#------------------------------------------------------------------------------- # Stage 2.5: 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 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 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 v_surfacetension file 2.5_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 v_surfacetension file 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.20692e-12 8304 2 103.7 8.55351e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.77 | 12.17 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-06 427.92672 92859.489 1.3074058 299.39882 42.395683 126.36111 0 0 20673.22 -171096.98 -448.40969 0 -150255 5650.9998 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.16731e-06 8304 2 103.7 9.083e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.38703e-06 8304 2 103.7 0.000135631 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.59317e-06 8304 2 103.7 0.000112974 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.57687e-06 8304 2 103.7 0.000143765 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.43819e-06 8304 2 103.7 0.000125341 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.35052e-06 8304 2 103.7 0.000106155 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.72935e-06 8304 2 103.7 0.000115404 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.99912e-06 8304 2 103.7 0.000119982 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.63255e-06 8304 2 103.7 0.000105651 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 2.25436e-06 8304 2 103.7 0.000138528 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.73669e-06 8304 2 103.7 0.000117634 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.23714e-06 8304 2 103.7 0.00010065 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.18785e-06 8304 2 103.7 0.000100183 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.74635e-06 8304 2 103.7 0.000132878 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.64442e-06 8304 2 103.7 0.000117616 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.14222e-06 8304 2 103.7 9.7673e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.13465e-06 8304 2 103.7 0.000129949 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.31579e-06 8304 2 103.7 0.000100276 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.32761e-06 8304 2 103.7 0.000103548 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.55466e-06 8304 2 103.7 0.000110201 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.35629e-06 8304 2 103.7 0.00010064 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.33893e-06 8304 2 103.7 0.000100279 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.25623e-06 8304 2 103.7 0.000110741 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.33881e-06 8304 2 103.7 0.000126178 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.32148e-06 8304 2 103.7 0.000118735 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.30844e-06 8304 2 103.7 0.000103993 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.91049e-06 8304 2 103.7 0.000105927 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.82144e-06 8304 2 103.7 0.000115485 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.36359e-06 8304 2 103.7 0.000106431 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.76005e-06 8304 2 103.7 9.96684e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.46376e-06 8304 2 103.7 0.000103267 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.76031e-06 8304 2 103.7 0.000111176 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.81906e-06 8304 2 103.7 0.000106981 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.41714e-06 8304 2 103.7 0.000100191 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.22486e-06 8304 2 103.7 0.000109157 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.39554e-06 8304 2 103.7 9.64575e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.81631e-06 8304 2 103.7 0.000115137 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.57199e-06 8304 2 103.7 9.90248e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.38493e-06 8304 2 103.7 0.000101872 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.64056e-06 8304 2 103.7 0.000135041 2768 2000000 2000000 -1657.5986 92859.489 1.3074058 299.26379 37.897546 123.26798 0 0 20736.69 -178833.19 -448.40969 0 -157935.33 5648.4513 Loop time of 5832.26 on 32 procs for 2000000 steps with 9101 atoms Performance: 29.628 ns/day, 0.810 hours/ns, 342.920 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3991.4 | 4397.5 | 4808.7 | 314.0 | 75.40 Bond | 1.4 | 3.8537 | 7.1568 | 80.4 | 0.07 Neigh | 292.55 | 293.51 | 294.16 | 2.4 | 5.03 Comm | 230.96 | 578.46 | 958.01 | 868.3 | 9.92 Output | 0.0089983 | 0.0113 | 0.013462 | 1.3 | 0.00 Modify | 433.55 | 532.88 | 704.21 | 328.8 | 9.14 Other | | 26.01 | | | 0.45 Nlocal: 284.406 ave 301 max 268 min Histogram: 4 2 1 6 2 4 6 2 2 3 Nghost: 4936.03 ave 5066 max 4802 min Histogram: 1 2 3 4 7 5 4 1 2 3 Neighs: 88282.6 ave 96088 max 80383 min Histogram: 1 5 3 2 5 6 2 1 3 4 Total # of neighbors = 2825044 Ave neighs/atom = 310.41028 Ave special neighs/atom = 1.8929788 Neighbor list builds = 95421 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.64056e-06 8304 2 103.7 0.000135041 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.77 | 12.17 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 -1656.6261 92859.489 1.3074058 299.26379 37.897546 123.26798 0 0 20736.69 -178833.19 -448.40969 0 -157935.33 5648.4513 Loop time of 7.26475e-06 on 32 procs for 0 steps with 9101 atoms 114.0% 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 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 | | 7.265e-06 | | |100.00 Nlocal: 284.406 ave 301 max 268 min Histogram: 4 2 1 6 2 4 6 2 2 3 Nghost: 4936.03 ave 5066 max 4802 min Histogram: 1 2 3 4 7 5 4 1 2 3 Neighs: 88282.6 ave 96088 max 80383 min Histogram: 1 5 3 2 5 6 2 1 3 4 Total # of neighbors = 2825044 Ave neighs/atom = 310.41028 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: 5:40:44