#------------------------------------------------------------------------------- # Stage 2.4: 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 3275 = # 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 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 2.4_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 2.4_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.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) = 0.25493894 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0037055622 estimated relative force accuracy = 1.115919e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00149 0.0772873 9825 1 97.5424 10.2626 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.28 | 13.65 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 -8661.3135 143778.81 1.3074423 420.87983 5.5974165 15.379855 0 0 40196.896 -93024.151 -318.5841 -317465.86 -370272.14 9933.6285 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.36049e-06 9825 1 103.7 0.0001048 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.2318e-06 9825 1 103.7 9.8361e-05 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.66425e-06 9825 1 103.7 9.33005e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.23778e-06 9825 1 103.7 0.000101818 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.44791e-06 9825 1 103.7 9.07685e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.22809e-06 9825 1 103.7 9.32085e-05 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.43661e-06 9825 1 103.7 9.46553e-05 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.18459e-06 9825 1 103.7 9.91035e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.28649e-06 9825 1 103.7 8.95084e-05 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.11492e-06 9825 1 103.7 9.1421e-05 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.11519e-06 9825 1 103.7 9.09356e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.29999e-06 9825 1 103.7 8.59868e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.20516e-06 9825 1 103.7 9.36713e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.08819e-06 9825 1 103.7 9.04497e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.4738e-06 9825 1 103.7 0.000106182 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.63015e-06 9825 1 103.7 0.000102009 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.45411e-06 9825 1 103.7 0.000110957 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.18656e-06 9825 1 103.7 9.27528e-05 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.24263e-06 9825 1 103.7 8.85529e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.14988e-06 9825 1 103.7 0.000103018 3275 1000000 1000000 -7562.9154 143778.81 1.3074423 301.09108 33.545652 62.832036 0 0 36721.172 -72798.849 -318.5841 -317330.15 -353311.45 7106.3679 Loop time of 9171.53 on 32 procs for 1000000 steps with 12250 atoms Performance: 9.420 ns/day, 2.548 hours/ns, 109.033 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 | 4302.3 | 5172.7 | 5671.5 | 555.0 | 56.40 Bond | 1.1266 | 2.6269 | 5.4111 | 69.8 | 0.03 Kspace | 2033.7 | 2537.6 | 3412.7 | 796.8 | 27.67 Neigh | 310.91 | 311.23 | 311.62 | 1.1 | 3.39 Comm | 509.99 | 540.37 | 562.43 | 77.3 | 5.89 Output | 0.013547 | 0.016361 | 0.018971 | 1.3 | 0.00 Modify | 561.9 | 580.85 | 606.85 | 69.1 | 6.33 Other | | 26.21 | | | 0.29 Nlocal: 382.812 ave 407 max 348 min Histogram: 3 1 3 3 1 3 4 3 7 4 Nghost: 7257.78 ave 7523 max 6956 min Histogram: 8 0 3 2 2 1 2 2 4 8 Neighs: 187525 ave 207911 max 153914 min Histogram: 4 0 4 0 0 2 5 6 5 6 Total # of neighbors = 6000786 Ave neighs/atom = 489.86008 Ave special neighs/atom = 1.6481633 Neighbor list builds = 49850 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25493894 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0037055622 estimated relative force accuracy = 1.115919e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.14988e-06 9825 1 103.7 0.000103018 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.42 | 13.65 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 -7562.0661 143778.81 1.3074423 301.09108 33.545652 62.832036 0 0 36721.172 -72798.849 -318.5841 -317330.15 -353311.45 7106.3679 Loop time of 1.35921e-05 on 32 procs for 0 steps with 12250 atoms 108.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.359e-05 | | |100.00 Nlocal: 382.812 ave 407 max 348 min Histogram: 3 1 3 3 1 3 4 3 7 4 Nghost: 7257.78 ave 7523 max 6956 min Histogram: 8 0 3 2 2 1 2 2 4 8 Neighs: 187525 ave 207911 max 153914 min Histogram: 4 0 4 0 0 2 5 6 5 6 Total # of neighbors = 6000786 Ave neighs/atom = 489.86008 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out