#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 = 0.001 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 300000 300000 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 2.5_averages.txt off 1 fix 3 movable ave/time 300 1 300 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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18700 7776 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 8.83515e-13 9825 1 103.7 1.0445e-10 3275 Per MPI rank memory allocation (min/avg/max) = 16.17 | 16.94 | 17.27 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 -7325.6343 143340.91 1.3114365 301.42215 42.503336 58.081086 0 0 36999.91 -73193.601 -319.55737 -317454.18 -353547.29 7114.1818 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.19083e-06 9825 1 103.7 9.23177e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.31164e-06 9825 1 103.7 0.000102581 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.26108e-06 9825 1 103.7 0.000103928 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.29164e-06 9825 1 103.7 0.000103652 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.0944e-06 9825 1 103.7 9.78896e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.25458e-06 9825 1 103.7 9.57536e-05 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.1052e-06 9825 1 103.7 9.59255e-05 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.3394e-06 9825 1 103.7 9.53086e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.31673e-06 9825 1 103.7 0.000102252 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.07955e-06 9825 1 103.7 9.69299e-05 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.27174e-06 9825 1 103.7 9.50723e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.35142e-06 9825 1 103.7 9.50867e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.10504e-06 9825 1 103.7 9.9261e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.31422e-06 9825 1 103.7 9.46324e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.13204e-06 9825 1 103.7 9.20585e-05 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.10269e-06 9825 1 103.7 9.03477e-05 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.15205e-06 9825 1 103.7 0.000104595 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.66103e-06 9825 1 103.7 0.00012498 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.29961e-06 9825 1 103.7 9.32176e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.19711e-06 9825 1 103.7 9.44909e-05 3275 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.30523e-06 9825 1 103.7 9.94428e-05 3275 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.12797e-06 9825 1 103.7 9.82944e-05 3275 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.31741e-06 9825 1 103.7 0.000106291 3275 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.13042e-06 9825 1 103.7 9.22164e-05 3275 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.15974e-06 9825 1 103.7 9.434e-05 3275 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.46782e-06 9825 1 103.7 0.000113003 3275 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.39857e-06 9825 1 103.7 0.000105015 3275 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.1821e-06 9825 1 103.7 9.70599e-05 3275 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.20273e-06 9825 1 103.7 0.000101749 3275 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.3192e-06 9825 1 103.7 9.95969e-05 3275 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.35458e-06 9825 1 103.7 9.82962e-05 3275 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.27399e-06 9825 1 103.7 9.10517e-05 3275 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.26751e-06 9825 1 103.7 9.80318e-05 3275 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.25561e-06 9825 1 103.7 9.7936e-05 3275 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.39879e-06 9825 1 103.7 0.00011103 3275 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.13619e-06 9825 1 103.7 0.000102332 3275 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.09971e-06 9825 1 103.7 9.8329e-05 3275 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.21199e-06 9825 1 103.7 8.87833e-05 3275 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.2961e-06 9825 1 103.7 9.48673e-05 3275 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.128e-06 9825 1 103.7 0.000116335 3275 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.08847e-06 9825 1 103.7 9.78836e-05 3275 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.17117e-06 9825 1 103.7 0.000107238 3275 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.43708e-06 9825 1 103.7 0.000109863 3275 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.09196e-06 9825 1 103.7 9.87872e-05 3275 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.47395e-06 9825 1 103.7 0.000104452 3275 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.46292e-06 9825 1 103.7 0.000118368 3275 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.06662e-06 9825 1 103.7 9.59431e-05 3275 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.85211e-06 9825 1 103.7 0.000122044 3275 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.18207e-06 9825 1 103.7 0.000102354 3275 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.1352e-06 9825 1 103.7 0.000112405 3275 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.71653e-06 9825 1 103.7 0.000120576 3275 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.26078e-06 9825 1 103.7 9.64518e-05 3275 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.29314e-06 9825 1 103.7 0.000109049 3275 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.8414e-06 9825 1 103.7 0.000130073 3275 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.23399e-06 9825 1 103.7 9.60461e-05 3275 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.34844e-06 9825 1 103.7 0.000118827 3275 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.3666e-06 9825 1 103.7 0.000101115 3275 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.43938e-06 9825 1 103.7 9.35365e-05 3275 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.31087e-06 9825 1 103.7 0.000136183 3275 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.118e-06 9825 1 103.7 9.06934e-05 3275 3000000 3000000 -7430.2533 143340.91 1.3114365 297.79106 40.902531 68.211228 0 0 36712.73 -72555.919 -319.55737 -317429.78 -353163.85 7028.4807 Loop time of 68568.9 on 8 procs for 3000000 steps with 12250 atoms Performance: 3.780 ns/day, 6.349 hours/ns, 43.752 timesteps/s 99.1% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42085 | 49875 | 53846 |1795.8 | 72.74 Bond | 4.3753 | 14.939 | 20.556 | 161.2 | 0.02 Kspace | 9860.3 | 13841 | 21647 |3414.7 | 20.19 Neigh | 2812.8 | 2814.7 | 2816.6 | 2.3 | 4.10 Comm | 652.02 | 670.33 | 690 | 47.6 | 0.98 Output | 0.02394 | 0.026648 | 0.029118 | 1.0 | 0.00 Modify | 1251.5 | 1263.1 | 1275.4 | 27.4 | 1.84 Other | | 89.74 | | | 0.13 Nlocal: 1531.25 ave 1586 max 1441 min Histogram: 2 0 0 0 0 1 0 1 2 2 Nghost: 12105.5 ave 12420 max 11932 min Histogram: 3 0 2 0 1 0 0 0 1 1 Neighs: 752353 ave 819627 max 645718 min Histogram: 2 0 0 0 0 0 1 3 0 2 Total # of neighbors = 6018822 Ave neighs/atom = 491.33241 Ave special neighs/atom = 1.6481633 Neighbor list builds = 149437 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 2.5.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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18700 7776 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.118e-06 9825 1 103.7 9.06934e-05 3275 Per MPI rank memory allocation (min/avg/max) = 16.17 | 16.93 | 17.27 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 3000000 3000000 -7429.455 143340.91 1.3114365 297.79106 40.902531 68.211228 0 0 36712.73 -72555.919 -319.55737 -317429.78 -353163.85 7028.4807 Loop time of 3.19e-06 on 8 procs for 0 steps with 12250 atoms 121.5% 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 | 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 | | 3.19e-06 | | |100.00 Nlocal: 1531.25 ave 1586 max 1441 min Histogram: 2 0 0 0 0 1 0 1 2 2 Nghost: 12105.5 ave 12420 max 11932 min Histogram: 3 0 2 0 1 0 0 0 1 1 Neighs: 752353 ave 819627 max 645718 min Histogram: 2 0 0 0 0 0 1 3 0 2 Total # of neighbors = 6018822 Ave neighs/atom = 491.33241 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 2.6_Custom.out