#------------------------------------------------------------------------------- # Stage 2.3: NVT integration for 1 ns 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # 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 100000 100000 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 100 1 100 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 1000000 2.3.restart dump sci all custom 100000 2.3.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24367668 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034817281 estimated relative force accuracy = 1.0485121e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 1 mixed pair_coeff terms from sixthpower 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 = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard SHAKE stats (type/ave/delta/count) on step 0 1 0.97 9.77953e-05 6600 1 103.7 0.00894552 2200 Per MPI rank memory allocation (min/avg/max) = 9.206 | 11.81 | 16.19 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-06 654.07668 200987.25 0.32745077 447.33389 0 0 0 0 5574.1416 82181.842 -37.551062 -110135.18 -22379.194 5865.703 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.51303e-06 6600 1 103.7 0.000115826 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.4154e-06 6600 1 103.7 9.89612e-05 2200 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.10993e-06 6600 1 103.7 9.51412e-05 2200 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.25409e-06 6600 1 103.7 9.59195e-05 2200 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.23257e-06 6600 1 103.7 0.000100047 2200 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.59202e-06 6600 1 103.7 0.000104867 2200 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.65724e-06 6600 1 103.7 0.00012192 2200 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.21761e-06 6600 1 103.7 9.15483e-05 2200 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.25071e-06 6600 1 103.7 9.52892e-05 2200 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.57198e-06 6600 1 103.7 8.99161e-05 2200 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.32582e-06 6600 1 103.7 9.12071e-05 2200 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.21555e-06 6600 1 103.7 8.98866e-05 2200 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 2.01015e-06 6600 1 103.7 0.000159365 2200 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.47305e-06 6600 1 103.7 9.28693e-05 2200 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.26828e-06 6600 1 103.7 9.21316e-05 2200 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.05849e-06 6600 1 103.7 9.55676e-05 2200 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.21924e-06 6600 1 103.7 0.000125505 2200 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.35818e-06 6600 1 103.7 9.69339e-05 2200 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.1523e-06 6600 1 103.7 9.37396e-05 2200 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.2654e-06 6600 1 103.7 9.37397e-05 2200 1000000 1000000 -52.703163 200987.25 0.32745077 295.747 0 0 0 0 5647.8678 81645.389 -37.551062 -110310.33 -23017.068 3878.0071 Loop time of 37040.8 on 8 procs for 1000000 steps with 6600 atoms Performance: 2.333 ns/day, 10.289 hours/ns, 26.997 timesteps/s 97.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55565 | 9960.5 | 30301 |12348.3 | 26.89 Bond | 0.87442 | 1.1717 | 1.5032 | 20.1 | 0.00 Kspace | 4106.6 | 24489 | 34530 |7896.7 | 66.11 Neigh | 1727.1 | 1732.7 | 1738.6 | 12.0 | 4.68 Comm | 53.707 | 219.67 | 327.81 | 726.1 | 0.59 Output | 0.033846 | 0.035617 | 0.037203 | 0.6 | 0.00 Modify | 545.34 | 602.21 | 682.28 | 218.3 | 1.63 Other | | 35.11 | | | 0.09 Nlocal: 825 ave 2258 max 0 min Histogram: 4 0 0 0 2 0 0 0 0 2 Nghost: 5576 ave 10985 max 0 min Histogram: 2 0 0 2 0 0 0 2 0 2 Neighs: 405724 ave 1.27623e+06 max 0 min Histogram: 4 0 1 1 0 0 0 0 0 2 Total # of neighbors = 3245789 Ave neighs/atom = 491.78621 Ave special neighs/atom = 2 Neighbor list builds = 50015 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.3.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) = 0.24367668 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034817281 estimated relative force accuracy = 1.0485121e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.2654e-06 6600 1 103.7 9.37397e-05 2200 Per MPI rank memory allocation (min/avg/max) = 9.208 | 12.1 | 16.21 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 1000000 1000000 -52.50294 200987.25 0.32745077 295.747 0 0 0 0 5647.8678 81645.389 -37.551062 -110310.33 -23017.068 3878.0071 Loop time of 4.0645e-06 on 8 procs for 0 steps with 6600 atoms 119.9% CPU use with 8 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 | | 4.064e-06 | | |100.00 Nlocal: 825 ave 2258 max 0 min Histogram: 4 0 0 0 2 0 0 0 0 2 Nghost: 5576 ave 10985 max 0 min Histogram: 2 0 0 2 0 0 0 2 0 2 Neighs: 405724 ave 1.27623e+06 max 0 min Histogram: 4 0 1 1 0 0 0 0 0 2 Total # of neighbors = 3245789 Ave neighs/atom = 491.78621 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.4_NVT.out