#------------------------------------------------------------------------------- # 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 8.42215e-13 8304 2 103.7 7.64402e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.13 | 12.56 | 12.72 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-06 313.56897 92859.489 1.3074058 297.80713 53.76728 135.84501 0 0 21687.058 -181474.63 -386.0007 0 -159597.96 5620.9574 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.43281e-06 8304 2 103.7 0.000104981 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.29891e-06 8304 2 103.7 9.2992e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.38714e-06 8304 2 103.7 0.000119958 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.43338e-06 8304 2 103.7 0.000106983 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.65685e-06 8304 2 103.7 0.000112757 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.52339e-06 8304 2 103.7 9.67995e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.29088e-06 8304 2 103.7 0.000107839 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.65562e-06 8304 2 103.7 9.46954e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.40264e-06 8304 2 103.7 9.65236e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 2.23492e-06 8304 2 103.7 0.000117726 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.62139e-06 8304 2 103.7 0.00010764 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.29239e-06 8304 2 103.7 0.000100389 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.92741e-06 8304 2 103.7 0.000158879 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.53344e-06 8304 2 103.7 0.00010359 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.67546e-06 8304 2 103.7 0.000100911 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.41468e-06 8304 2 103.7 0.000127141 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.73119e-06 8304 2 103.7 0.000126596 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.47666e-06 8304 2 103.7 0.00010218 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.36289e-06 8304 2 103.7 0.000105827 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.44816e-06 8304 2 103.7 0.000100566 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.38138e-06 8304 2 103.7 0.000114579 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.32433e-06 8304 2 103.7 9.26092e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.61131e-06 8304 2 103.7 0.000108411 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.77945e-06 8304 2 103.7 0.000104082 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.19759e-06 8304 2 103.7 0.000106272 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.42742e-06 8304 2 103.7 0.000110676 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.57551e-06 8304 2 103.7 0.000106181 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.53739e-06 8304 2 103.7 0.000113015 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.39554e-06 8304 2 103.7 0.000100272 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.67247e-06 8304 2 103.7 0.00011205 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 2.07129e-06 8304 2 103.7 0.000139695 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.71758e-06 8304 2 103.7 9.50646e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.71423e-06 8304 2 103.7 0.000126384 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.42681e-06 8304 2 103.7 0.000113205 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.63371e-06 8304 2 103.7 0.000114683 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.25564e-06 8304 2 103.7 0.000105828 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.39893e-06 8304 2 103.7 0.000119771 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.32328e-06 8304 2 103.7 0.000101463 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.41842e-06 8304 2 103.7 0.000132931 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.45906e-06 8304 2 103.7 0.000102083 2768 2000000 2000000 44.033721 92859.489 1.3074058 302.57357 48.631498 114.14584 0 0 21277.465 -177891.89 -386.0007 0 -156451.65 5710.9215 Loop time of 11690.4 on 16 procs for 2000000 steps with 9101 atoms Performance: 14.781 ns/day, 1.624 hours/ns, 171.081 timesteps/s 99.5% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8695.1 | 9632.1 | 10227 | 398.0 | 82.39 Bond | 2.3761 | 6.8234 | 9.7397 | 67.7 | 0.06 Neigh | 599.87 | 600.27 | 600.85 | 1.0 | 5.13 Comm | 279.49 | 794.48 | 1561.3 |1268.9 | 6.80 Output | 0.013739 | 0.015479 | 0.017022 | 0.8 | 0.00 Modify | 537.98 | 623.23 | 794.11 | 331.9 | 5.33 Other | | 33.48 | | | 0.29 Nlocal: 568.812 ave 590 max 544 min Histogram: 1 3 0 1 1 3 1 3 0 3 Nghost: 6746.25 ave 6840 max 6618 min Histogram: 1 0 0 2 1 3 5 2 0 2 Neighs: 200806 ave 213329 max 183262 min Histogram: 1 0 0 3 2 3 1 2 1 3 Total # of neighbors = 3212896 Ave neighs/atom = 353.0267 Ave special neighs/atom = 1.8929788 Neighbor list builds = 95574 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 1.45906e-06 8304 2 103.7 0.000102083 2768 Per MPI rank memory allocation (min/avg/max) = 12.13 | 12.56 | 12.72 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 45.192314 92859.489 1.3074058 302.57357 48.631498 114.14584 0 0 21277.465 -177891.89 -386.0007 0 -156451.65 5710.9215 Loop time of 4.23069e-06 on 16 procs for 0 steps with 9101 atoms 116.7% 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 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 | | 4.231e-06 | | |100.00 Nlocal: 568.812 ave 590 max 544 min Histogram: 1 3 0 1 1 3 1 3 0 3 Nghost: 6746.25 ave 6840 max 6618 min Histogram: 1 0 0 2 1 3 5 2 0 2 Neighs: 200806 ave 213329 max 183262 min Histogram: 1 0 0 3 2 3 1 2 1 3 Total # of neighbors = 3212896 Ave neighs/atom = 353.0267 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: 3:24:43