#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 4 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 400000 400000 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 400 1 400 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 4000000 2.5.restart dump sci all custom 400000 2.5.xyz id mol type q xs ys zs timestep 1 run 4000000 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 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.36315e-06 9825 1 103.7 9.47833e-05 3275 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.30922e-06 9825 1 103.7 9.67811e-05 3275 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.21641e-06 9825 1 103.7 0.000103324 3275 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.13319e-06 9825 1 103.7 9.29652e-05 3275 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.62244e-06 9825 1 103.7 9.85533e-05 3275 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.16014e-06 9825 1 103.7 8.88038e-05 3275 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.15797e-06 9825 1 103.7 9.09754e-05 3275 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.14512e-06 9825 1 103.7 0.000102839 3275 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.17292e-06 9825 1 103.7 0.000103338 3275 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.90824e-06 9825 1 103.7 0.000108601 3275 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.12357e-06 9825 1 103.7 0.000101098 3275 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.65848e-06 9825 1 103.7 0.000120528 3275 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.10763e-06 9825 1 103.7 0.000109868 3275 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.20516e-06 9825 1 103.7 9.39288e-05 3275 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.32521e-06 9825 1 103.7 0.000103782 3275 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.1895e-06 9825 1 103.7 9.45272e-05 3275 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.26388e-06 9825 1 103.7 9.56955e-05 3275 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.23585e-06 9825 1 103.7 9.4926e-05 3275 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.31631e-06 9825 1 103.7 0.000121448 3275 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.31739e-06 9825 1 103.7 8.71978e-05 3275 4000000 4000000 -7540.2018 143340.91 1.3114365 297.30532 33.092082 61.191263 0 0 36766.202 -72824.281 -319.55737 -317431.28 -353395.08 7017.0163 Loop time of 100025 on 8 procs for 4000000 steps with 12250 atoms Performance: 3.455 ns/day, 6.946 hours/ns, 39.990 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 58109 | 71222 | 78816 |2446.9 | 71.20 Bond | 6.9375 | 22.659 | 30.969 | 190.7 | 0.02 Kspace | 14056 | 21659 | 34796 |4444.7 | 21.65 Neigh | 4133.4 | 4136.5 | 4139.4 | 3.5 | 4.14 Comm | 982.71 | 999.06 | 1015.2 | 42.8 | 1.00 Output | 0.026063 | 0.028976 | 0.031685 | 1.1 | 0.00 Modify | 1840.4 | 1847.7 | 1853.9 | 10.8 | 1.85 Other | | 138.2 | | | 0.14 Nlocal: 1531.25 ave 1597 max 1423 min Histogram: 2 0 0 0 0 1 0 2 1 2 Nghost: 12108.5 ave 12458 max 11819 min Histogram: 1 1 1 1 2 0 0 0 0 2 Neighs: 752534 ave 831083 max 637144 min Histogram: 2 0 0 0 0 0 1 3 1 1 Total # of neighbors = 6020269 Ave neighs/atom = 491.45053 Ave special neighs/atom = 1.6481633 Neighbor list builds = 199273 Dangerous builds = 0 undump sci restart 0 dump sci all custom 4000000 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 4000000 1 0.97 1.31739e-06 9825 1 103.7 8.71978e-05 3275 Per MPI rank memory allocation (min/avg/max) = 16.17 | 16.96 | 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 4000000 4000000 -7539.3929 143340.91 1.3114365 297.30532 33.092082 61.191263 0 0 36766.202 -72824.281 -319.55737 -317431.28 -353395.08 7017.0163 Loop time of 3.22275e-06 on 8 procs for 0 steps with 12250 atoms 120.2% 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 | | 3.223e-06 | | |100.00 Nlocal: 1531.25 ave 1597 max 1423 min Histogram: 2 0 0 0 0 1 0 2 1 2 Nghost: 12108.5 ave 12458 max 11819 min Histogram: 1 1 1 1 2 0 0 0 0 2 Neighs: 752534 ave 831083 max 637144 min Histogram: 2 0 0 0 0 0 1 3 1 1 Total # of neighbors = 6020269 Ave neighs/atom = 491.45053 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