#------------------------------------------------------------------------------- # Stage 2.4: 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 8303 = # of frozen angles find clusters CPU = 0.002 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 file 2.4_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 2.4_instantaneous.txt restart 200000 2.4.restart dump sci all custom 20000 2.4.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 0.994869 0.818103 24909 2 96.5257 95.1836 8303 Per MPI rank memory allocation (min/avg/max) = 12.59 | 12.73 | 13.19 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 34829.23 280706.73 1.2973928 428.54084 131.26044 992.54333 0 0 89338.355 -464441.87 0 0 -373979.71 24265.468 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.58485e-06 24909 2 103.7 0.000124578 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.36454e-06 24909 2 103.7 0.000119435 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.63503e-06 24909 2 103.7 0.000125805 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.50135e-06 24909 2 103.7 0.000109457 8303 200000 200000 756.75225 329121.76 1.1065415 298.2021 159.9552 360.44872 0 0 64367.695 -521377.28 0 0 -456489.18 16885.237 Loop time of 1549.54 on 32 procs for 200000 steps with 27300 atoms Performance: 11.152 ns/day, 2.152 hours/ns, 129.070 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 962.7 | 1146.9 | 1309.3 | 335.0 | 74.01 Bond | 0.24168 | 0.85571 | 1.4499 | 33.6 | 0.06 Neigh | 85.514 | 85.718 | 85.903 | 1.1 | 5.53 Comm | 52.75 | 211.38 | 404 | 793.5 | 13.64 Output | 0.025038 | 0.029836 | 0.034507 | 1.7 | 0.00 Modify | 90.77 | 99.761 | 119.4 | 68.5 | 6.44 Other | | 4.928 | | | 0.32 Nlocal: 853.125 ave 905 max 804 min Histogram: 3 3 3 5 4 2 2 5 3 2 Nghost: 5275.53 ave 5399 max 5122 min Histogram: 1 0 2 5 6 6 5 1 3 3 Neighs: 239822 ave 276930 max 199056 min Histogram: 3 6 4 2 1 0 3 3 3 7 Total # of neighbors = 7674310 Ave neighs/atom = 281.11026 Ave special neighs/atom = 1.892967 Neighbor list builds = 10612 Dangerous builds = 1 undump sci restart 0 dump sci all custom 200000 2.4.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 1.50135e-06 24909 2 103.7 0.000109457 8303 Per MPI rank memory allocation (min/avg/max) = 12.59 | 12.8 | 13.19 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 757.62068 329121.76 1.1065415 298.2021 159.9552 360.44872 0 0 64367.695 -521377.28 0 0 -456489.18 16885.237 Loop time of 8.0025e-06 on 32 procs for 0 steps with 27300 atoms 108.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.002e-06 | | |100.00 Nlocal: 853.125 ave 905 max 804 min Histogram: 3 3 3 5 4 2 2 5 3 2 Nghost: 5275.53 ave 5399 max 5122 min Histogram: 1 0 2 5 6 6 5 1 3 3 Neighs: 239822 ave 276930 max 199056 min Histogram: 3 6 4 2 1 0 3 3 3 7 Total # of neighbors = 7674310 Ave neighs/atom = 281.11026 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out