#------------------------------------------------------------------------------- # 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 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2812 = # 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00022 0.0683891 8436 2 97.8065 10.268 2812 Per MPI rank memory allocation (min/avg/max) = 12.46 | 13.16 | 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 -2348.6164 141184.09 1.4079299 407.8254 6.8547611 32.216806 0 0 34634.878 -53383.538 -312.04795 -284230.21 -302939.8 9325.2516 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.42271e-06 8436 2 103.7 0.000110145 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.10534e-06 8436 2 103.7 0.000104613 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.3341e-06 8436 2 103.7 9.77796e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16126e-06 8436 2 103.7 8.96267e-05 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.72146e-06 8436 2 103.7 9.41027e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.1547e-06 8436 2 103.7 0.000102626 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.578e-06 8436 2 103.7 0.0001168 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.64001e-06 8436 2 103.7 9.57073e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.24015e-06 8436 2 103.7 9.78924e-05 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.27297e-06 8436 2 103.7 9.68016e-05 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.41355e-06 8436 2 103.7 0.000108049 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.31778e-06 8436 2 103.7 0.000100678 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.30948e-06 8436 2 103.7 9.71683e-05 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.26389e-06 8436 2 103.7 9.00371e-05 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.47326e-06 8436 2 103.7 0.00010264 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.17259e-06 8436 2 103.7 9.25774e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.4142e-06 8436 2 103.7 0.000111028 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.23092e-06 8436 2 103.7 9.5375e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.52397e-06 8436 2 103.7 8.84745e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.39569e-06 8436 2 103.7 0.000110162 2812 1000000 1000000 -378.32924 141184.09 1.4079299 296.90938 46.210832 60.947133 0 0 31839.334 -35569.255 -312.04795 -284064.65 -287687.41 6789.0687 Loop time of 9486.05 on 32 procs for 1000000 steps with 10808 atoms Performance: 9.108 ns/day, 2.635 hours/ns, 105.418 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1283.3 | 4447.3 | 6189.3 |2791.9 | 46.88 Bond | 0.98344 | 2.5599 | 5.8287 | 79.8 | 0.03 Kspace | 1813.8 | 3565.9 | 6749.9 |3130.8 | 37.59 Neigh | 447.59 | 448.47 | 449.79 | 3.3 | 4.73 Comm | 347.37 | 466.27 | 510.04 | 241.7 | 4.92 Output | 0.013575 | 0.01613 | 0.018469 | 1.2 | 0.00 Modify | 498.97 | 533.38 | 630.5 | 190.8 | 5.62 Other | | 22.09 | | | 0.23 Nlocal: 337.75 ave 413 max 160 min Histogram: 4 4 0 0 0 0 0 1 7 16 Nghost: 6440.94 ave 7689 max 4773 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 158254 ave 225894 max 43568 min Histogram: 8 0 0 0 0 1 3 2 9 9 Total # of neighbors = 5064121 Ave neighs/atom = 468.55302 Ave special neighs/atom = 1.6184308 Neighbor list builds = 49804 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.39569e-06 8436 2 103.7 0.000110162 2812 Per MPI rank memory allocation (min/avg/max) = 12.46 | 13.25 | 13.66 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 -377.84176 141184.09 1.4079299 296.90938 46.210832 60.947133 0 0 31839.334 -35569.255 -312.04795 -284064.65 -287687.41 6789.0687 Loop time of 7.33769e-06 on 32 procs for 0 steps with 10808 atoms 124.8% 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 | | 7.338e-06 | | |100.00 Nlocal: 337.75 ave 413 max 160 min Histogram: 4 4 0 0 0 0 0 1 7 16 Nghost: 6440.94 ave 7689 max 4773 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 158254 ave 225894 max 43568 min Histogram: 8 0 0 0 0 1 3 2 9 9 Total # of neighbors = 5064121 Ave neighs/atom = 468.55302 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_Custom.out