#------------------------------------------------------------------------------- # 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 2 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3659 = # 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 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00484 0.0885813 10977 2 97.6633 10.2851 3659 Per MPI rank memory allocation (min/avg/max) = 14.83 | 15.11 | 15.84 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 338596.22 142807.9 1.3823791 416.85345 44.188121 265.24192 0 0 277771.87 -89850.048 -383.2647 -382578.95 -194347.7 11329.671 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.21189e-06 10977 2 103.7 8.74406e-05 3659 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.19345e-06 10977 2 103.7 9.22378e-05 3659 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.2933e-06 10977 2 103.7 9.24356e-05 3659 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.13482e-06 10977 2 103.7 8.99444e-05 3659 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.21267e-06 10977 2 103.7 9.71757e-05 3659 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.20366e-06 10977 2 103.7 9.92342e-05 3659 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.07458e-06 10977 2 103.7 9.32213e-05 3659 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.40466e-06 10977 2 103.7 0.000104346 3659 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.20333e-06 10977 2 103.7 8.8841e-05 3659 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.0886e-06 10977 2 103.7 9.2791e-05 3659 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.33838e-06 10977 2 103.7 9.4628e-05 3659 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.25049e-06 10977 2 103.7 0.000107116 3659 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.40893e-06 10977 2 103.7 9.2373e-05 3659 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.46421e-06 10977 2 103.7 0.000111663 3659 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.26696e-06 10977 2 103.7 9.68922e-05 3659 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.31345e-06 10977 2 103.7 0.000109684 3659 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.2441e-06 10977 2 103.7 0.000107771 3659 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.61835e-06 10977 2 103.7 0.000133302 3659 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.39847e-06 10977 2 103.7 9.41702e-05 3659 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.26314e-06 10977 2 103.7 0.000111357 3659 1000000 1000000 337951.67 142807.9 1.3823791 298.24549 282.68739 377.368 0 0 272984.17 -64853.633 -383.2647 -382421.77 -173631.18 8106.022 Loop time of 21260.3 on 16 procs for 1000000 steps with 13738 atoms Performance: 4.064 ns/day, 5.906 hours/ns, 47.036 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 | 9564.1 | 12080 | 16929 |2372.6 | 56.82 Bond | 2.3762 | 11.987 | 31.054 | 299.8 | 0.06 Kspace | 2540.2 | 7411.9 | 9940.5 |3043.1 | 34.86 Neigh | 897.85 | 899.06 | 900.52 | 2.7 | 4.23 Comm | 322.12 | 339.78 | 358.89 | 63.2 | 1.60 Output | 0.020084 | 0.022441 | 0.024633 | 1.0 | 0.00 Modify | 474.35 | 485.49 | 496.21 | 32.8 | 2.28 Other | | 31.72 | | | 0.15 Nlocal: 858.625 ave 1032 max 764 min Histogram: 4 4 3 1 0 0 0 0 0 4 Nghost: 10329.8 ave 10948 max 9360 min Histogram: 4 0 0 0 0 0 4 4 0 4 Neighs: 480235 ave 666422 max 381242 min Histogram: 4 5 3 0 0 0 0 0 0 4 Total # of neighbors = 7683759 Ave neighs/atom = 559.30696 Ave special neighs/atom = 1.8702868 Neighbor list builds = 49943 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.26314e-06 10977 2 103.7 0.000111357 3659 Per MPI rank memory allocation (min/avg/max) = 14.83 | 15.11 | 15.84 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 337952.67 142807.9 1.3823791 298.24549 282.68739 377.368 0 0 272984.17 -64853.633 -383.2647 -382421.77 -173631.18 8106.022 Loop time of 4.1805e-06 on 16 procs for 0 steps with 13738 atoms 121.1% 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 | | 4.181e-06 | | |100.00 Nlocal: 858.625 ave 1032 max 764 min Histogram: 4 4 3 1 0 0 0 0 0 4 Nghost: 10329.8 ave 10948 max 9360 min Histogram: 4 0 0 0 0 0 4 4 0 4 Neighs: 480235 ave 666422 max 381242 min Histogram: 4 5 3 0 0 0 0 0 0 4 Total # of neighbors = 7683759 Ave neighs/atom = 559.30696 Ave special neighs/atom = 1.8702868 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out