#------------------------------------------------------------------------------- # 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 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # 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_O(H2O)_1 2782 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 group rdfgroup_14 union subset_Li_1 subset_S(SO4)_1 41 atoms in group rdfgroup_14 compute rdf_14 rdfgroup_14 rdf 200 4 9 fix rdf_14 rdfgroup_14 ave/time 1 30000 30000 c_rdf_14[*] file 2.5_PairCorrelation_all_14.out mode vector group rdfgroup_15 union subset_Na_1 subset_S(SO4)_1 33 atoms in group rdfgroup_15 compute rdf_15 rdfgroup_15 rdf 200 6 9 fix rdf_15 rdfgroup_15 ave/time 1 30000 30000 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector group rdfgroup_16 union subset_K_1 subset_S(SO4)_1 62 atoms in group rdfgroup_16 compute rdf_16 rdfgroup_16 rdf 200 3 9 fix rdf_16 rdfgroup_16 ave/time 1 30000 30000 c_rdf_16[*] file 2.5_PairCorrelation_all_16.out mode vector group rdfgroup_17 union subset_Mg_1 subset_S(SO4)_1 237 atoms in group rdfgroup_17 compute rdf_17 rdfgroup_17 rdf 200 5 9 fix rdf_17 rdfgroup_17 ave/time 1 30000 30000 c_rdf_17[*] file 2.5_PairCorrelation_all_17.out mode vector timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 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 = 6 6 16 6 neighbor lists, perpetual/occasional/extra = 1 5 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 (3) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (4) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (5) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (6) 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 2 0.97 5.84532e-13 8304 2 103.7 7.59286e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.42 | 13.19 | 13.75 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 -847.89093 143908.11 1.3942094 302.35034 48.233812 75.604521 0 0 29166.191 -19738.763 -320.88394 -277689.38 -268138.11 6629.5871 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.28152e-06 8304 2 103.7 9.65223e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.16554e-06 8304 2 103.7 0.00010038 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.09194e-06 8304 2 103.7 9.01335e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.21467e-06 8304 2 103.7 0.00010025 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.21609e-06 8304 2 103.7 0.000103117 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.38802e-06 8304 2 103.7 9.51834e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.13362e-06 8304 2 103.7 8.8556e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.17968e-06 8304 2 103.7 9.73628e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.29325e-06 8304 2 103.7 9.82182e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.2096e-06 8304 2 103.7 9.13068e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.25291e-06 8304 2 103.7 9.9079e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.13977e-06 8304 2 103.7 0.000101455 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.12964e-06 8304 2 103.7 0.000101564 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.41447e-06 8304 2 103.7 0.000116459 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.2197e-06 8304 2 103.7 9.27192e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.3412e-06 8304 2 103.7 0.00010133 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.08034e-06 8304 2 103.7 9.22543e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.11746e-06 8304 2 103.7 9.81936e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.03557e-06 8304 2 103.7 9.35205e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.23877e-06 8304 2 103.7 9.62452e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.30871e-06 8304 2 103.7 0.000100155 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.1737e-06 8304 2 103.7 9.33245e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.23047e-06 8304 2 103.7 9.68055e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.03938e-06 8304 2 103.7 9.06116e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17158e-06 8304 2 103.7 9.42966e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.26497e-06 8304 2 103.7 0.000103959 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.27732e-06 8304 2 103.7 9.51648e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.22568e-06 8304 2 103.7 9.73593e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.3808e-06 8304 2 103.7 0.000104887 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.19247e-06 8304 2 103.7 9.24393e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.47393e-06 8304 2 103.7 