#------------------------------------------------------------------------------- # 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 2699 = # 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_18 union subset_Li_1 subset_Cl_1 460 atoms in group rdfgroup_18 compute rdf_18 rdfgroup_18 rdf 200 4 1 fix rdf_18 rdfgroup_18 ave/time 1 30000 30000 c_rdf_18[*] file 2.5_PairCorrelation_all_18.out mode vector group rdfgroup_19 union subset_Li_1 subset_O(H2O)_1 2713 atoms in group rdfgroup_19 compute rdf_19 rdfgroup_19 rdf 200 4 7 fix rdf_19 rdfgroup_19 ave/time 1 30000 30000 c_rdf_19[*] file 2.5_PairCorrelation_all_19.out mode vector group rdfgroup_20 union subset_K_1 subset_Cl_1 452 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 200 3 1 fix rdf_20 rdfgroup_20 ave/time 1 30000 30000 c_rdf_20[*] file 2.5_PairCorrelation_all_20.out mode vector group rdfgroup_21 union subset_K_1 subset_O(H2O)_1 2705 atoms in group rdfgroup_21 compute rdf_21 rdfgroup_21 rdf 200 3 7 fix rdf_21 rdfgroup_21 ave/time 1 30000 30000 c_rdf_21[*] file 2.5_PairCorrelation_all_21.out mode vector group rdfgroup_22 union subset_Mg_1 subset_Cl_1 686 atoms in group rdfgroup_22 compute rdf_22 rdfgroup_22 rdf 200 5 1 fix rdf_22 rdfgroup_22 ave/time 1 30000 30000 c_rdf_22[*] file 2.5_PairCorrelation_all_22.out mode vector group rdfgroup_23 union subset_Mg_1 subset_O(H2O)_1 2939 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 200 5 7 fix rdf_23 rdfgroup_23 ave/time 1 30000 30000 c_rdf_23[*] file 2.5_PairCorrelation_all_23.out mode vector group rdfgroup_24 union subset_Cl_1 subset_O(H2O)_1 3145 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 200 1 7 fix rdf_24 rdfgroup_24 ave/time 1 30000 30000 c_rdf_24[*] file 2.5_PairCorrelation_all_24.out mode vector group rdfgroup_25 union subset_Cl_1 subset_H(H2O)_1 5844 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 1 2 fix rdf_25 rdfgroup_25 ave/time 1 30000 30000 c_rdf_25[*] file 2.5_PairCorrelation_all_25.out mode vector group rdfgroup_26 union subset_S(SO4)_1 subset_O(H2O)_1 2726 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 200 9 7 fix rdf_26 rdfgroup_26 ave/time 1 30000 30000 c_rdf_26[*] file 2.5_PairCorrelation_all_26.out mode vector group rdfgroup_27 union subset_O(SO4)_1 subset_H(H2O)_1 5506 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 200 8 2 fix rdf_27 rdfgroup_27 ave/time 1 30000 30000 c_rdf_27[*] file 2.5_PairCorrelation_all_27.out mode vector group rdfgroup_28 union subset_jiemian-mg subset_jiemian-Cl 17 atoms in group rdfgroup_28 compute rdf_28 rdfgroup_28 rdf 200 5 1 fix rdf_28 rdfgroup_28 ave/time 1 30000 30000 c_rdf_28[*] file 2.5_PairCorrelation_all_28.out mode vector group rdfgroup_29 union subset_jiemian-mg subset_jiemian-OH 99 atoms in group rdfgroup_29 compute rdf_29 rdfgroup_29 rdf 200 5 7 fix rdf_29 rdfgroup_29 ave/time 1 30000 30000 c_rdf_29[*] file 2.5_PairCorrelation_all_29.out mode vector group rdfgroup_30 union subset_jiemian-Cl subset_jiemian-OH 106 atoms in group rdfgroup_30 compute rdf_30 rdfgroup_30 rdf 200 1 7 fix rdf_30 rdfgroup_30 ave/time 1 30000 30000 c_rdf_30[*] file 2.5_PairCorrelation_all_30.out mode vector group rdfgroup_31 union subset_jiemian-Cl subset_jiemian-H 208 atoms in group rdfgroup_31 compute rdf_31 rdfgroup_31 rdf 200 1 2 fix rdf_31 rdfgroup_31 ave/time 1 30000 30000 c_rdf_31[*] file 2.5_PairCorrelation_all_31.out mode vector timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 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 15 15 neighbor lists, perpetual/occasional/extra = 1 14 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 (7) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (8) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (9) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (10) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (11) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (12) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (13) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (14) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (15) 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 7.63389e-13 8097 2 103.7 1.00442e-10 2699 