#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 200 ps with a timestep of 1 fs # Temperature 298.15 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 8303 = # 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 298.15 298.15 100 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 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.63836e-12 24909 2 103.7 1.24714e-10 8303 Per MPI rank memory allocation (min/avg/max) = 12.6 | 12.77 | 13.18 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 -372.07471 322479.38 1.1293339 302.1865 141.35434 391.92751 0 0 63348.08 -526074.12 0 0 -462192.76 17110.848 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.54704e-06 24909 2 103.7 0.000112903 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.79565e-06 24909 2 103.7 0.000118388 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.50426e-06 24909 2 103.7 0.000110567 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.30917e-06 24909 2 103.7 0.000126302 8303 200000 200000 -986.93744 327386.35 1.1124071 299.47152 152.85334 379.6362 0 0 63176.619 -533401.69 0 0 -469692.59 16957.116 Loop time of 1593.7 on 32 procs for 200000 steps with 27300 atoms Performance: 10.843 ns/day, 2.213 hours/ns, 125.494 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 979.93 | 1132.1 | 1359.3 | 288.8 | 71.03 Bond | 0.37819 | 0.85632 | 1.6168 | 33.9 | 0.05 Neigh | 85.948 | 86.132 | 86.379 | 1.1 | 5.40 Comm | 46.705 | 246.38 | 430.74 | 640.8 | 15.46 Output | 0.022558 | 0.027321 | 0.031878 | 1.7 | 0.00 Modify | 91.104 | 123.38 | 211.55 | 326.1 | 7.74 Other | | 4.865 | | | 0.31 Nlocal: 853.125 ave 919 max 800 min Histogram: 2 3 4 4 7 3 5 2 1 1 Nghost: 5291.66 ave 5421 max 5163 min Histogram: 3 1 3 3 6 3 5 4 3 1 Neighs: 238441 ave 288934 max 204799 min Histogram: 4 8 2 1 6 2 5 2 1 1 Total # of neighbors = 7630117 Ave neighs/atom = 279.49147 Ave special neighs/atom = 1.892967 Neighbor list builds = 10574 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.5.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.30917e-06 24909 2 103.7 0.000126302 8303 Per MPI rank memory allocation (min/avg/max) = 12.59 | 12.76 | 13.18 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 -986.06449 327386.35 1.1124071 299.47152 152.85334 379.6362 0 0 63176.619 -533401.69 0 0 -469692.59 16957.116 Loop time of 9.74584e-06 on 32 procs for 0 steps with 27300 atoms 109.3% 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 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 | | 9.746e-06 | | |100.00 Nlocal: 853.125 ave 919 max 800 min Histogram: 2 3 4 4 7 3 5 2 1 1 Nghost: 5291.66 ave 5421 max 5163 min Histogram: 3 1 3 3 6 3 5 4 3 1 Neighs: 238441 ave 288934 max 204799 min Histogram: 4 8 2 1 6 2 5 2 1 1 Total # of neighbors = 7630117 Ave neighs/atom = 279.49147 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 0:52:33