#------------------------------------------------------------------------------- # 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) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.991854 0.602613 8436 2 96.9689 39.7099 2812 Per MPI rank memory allocation (min/avg/max) = 12.75 | 13.98 | 14.61 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 6316.6931 130091.43 1.4011632 415.64004 111.0517 404.90865 0 0 31846.584 -14834.533 -295.4552 -266249.55 -248721.54 8849.777 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.16841e-06 8436 2 103.7 0.000103998 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.38156e-06 8436 2 103.7 9.64157e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.2433e-06 8436 2 103.7 0.000101216 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.0656e-06 8436 2 103.7 9.30132e-05 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.37468e-06 8436 2 103.7 0.000110002 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.15523e-06 8436 2 103.7 9.73557e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.22557e-06 8436 2 103.7 9.54956e-05 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.33948e-06 8436 2 103.7 9.51544e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.20778e-06 8436 2 103.7 0.000115242 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.17642e-06 8436 2 103.7 0.000107063 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.18622e-06 8436 2 103.7 0.0001134 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.34399e-06 8436 2 103.7 0.000103342 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.25464e-06 8436 2 103.7 9.88688e-05 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.77214e-06 8436 2 103.7 0.000120517 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.30816e-06 8436 2 103.7 0.000106058 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16045e-06 8436 2 103.7 0.00010435 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.2117e-06 8436 2 103.7 9.5843e-05 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.29317e-06 8436 2 103.7 9.42414e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.22371e-06 8436 2 103.7 9.32087e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.33248e-06 8436 2 103.7 0.000116879 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.35456e-06 8436 2 103.7 8.98152e-05 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.53315e-06 8436 2 103.7 9.60685e-05 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.95527e-06 8436 2 103.7 0.000160342 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.56072e-06 8436 2 103.7 9.259e-05 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.48458e-06 8436 2 103.7 0.000101752 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.2587e-06 8436 2 103.7 9.67912e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.39055e-06 8436 2 103.7 9.92678e-05 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.50696e-06 8436 2 103.7 0.000111706 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.22385e-06 8436 2 103.7 0.000107233 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.34585e-06 8436 2 103.7 0.000103108 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.29542e-06 8436 2 103.7 0.00011332 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.22684e-06 8436 2 103.7 0.000100619 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.16692e-06 8436 2 103.7 9.27245e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.16496e-06 8436 2 103.7 0.000106337 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.10988e-06 8436 2 103.7 9.30134e-05 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.24515e-06 8436 2 103.7 9.29051e-05 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.53198e-06 8436 2 103.7 0.000105343 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.15937e-06 8436 2 103.7 8.8915e-05 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.26379e-06 8436 2 103.7 9.64079e-05 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.45077e-06 8436 2 103.7 9.10322e-05 2812 2000000 2000000 118.5589 130091.43 1.4011632 297.38395 49.381797 237.30931 0 0 29348.852 -19074.661 -295.4552 -267614.11 -257053.23 6331.8771 Loop time of 30652.6 on 16 procs for 2000000 steps with 10468 atoms Performance: 5.637 ns/day, 4.257 hours/ns, 65.247 timesteps/s 99.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6218.4 | 17317 | 22407 |4918.4 | 56.50 Bond | 2.7237 | 8.6978 | 16.426 | 137.7 | 0.03 Kspace | 5011 | 10106 | 21232 |6453.5 | 32.97 Neigh | 1252.1 | 1253.9 | 1256.3 | 3.9 | 4.09 Comm | 707.12 | 847.42 | 911.98 | 271.2 | 2.76 Output | 0.017455 | 0.019666 | 0.021596 | 0.9 | 0.00 Modify | 1019.3 | 1061.3 | 1175.2 | 200.6 | 3.46 Other | | 57.93 | | | 0.19 Nlocal: 654.25 ave 797 max 369 min Histogram: 4 0 0 0 0 0 0 2 4 6 Nghost: 8606.38 ave 10013 max 7291 min Histogram: 4 0 0 3 1 4 0 0 0 4 Neighs: 320328 ave 427611 max 112131 min Histogram: 4 0 0 0 0 0 0 3 4 5 Total # of neighbors = 5125250 Ave neighs/atom = 489.6112 Ave special neighs/atom = 1.6709973 Neighbor list builds = 99432 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) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.45077e-06 8436 2 103.7 9.10322e-05 2812 Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.18 | 14.69 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 119.18442 130091.43 1.4011632 297.38395 49.381797 237.30931 0 0 29348.852 -19074.661 -295.4552 -267614.11 -257053.23 6331.8771 Loop time of 4.30712e-06 on 16 procs for 0 steps with 10468 atoms 124.8% 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 | | 4.307e-06 | | |100.00 Nlocal: 654.25 ave 797 max 369 min Histogram: 4 0 0 0 0 0 0 2 4 6 Nghost: 8606.38 ave 10013 max 7291 min Histogram: 4 0 0 3 1 4 0 0 0 4 Neighs: 320328 ave 427611 max 112131 min Histogram: 4 0 0 0 0 0 0 3 4 5 Total # of neighbors = 5125250 Ave neighs/atom = 489.6112 Ave special neighs/atom = 1.6709973 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out