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.06 | 14.78 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 -370.75965 138878.49 1.4411859 295.14439 36.187694 64.059394 0 0 35953.424 -63507.872 -317.08001 -295419.68 -322873.88 6628.1823 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.1353e-06 8097 2 103.7 9.26529e-05 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26749e-06 8097 2 103.7 9.19331e-05 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.34681e-06 8097 2 103.7 0.000101694 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.45785e-06 8097 2 103.7 8.99179e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.51069e-06 8097 2 103.7 0.000108771 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.29829e-06 8097 2 103.7 9.42683e-05 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.08639e-06 8097 2 103.7 0.00010409 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.22479e-06 8097 2 103.7 9.93475e-05 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.23675e-06 8097 2 103.7 9.97567e-05 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.4451e-06 8097 2 103.7 0.000102241 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2563e-06 8097 2 103.7 0.000100976 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.32743e-06 8097 2 103.7 9.54571e-05 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.37835e-06 8097 2 103.7 9.40603e-05 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.47884e-06 8097 2 103.7 0.000118331 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.3837e-06 8097 2 103.7 0.000109916 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.12691e-06 8097 2 103.7 0.000104981 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.26471e-06 8097 2 103.7 9.44344e-05 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.30755e-06 8097 2 103.7 9.33155e-05 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.09136e-06 8097 2 103.7 0.000102103 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.20402e-06 8097 2 103.7 0.000105997 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.11623e-06 8097 2 103.7 8.94995e-05 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.19986e-06 8097 2 103.7 9.38338e-05 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.14812e-06 8097 2 103.7 9.09387e-05 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.3025e-06 8097 2 103.7 0.000110804 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17676e-06 8097 2 103.7 0.0001012 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.2816e-06 8097 2 103.7 9.12844e-05 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.40736e-06 8097 2 103.7 0.000103052 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.16191e-06 8097 2 103.7 9.0527e-05 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.16274e-06 8097 2 103.7 0.00011103 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.42081e-06 8097 2 103.7 0.000109437 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.26956e-06 8097 2 103.7 0.00010423 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.21075e-06 8097 2 103.7 0.000101337 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.11192e-06 8097 2 103.7 9.07518e-05 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.46561e-06 8097 2 103.7 9.94107e-05 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.14185e-06 8097 2 103.7 9.63201e-05 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19739e-06 8097 2 103.7 9.9977e-05 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.70802e-06 8097 2 103.7 0.000105149 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.19151e-06 8097 2 103.7 0.00010014 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.15143e-06 8097 2 103.7 8.99357e-05 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.11601e-06 8097 2 103.7 9.05294e-05 2699 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.30866e-06 8097 2 103.7 0.000109976 2699 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.53279e-06 8097 2 103.7 9.02989e-05 2699 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.77563e-06 8097 2 103.7 0.000113685 2699 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.3617e-06 8097 2 103.7 0.000108828 2699 