#------------------------------------------------------------------------------- # 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 2 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3728 = # 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 group rdfgroup_13 union subset_jiemian-Cl subset_jiemian-O 155 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 200 1 7 fix rdf_13 rdfgroup_13 ave/time 1 30000 30000 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 5 7 13 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard (2) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.85341e-13 11184 2 103.7 8.0334e-11 3728 Per MPI rank memory allocation (min/avg/max) = 13.11 | 13.63 | 14.11 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 335929.19 143799.62 1.371895 297.37957 276.1468 362.97776 0 0 271595.53 -52433.342 -383.45046 -378985.51 -159184.19 8165.8117 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.33419e-06 11184 2 103.7 9.59926e-05 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.23862e-06 11184 2 103.7 9.07758e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.27856e-06 11184 2 103.7 0.000103604 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.45339e-06 11184 2 103.7 0.000106557 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.15835e-06 11184 2 103.7 9.09732e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.29304e-06 11184 2 103.7 9.09013e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2671e-06 11184 2 103.7 9.77907e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.78007e-06 11184 2 103.7 0.000114019 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.28558e-06 11184 2 103.7 9.06464e-05 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.2439e-06 11184 2 103.7 9.41551e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.19062e-06 11184 2 103.7 8.94261e-05 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.2307e-06 11184 2 103.7 9.92265e-05 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.59308e-06 11184 2 103.7 9.54923e-05 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.3877e-06 11184 2 103.7 9.50957e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.75965e-06 11184 2 103.7 0.00010714 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.13028e-06 11184 2 103.7 9.31246e-05 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.41742e-06 11184 2 103.7 0.000107258 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.62613e-06 11184 2 103.7 0.000110202 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.51357e-06 11184 2 103.7 0.000107031 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.36271e-06 11184 2 103.7 9.55281e-05 3728 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.33238e-06 11184 2 103.7 9.12286e-05 3728 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.52611e-06 11184 2 103.7 0.000121804 3728 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.37379e-06 11184 2 103.7 0.00010451 3728 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.64211e-06 11184 2 103.7 0.000112631 3728 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.39624e-06 11184 2 103.7 9.55039e-05 3728 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.67364e-06 11184 2 103.7 0.000105457 3728 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.23093e-06 11184 2 103.7 9.05454e-05 3728 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.35748e-06 11184 2 103.7 9.68061e-05 3728 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.4899e-06 11184 2 103.7 9.44574e-05 3728 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.49336e-06 11184 2 103.7 9.5904e-05 3728 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.09572e-06 11184 2 103.7 9.31758e-05 3728 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.25882e-06 11184 2 103.7 9.70951e-05 3728 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.46479e-06 11184 2 103.7 0.000101265 3728 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.29527e-06 11184 2 103.7 9.77513e-05 3728 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.05697e-06 11184 2 103.7 0.000100752 3728 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.40357e-06 11184 2 103.7 9.09801e-05 3728 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.50592e-06 11184 2 103.7 9.78738e-05 3728 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.39918e-06 11184 2 103.7 0.000103527 3728 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.37868e-06 11184 2 103.7 9.02347e-05 3728 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.14876e-06 11184 2 103.7 9.7484e-05 3728 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.47109e-06 11184 2 103.7 0.000101314 3728 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.26409e-06 11184 2 103.7 0.000105611 3728 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.53022e-06 11184 2 103.7 0.000103568 3728 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.17954e-06 11184 2 103.7 0.00010442 3728 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.5174e-06 11184 2 103.7 0.000114671 3728 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.14659e-06 11184 2 103.7 9.17162e-05 3728 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.36299e-06 11184 2 103.7 0.000118708 3728 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.22356e-06 11184 2 103.7 9.41725e-05 3728 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.21065e-06 11184 2 103.7 0.000106098 3728 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.18359e-06 11184 2 103.7 9.60096e-05 3728 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.28911e-06 11184 2 103.7 0.000102484 3728 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.58981e-06 11184 2 103.7 0.000106273 3728 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.19135e-06 11184 2 103.7 9.26167e-05 3728 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.16548e-06 11184 2 103.7 8.90027e-05 3728 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.24844e-06 11184 2 103.7 9.15284e-05 3728 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.54302e-06 11184 2 103.7 9.03815e-05 3728 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.32003e-06 11184 2 103.7 0.000106277 3728 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.16335e-06 11184 2 103.7 0.000104812 3728 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.32652e-06 11184 2 103.7 0.000100151 3728 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.23924e-06 11184 2 103.7 9.63951e-05 3728 3000000 3000000 335529.9 143799.62 1.371895 300.11972 287.54571 372.43919 0 0 271339.09 -52207.03 -383.45046 -378991.89 -159199.85 8241.054 Loop time of 40002.6 on 32 procs for 3000000 steps with 13901 atoms Performance: 6.480 ns/day, 3.704 hours/ns, 74.995 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16371 | 19805 | 27415 |2868.6 | 49.51 Bond | 6.5387 | 22.142 | 55.197 | 356.4 | 0.06 Kspace | 6905.4 | 14583 | 18083 |3368.6 | 36.45 Neigh | 1450.2 | 1453.7 | 1457.5 | 5.6 | 3.63 Comm | 1643.8 | 1765.6 | 1919.7 | 201.5 | 4.41 Output | 0.016597 | 0.019438 | 0.022327 | 1.2 | 0.00 Modify | 2166.3 | 2263.8 | 2332.9 | 121.4 | 5.66 Other | | 109.2 | | | 0.27 Nlocal: 434.406 ave 526 max 379 min Histogram: 4 9 9 2 0 0 0 0 1 7 Nghost: 8234.78 ave 8691 max 7554 min Histogram: 8 0 0 0 0 0 7 9 0 8 Neighs: 243696 ave 342974 max 190687 min Histogram: 8 10 4 2 0 0 0 0 3 5 Total # of neighbors = 7798282 Ave neighs/atom = 560.98712 Ave special neighs/atom = 1.8838932 Neighbor list builds = 150147 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.23924e-06 11184 2 103.7 9.63951e-05 3728 Per MPI rank memory allocation (min/avg/max) = 14.61 | 14.89 | 15.63 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 335530.89 143799.62 1.371895 300.11972 287.54571 372.43919 0 0 271339.09 -52207.03 -383.45046 -378991.89 -159199.85 8241.054 Loop time of 7.57572e-06 on 32 procs for 0 steps with 13901 atoms 113.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.576e-06 | | |100.00 Nlocal: 434.406 ave 526 max 379 min Histogram: 4 9 9 2 0 0 0 0 1 7 Nghost: 8234.78 ave 8691 max 7554 min Histogram: 8 0 0 0 0 0 7 9 0 8 Neighs: 243696 ave 342974 max 190687 min Histogram: 8 10 4 2 0 0 0 0 3 5 Total # of neighbors = 7798282 Ave neighs/atom = 560.98712 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_13 unfix rdf_13 group rdfgroup_13 delete unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 14:49:17