#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 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 200000 200000 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 200 1 200 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 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 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.33288e-06 8436 2 103.7 9.58046e-05 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.1759e-06 8436 2 103.7 9.06128e-05 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.28833e-06 8436 2 103.7 0.000127897 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.35043e-06 8436 2 103.7 0.000102568 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.05274e-06 8436 2 103.7 9.58548e-05 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.58552e-06 8436 2 103.7 9.8799e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.55112e-06 8436 2 103.7 0.000100911 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.28043e-06 8436 2 103.7 9.49577e-05 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.48565e-06 8436 2 103.7 0.000102601 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.53135e-06 8436 2 103.7 0.000107154 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.06541e-06 8436 2 103.7 9.94272e-05 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.37514e-06 8436 2 103.7 9.7237e-05 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.3257e-06 8436 2 103.7 0.000102848 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.21352e-06 8436 2 103.7 9.44142e-05 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.16597e-06 8436 2 103.7 0.000102835 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.57835e-06 8436 2 103.7 0.00012155 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.2251e-06 8436 2 103.7 9.8598e-05 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.18462e-06 8436 2 103.7 0.000113221 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.19717e-06 8436 2 103.7 9.94068e-05 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.69479e-06 8436 2 103.7 0.000102854 2812 2000000 2000000 -551.86971 141184.09 1.4079299 301.22095 54.297706 64.607203 0 0 31817.829 -35637.769 -312.04795 -284059.3 -287760.34 6887.6563 Loop time of 18991.4 on 32 procs for 2000000 steps with 10808 atoms Performance: 9.099 ns/day, 2.638 hours/ns, 105.311 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 | 2553.5 | 8903.6 | 12267 |3958.6 | 46.88 Bond | 1.9918 | 5.2641 | 11.316 | 103.8 | 0.03 Kspace | 3761.5 | 7129.8 | 13514 |4443.2 | 37.54 Neigh | 892.28 | 893.76 | 896.45 | 4.6 | 4.71 Comm | 708.42 | 941.31 | 1036.4 | 339.5 | 4.96 Output | 0.01287 | 0.015348 | 0.017683 | 1.2 | 0.00 Modify | 998.89 | 1073.1 | 1259.8 | 266.6 | 5.65 Other | | 44.62 | | | 0.23 Nlocal: 337.75 ave 415 max 160 min Histogram: 4 4 0 0 0 0 0 4 5 15 Nghost: 6439.38 ave 7767 max 4723 min Histogram: 8 0 0 4 4 0 0 0 5 11 Neighs: 158717 ave 223566 max 43443 min Histogram: 8 0 0 0 0 3 1 2 6 12 Total # of neighbors = 5078932 Ave neighs/atom = 469.92339 Ave special neighs/atom = 1.6184308 Neighbor list builds = 99579 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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 2000000 2 0.97 1.69479e-06 8436 2 103.7 0.000102854 2812 Per MPI rank memory allocation (min/avg/max) = 12.46 | 13.27 | 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 2000000 2000000 -551.37521 141184.09 1.4079299 301.22095 54.297706 64.607203 0 0 31817.829 -35637.769 -312.04795 -284059.3 -287760.34 6887.6563 Loop time of 1.29167e-05 on 32 procs for 0 steps with 10808 atoms 107.2% 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 | | 1.292e-05 | | |100.00 Nlocal: 337.75 ave 415 max 160 min Histogram: 4 4 0 0 0 0 0 4 5 15 Nghost: 6439.38 ave 7767 max 4723 min Histogram: 8 0 0 4 4 0 0 0 5 11 Neighs: 158717 ave 223566 max 43443 min Histogram: 8 0 0 0 0 3 1 2 6 12 Total # of neighbors = 5078932 Ave neighs/atom = 469.92339 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