9.12552e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.29335e-06 8304 2 103.7 0.00010696 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.0778e-06 8304 2 103.7 8.83765e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.85728e-06 8304 2 103.7 0.000119287 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.27296e-06 8304 2 103.7 9.6574e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.14343e-06 8304 2 103.7 0.000112188 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.21106e-06 8304 2 103.7 9.49517e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.20805e-06 8304 2 103.7 9.87744e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.38745e-06 8304 2 103.7 0.0001195 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.41188e-06 8304 2 103.7 0.000118758 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.12975e-06 8304 2 103.7 9.59149e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.19465e-06 8304 2 103.7 9.97444e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.31678e-06 8304 2 103.7 0.000113799 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.45489e-06 8304 2 103.7 0.000123181 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.07114e-06 8304 2 103.7 8.77045e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.3094e-06 8304 2 103.7 0.000119958 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.54693e-06 8304 2 103.7 0.000121362 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.64389e-06 8304 2 103.7 0.000137968 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.14242e-06 8304 2 103.7 9.55904e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.2629e-06 8304 2 103.7 0.000110535 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.51641e-06 8304 2 103.7 0.000116948 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.43154e-06 8304 2 103.7 0.000118313 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.33738e-06 8304 2 103.7 9.72143e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.22718e-06 8304 2 103.7 9.81605e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.281e-06 8304 2 103.7 9.85203e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.73535e-06 8304 2 103.7 0.00012691 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.20634e-06 8304 2 103.7 9.46023e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.28391e-06 8304 2 103.7 9.60481e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.42905e-06 8304 2 103.7 0.000102389 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.35115e-06 8304 2 103.7 9.00208e-05 2768 3000000 3000000 -897.07781 143908.11 1.3942094 297.64425 41.201175 71.924942 0 0 29181.472 -19673.407 -320.88394 -277698.7 -268077.51 6526.3976 Loop time of 30660 on 32 procs for 3000000 steps with 10381 atoms Performance: 8.454 ns/day, 2.839 hours/ns, 97.847 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 | 2726.5 | 12644 | 18013 |5329.1 | 41.24 Bond | 2.9967 | 8.028 | 15.45 | 138.8 | 0.03 Kspace | 6356.1 | 11753 | 21713 |5550.1 | 38.33 Neigh | 1287 | 1289.4 | 1292.2 | 4.4 | 4.21 Comm | 979.51 | 1357.9 | 1506.4 | 458.6 | 4.43 Output | 0.012349 | 0.014657 | 0.017033 | 1.1 | 0.00 Modify | 3396.2 | 3527.5 | 3835 | 241.2 | 11.51 Other | | 80.08 | | | 0.26 Nlocal: 324.406 ave 415 max 128 min Histogram: 8 0 0 0 0 0 1 3 5 15 Nghost: 6018.56 ave 7531 max 3823 min Histogram: 8 0 0 2 6 0 0 0 4 12 Neighs: 148747 ave 216773 max 26587 min Histogram: 8 0 0 0 0 2 3 3 1 15 Total # of neighbors = 4759898 Ave neighs/atom = 458.52018 Ave special neighs/atom = 1.6595704 Neighbor list builds = 149078 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.35115e-06 8304 2 103.7 9.00208e-05 2768 Per MPI rank memory allocation (min/avg/max) = 14.33 | 17.53 | 19.48 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 -896.48494 143908.11 1.3942094 297.64425 41.201175 71.924942 0 0 29181.472 -19673.407 -320.88394 -277698.7 -268077.51 6526.3976 Loop time of 1.53257e-05 on 32 procs for 0 steps with 10381 atoms 109.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.533e-05 | | |100.00 Nlocal: 324.406 ave 415 max 128 min Histogram: 8 0 0 0 0 0 1 3 5 15 Nghost: 6018.56 ave 7531 max 3823 min Histogram: 8 0 0 2 6 0 0 0 4 12 Neighs: 148747 ave 216773 max 26587 min Histogram: 8 0 0 0 0 2 3 3 1 15 Total # of neighbors = 4759898 Ave neighs/atom = 458.52018 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_13 unfix rdf_13 group rdfgroup_13 delete uncompute rdf_14 unfix rdf_14 group rdfgroup_14 delete uncompute rdf_15 unfix rdf_15 group rdfgroup_15 delete uncompute rdf_16 unfix rdf_16 group rdfgroup_16 delete uncompute rdf_17 unfix rdf_17 group rdfgroup_17 delete unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out