#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 10 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 2699 = # 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 1000 1000 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 1 1 1 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 10000 2.4.restart dump sci all custom 1000 2.4.xyz id mol type q xs ys zs timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.99539 0.781566 8097 2 96.4565 47.4908 2699 Per MPI rank memory allocation (min/avg/max) = 13.7 | 14.09 | 14.27 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 18705.812 91446.309 1.3291045 427.22241 141.31641 221.96479 0 0 27811.123 35668.162 -226.3957 -218591.6 -154749.03 7943.8987 10000 10000 3969.5439 91446.309 1.3291045 300.12154 39.049396 103.72601 0 0 24323.594 20085.263 -226.3957 -220255.76 -175704.13 5580.5478 Loop time of 122.623 on 16 procs for 10000 steps with 8938 atoms Performance: 7.046 ns/day, 3.406 hours/ns, 81.551 timesteps/s 98.7% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 80.07 | 84.784 | 89.281 | 28.0 | 69.14 Bond | 0.02905 | 0.050624 | 0.072958 | 4.9 | 0.04 Kspace | 19.879 | 24.396 | 29.049 | 51.8 | 19.90 Neigh | 4.8381 | 4.85 | 4.8563 | 0.3 | 3.96 Comm | 2.7548 | 2.8749 | 3.0611 | 4.6 | 2.34 Output | 0.013757 | 0.015478 | 0.017054 | 0.9 | 0.01 Modify | 5.0293 | 5.1404 | 5.5025 | 4.7 | 4.19 Other | | 0.5113 | | | 0.42 Nlocal: 558.625 ave 578 max 537 min Histogram: 2 1 0 0 5 1 2 3 0 2 Nghost: 8992.94 ave 9115 max 8841 min Histogram: 1 1 1 3 0 4 0 2 1 3 Neighs: 313602 ave 330025 max 295215 min Histogram: 1 2 0 0 4 3 0 3 2 1 Total # of neighbors = 5017629 Ave neighs/atom = 561.38163 Ave special neighs/atom = 1.8722309 Neighbor list builds = 508 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 2.4.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.97 1.52612e-06 8097 2 103.7 0.000106617 2699 Per MPI rank memory allocation (min/avg/max) = 14.02 | 14.13 | 14.28 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 10000 10000 3970.507 91446.309 1.3291045 300.12154 39.049396 103.72601 0 0 24323.594 20085.263 -226.3957 -220255.76 -175704.13 5580.5478 Loop time of 4.33075e-06 on 16 procs for 0 steps with 8938 atoms 121.2% 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 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 | | 4.331e-06 | | |100.00 Nlocal: 558.625 ave 578 max 537 min Histogram: 2 1 0 0 5 1 2 3 0 2 Nghost: 8992.94 ave 9115 max 8841 min Histogram: 1 1 1 3 0 4 0 2 1 3 Neighs: 313602 ave 330025 max 295215 min Histogram: 1 2 0 0 4 3 0 3 2 1 Total # of neighbors = 5017629 Ave neighs/atom = 561.38163 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out