#------------------------------------------------------------------------------- # 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 2768 = # 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 Ewald initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.31948988 estimated absolute RMS force accuracy = 0.0038193567 estimated relative force accuracy = 1.1501879e-05 KSpace vectors: actual max1d max3d = 10160 24 58824 kxmax kymax kzmax = 24 23 6 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.994493 1.08382 8304 2 96.7812 47.1697 2768 Per MPI rank memory allocation (min/avg/max) = 55.66 | 55.74 | 56.06 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 19561.077 92859.489 1.3074058 428.55654 88.202692 247.6823 0 0 24589.963 96909.922 -448.40969 -264784.47 -142948.7 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.27392e-06 8304 2 103.7 0.000105702 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.25008e-06 8304 2 103.7 0.000110009 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.21312e-06 8304 2 103.7 9.48295e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.49117e-06 8304 2 103.7 9.83373e-05 2768 200000 200000 3211.8022 92859.489 1.3074058 299.10805 43.83841 109.63999 0 0 22495.785 83067.816 -448.40969 -267354.04 -161636.96 5645.5116 Loop time of 6480.43 on 32 procs for 200000 steps with 9101 atoms Performance: 2.666 ns/day, 9.001 hours/ns, 30.862 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 427.82 | 474.83 | 509.63 | 82.3 | 7.33 Bond | 0.36928 | 1.0862 | 2.0889 | 45.1 | 0.02 Kspace | 4243.2 | 4464.2 | 4654.2 | 131.7 | 68.89 Neigh | 30.456 | 30.569 | 30.707 | 1.4 | 0.47 Comm | 669.84 | 874.33 | 1222.7 | 436.0 | 13.49 Output | 0.0096741 | 0.011989 | 0.014163 | 1.3 | 0.00 Modify | 483.15 | 631.58 | 810.71 | 299.9 | 9.75 Other | | 3.864 | | | 0.06 Nlocal: 284.406 ave 302 max 266 min Histogram: 1 4 3 3 4 5 5 3 2 2 Nghost: 4928.22 ave 5027 max 4811 min Histogram: 2 2 1 4 5 7 1 4 4 2 Neighs: 88659.6 ave 97155 max 79787 min Histogram: 1 2 4 4 4 4 6 3 2 2 Total # of neighbors = 2837108 Ave neighs/atom = 311.73585 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9851 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.4.xyz id mol type q xs ys zs run 0 Ewald initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.31948988 estimated absolute RMS force accuracy = 0.0038193567 estimated relative force accuracy = 1.1501879e-05 KSpace vectors: actual max1d max3d = 10160 24 58824 kxmax kymax kzmax = 24 23 6 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.49117e-06 8304 2 103.7 9.83373e-05 2768 Per MPI rank memory allocation (min/avg/max) = 55.66 | 55.96 | 56.25 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 3212.6745 92859.489 1.3074058 299.10805 43.83841 109.63999 0 0 22495.785 83067.816 -448.40969 -267354.04 -161636.96 5645.5116 Loop time of 8.27547e-06 on 32 procs for 0 steps with 9101 atoms 112.9% 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 Kspace | 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 | | 8.275e-06 | | |100.00 Nlocal: 284.406 ave 302 max 266 min Histogram: 1 4 3 3 4 5 5 3 2 2 Nghost: 4928.22 ave 5027 max 4811 min Histogram: 2 2 1 4 5 7 1 4 4 2 Neighs: 88659.6 ave 97155 max 79787 min Histogram: 1 2 4 4 4 4 6 3 2 2 Total # of neighbors = 2837108 Ave neighs/atom = 311.73585 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out