5 2 2 3 1 1 Neighs: 88630 ave 94954 max 81211 min Histogram: 1 2 2 3 2 10 4 4 2 2 Total # of neighbors = 2836159 Ave neighs/atom = 311.63158 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 3:36:28