#------------------------------------------------------------------------------- # Stage 2.3: NVT integration for 100 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 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 10000 10000 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 v_surfacetension file 2.3_averages.txt off 1 fix 3 movable ave/time 10 1 10 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 v_surfacetension file 2.3_instantaneous.txt restart 100000 2.3.restart dump sci all custom 10000 2.3.xyz id mol type q xs ys zs timestep 1 run 100000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24355723 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035057422 estimated relative force accuracy = 1.0557438e-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 0.996 0.052036 6600 1 98.4199 11.2871 2200 Per MPI rank memory allocation (min/avg/max) = 9.242 | 12.06 | 17.32 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 -1084.0554 201600 0.32645551 447.33389 0 0 0 0 6559.6273 72893.286 -37.436928 -110299.04 -30846.131 5865.703 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.05118e-06 6600 1 103.7 9.2726e-05 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.24467e-06 6600 1 103.7 9.4752e-05 2200 100000 100000 -184.45893 201600 0.32645551 298.25472 0 0 0 0 5466.2077 81721.008 -37.436928 -110256.53 -23069.318 3910.8899 Loop time of 4204.82 on 8 procs for 100000 steps with 6600 atoms Performance: 2.055 ns/day, 11.680 hours/ns, 23.782 timesteps/s 97.5% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.056326 | 1061.6 | 3492.3 |4365.0 | 25.25 Bond | 0.09277 | 0.14154 | 0.19632 | 9.5 | 0.00 Kspace | 418.46 | 2854.9 | 3927.6 |2669.6 | 67.90 Neigh | 190.88 | 191.49 | 192.31 | 4.3 | 4.55 Comm | 2.7831 | 22.985 | 35.3 | 258.7 | 0.55 Output | 0.03848 | 0.039815 | 0.040854 | 0.5 | 0.00 Modify | 63.139 | 69.356 | 78.17 | 65.5 | 1.65 Other | | 4.32 | | | 0.10 Nlocal: 825 ave 2438 max 0 min Histogram: 4 0 0 2 0 0 0 0 0 2 Nghost: 5638.62 ave 11073 max 0 min Histogram: 2 0 0 0 2 0 2 0 0 2 Neighs: 404837 ave 1.35662e+06 max 0 min Histogram: 4 2 0 0 0 0 0 0 0 2 Total # of neighbors = 3238696 Ave neighs/atom = 490.71152 Ave special neighs/atom = 2 Neighbor list builds = 5012 Dangerous builds = 0 undump sci restart 0 dump sci all custom 100000 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) = 0.24355723 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035057422 estimated relative force accuracy = 1.0557438e-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 100000 1 0.97 1.24467e-06 6600 1 103.7 9.4752e-05 2200 Per MPI rank memory allocation (min/avg/max) = 9.222 | 12.3 | 17.31 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 100000 100000 -184.28213 201600 0.32645551 298.25472 0 0 0 0 5466.2077 81721.008 -37.436928 -110256.53 -23069.318 3910.8899 Loop time of 3.26288e-06 on 8 procs for 0 steps with 6600 atoms 122.6% 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 | | 3.263e-06 | | |100.00 Nlocal: 825 ave 2438 max 0 min Histogram: 4 0 0 2 0 0 0 0 0 2 Nghost: 5638.62 ave 11073 max 0 min Histogram: 2 0 0 0 2 0 2 0 0 2 Neighs: 404837 ave 1.35662e+06 max 0 min Histogram: 4 2 0 0 0 0 0 0 0 2 Total # of neighbors = 3238696 Ave neighs/atom = 490.71152 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 1:10:05