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.10855e-06 8097 2 103.7 9.63621e-05 2699 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.09029e-06 8097 2 103.7 9.04815e-05 2699 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.1571e-06 8097 2 103.7 9.42768e-05 2699 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.58862e-06 8097 2 103.7 9.01952e-05 2699 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.2743e-06 8097 2 103.7 0.00011912 2699 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.12984e-06 8097 2 103.7 9.92063e-05 2699 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.32098e-06 8097 2 103.7 9.55442e-05 2699 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.59463e-06 8097 2 103.7 0.000130429 2699 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.11754e-06 8097 2 103.7 0.000108043 2699 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.37926e-06 8097 2 103.7 9.48982e-05 2699 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.37802e-06 8097 2 103.7 0.000109085 2699 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.16136e-06 8097 2 103.7 9.5282e-05 2699 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.29412e-06 8097 2 103.7 0.000107115 2699 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.24126e-06 8097 2 103.7 0.0001014 2699 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.12046e-06 8097 2 103.7 0.000104593 2699 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.36021e-06 8097 2 103.7 9.97278e-05 2699 3000000 3000000 108.20773 138878.49 1.4411859 298.3607 40.34364 40.89792 0 0 36221.87 -63588.6 -317.08001 -295421.59 -322707.07 6700.4125 Loop time of 71061.8 on 16 procs for 3000000 steps with 10558 atoms Performance: 3.648 ns/day, 6.580 hours/ns, 42.217 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7165.1 | 24387 | 32021 |6357.2 | 34.32 Bond | 4.1637 | 12.046 | 18.992 | 151.3 | 0.02 Kspace | 6746.8 | 14419 | 31684 |8291.6 | 20.29 Neigh | 1654.7 | 1658.4 | 1662.5 | 6.1 | 2.33 Comm | 1000.3 | 1184.1 | 1279.1 | 305.1 | 1.67 Output | 0.01831 | 0.020203 | 0.022072 | 0.8 | 0.00 Modify | 29216 | 29280 | 29421 | 45.7 | 41.20 Other | | 120.7 | | | 0.17 Nlocal: 659.875 ave 809 max 350 min Histogram: 4 0 0 0 0 0 0 0 7 5 Nghost: 8167.88 ave 9734 max 6925 min Histogram: 4 0 0 7 1 0 0 0 0 4 Neighs: 307270 ave 406684 max 87912 min Histogram: 4 0 0 0 0 0 0 1 3 8 Total # of neighbors = 4916315 Ave neighs/atom = 465.64832 Ave special neighs/atom = 1.5849593 Neighbor list builds = 148309 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.36021e-06 8097 2 103.7 9.97278e-05 2699 Per MPI rank memory allocation (min/avg/max) = 18.16 | 34.52 | 41.48 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 108.75064 138878.49 1.4411859 298.3607 40.34364 40.89792 0 0 36221.87 -63588.6 -317.08001 -295421.59 -322707.07 6700.4125 Loop time of 5.1475e-06 on 16 procs for 0 steps with 10558 atoms 120.2% 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 | | 5.148e-06 | | |100.00 Nlocal: 659.875 ave 809 max 350 min Histogram: 4 0 0 0 0 0 0 0 7 5 Nghost: 8167.88 ave 9734 max 6925 min Histogram: 4 0 0 7 1 0 0 0 0 4 Neighs: 307270 ave 406684 max 87912 min Histogram: 4 0 0 0 0 0 0 1 3 8 Total # of neighbors = 4916315 Ave neighs/atom = 465.64832 Ave special neighs/atom = 1.5849593 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_18 unfix rdf_18 group rdfgroup_18 delete uncompute rdf_19 unfix rdf_19 group rdfgroup_19 delete uncompute rdf_20 unfix rdf_20 group rdfgroup_20 delete uncompute rdf_21 unfix rdf_21 group rdfgroup_21 delete uncompute rdf_22 unfix rdf_22 group rdfgroup_22 delete uncompute rdf_23 unfix rdf_23 group rdfgroup_23 delete uncompute rdf_24 unfix rdf_24 group rdfgroup_24 delete uncompute rdf_25 unfix rdf_25 group rdfgroup_25 delete uncompute rdf_26 unfix rdf_26 group rdfgroup_26 delete uncompute rdf_27 unfix rdf_27 group rdfgroup_27 delete uncompute rdf_28 unfix rdf_28 group rdfgroup_28 delete uncompute rdf_29 unfix rdf_29 group rdfgroup_29 delete uncompute rdf_30 unfix rdf_30 group rdfgroup_30 delete uncompute rdf_31 unfix rdf_31 group rdfgroup_31 delete unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 24:09:21