#------------------------------------------------------------------------------- # Stage 2.3: 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 WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) 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 file 2.3_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 file 2.3_instantaneous.txt restart 200000 2.3.restart dump sci all custom 20000 2.3.xyz id mol type q xs ys zs timestep 1 run 200000 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 7 7 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 0 2 1.00023 0.089284 8304 2 97.8686 12.7643 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.79 | 12.21 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 7957.1062 83832.935 1.4481783 428.55654 9.26327 70.922677 0 0 25449.614 -179260.07 0 0 -153730.27 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.20348e-06 8304 2 103.7 9.09449e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.72926e-06 8304 2 103.7 0.000124504 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.38393e-06 8304 2 103.7 0.000113668 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.20538e-06 8304 2 103.7 0.00011712 2768 200000 200000 3344.0198 95857.347 1.2665178 299.01337 39.543572 158.60405 0 0 23353.632 -183486.94 0 0 -159935.16 5643.7247 Loop time of 724.977 on 32 procs for 200000 steps with 9101 atoms Performance: 23.835 ns/day, 1.007 hours/ns, 275.871 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 266.49 | 438.16 | 591.01 | 514.1 | 60.44 Bond | 0.15589 | 0.38784 | 0.72773 | 25.4 | 0.05 Neigh | 35 | 35.101 | 35.254 | 1.3 | 4.84 Comm | 47.263 | 188.04 | 331.71 | 685.5 | 25.94 Output | 0.011935 | 0.0142 | 0.016322 | 1.1 | 0.00 Modify | 48.195 | 60.324 | 88.229 | 209.0 | 8.32 Other | | 2.949 | | | 0.41 Nlocal: 284.406 ave 336 max 231 min Histogram: 3 6 3 4 0 0 1 6 6 3 Nghost: 4260.94 ave 5315 max 3198 min Histogram: 16 0 0 0 0 0 0 0 0 16 Neighs: 86253 ave 116463 max 48159 min Histogram: 6 2 0 2 6 0 1 3 6 6 Total # of neighbors = 2760097 Ave neighs/atom = 303.27404 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9535 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.3.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 1.20538e-06 8304 2 103.7 0.00011712 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.88 | 12.21 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 3345.1783 95857.347 1.2665178 299.01337 39.543572 158.60405 0 0 23353.632 -183486.94 0 0 -159935.16 5643.7247 Loop time of 7.62106e-06 on 32 procs for 0 steps with 9101 atoms 113.6% 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 | | 7.621e-06 | | |100.00 Nlocal: 284.406 ave 336 max 231 min Histogram: 3 6 3 4 0 0 1 6 6 3 Nghost: 4260.94 ave 5315 max 3198 min Histogram: 16 0 0 0 0 0 0 0 0 16 Neighs: 86253 ave 116463 max 48159 min Histogram: 6 2 0 2 6 0 1 3 6 6 Total # of neighbors = 2760097 Ave neighs/atom = 303.27404 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.4_NVT.out