#------------------------------------------------------------------------------- # 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 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 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 restart 3000000 2.5.restart dump trj all custom 30000 2.5.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 30000 1 30000 v_etotal v_pe v_ke file 2.5.energies.txt dump sci all custom 300000 2.5.xyz id mol type q xs ys zs group rdfgroup_1 union subset_Li subset_Cl 350 atoms in group rdfgroup_1 compute rdf_1 rdfgroup_1 rdf 100 4 1 fix rdf_1 rdfgroup_1 ave/time 1 300000 300000 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector group rdfgroup_2 union subset_Li subset_O(SO4) 131 atoms in group rdfgroup_2 compute rdf_2 rdfgroup_2 rdf 100 4 8 fix rdf_2 rdfgroup_2 ave/time 1 300000 300000 c_rdf_2[*] file 2.5_PairCorrelation_all_2.out mode vector group rdfgroup_5 union subset_Li subset_O(H2O) 2819 atoms in group rdfgroup_5 compute rdf_5 rdfgroup_5 rdf 100 4 7 fix rdf_5 rdfgroup_5 ave/time 1 300000 300000 c_rdf_5[*] file 2.5_PairCorrelation_all_5.out mode vector group rdfgroup_6 union subset_Na subset_Cl 399 atoms in group rdfgroup_6 compute rdf_6 rdfgroup_6 rdf 100 6 1 fix rdf_6 rdfgroup_6 ave/time 1 300000 300000 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector group rdfgroup_7 union subset_Na subset_O(SO4) 180 atoms in group rdfgroup_7 compute rdf_7 rdfgroup_7 rdf 100 6 8 fix rdf_7 rdfgroup_7 ave/time 1 300000 300000 c_rdf_7[*] file 2.5_PairCorrelation_all_7.out mode vector group rdfgroup_9 union subset_Na subset_O(H2O) 2868 atoms in group rdfgroup_9 compute rdf_9 rdfgroup_9 rdf 100 6 7 fix rdf_9 rdfgroup_9 ave/time 1 300000 300000 c_rdf_9[*] file 2.5_PairCorrelation_all_9.out mode vector group rdfgroup_11 union subset_K subset_Cl 383 atoms in group rdfgroup_11 compute rdf_11 rdfgroup_11 rdf 100 3 1 fix rdf_11 rdfgroup_11 ave/time 1 300000 300000 c_rdf_11[*] file 2.5_PairCorrelation_all_11.out mode vector group rdfgroup_12 union subset_K subset_O(SO4) 164 atoms in group rdfgroup_12 compute rdf_12 rdfgroup_12 rdf 100 3 8 fix rdf_12 rdfgroup_12 ave/time 1 300000 300000 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector group rdfgroup_13 union subset_K subset_O(H2O) 2852 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 100 3 7 fix rdf_13 rdfgroup_13 ave/time 1 300000 300000 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector group rdfgroup_15 union subset_Mg subset_Cl 494 atoms in group rdfgroup_15 compute rdf_15 rdfgroup_15 rdf 100 5 1 fix rdf_15 rdfgroup_15 ave/time 1 300000 300000 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector group rdfgroup_16 union subset_Mg subset_O(SO4) 275 atoms in group rdfgroup_16 compute rdf_16 rdfgroup_16 rdf 100 5 8 fix rdf_16 rdfgroup_16 ave/time 1 300000 300000 c_rdf_16[*] file 2.5_PairCorrelation_all_16.out mode vector group rdfgroup_18 union subset_Mg subset_O(H2O) 2963 atoms in group rdfgroup_18 compute rdf_18 rdfgroup_18 rdf 100 5 7 fix rdf_18 rdfgroup_18 ave/time 1 300000 300000 c_rdf_18[*] file 2.5_PairCorrelation_all_18.out mode vector group rdfgroup_20 union subset_Cl subset_O(H2O) 3155 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 100 1 7 fix rdf_20 rdfgroup_20 ave/time 1 300000 300000 c_rdf_20[*] file 2.5_PairCorrelation_all_20.out mode vector group rdfgroup_21 union subset_Cl subset_H(H2O) 5967 atoms in group rdfgroup_21 compute rdf_21 rdfgroup_21 rdf 100 1 2 fix rdf_21 rdfgroup_21 ave/time 1 300000 300000 c_rdf_21[*] file 2.5_PairCorrelation_all_21.out mode vector group rdfgroup_23 union subset_S(SO4) subset_H(H2O) 5655 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 100 9 2 fix rdf_23 rdfgroup_23 ave/time 1 300000 300000 c_rdf_23[*] file 2.5_PairCorrelation_all_23.out mode vector group rdfgroup_24 union subset_S(SO4) subset_O(H2O) 2843 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 100 9 7 fix rdf_24 rdfgroup_24 ave/time 1 300000 300000 c_rdf_24[*] file 2.5_PairCorrelation_all_24.out mode vector group rdfgroup_25 union subset_O(SO4) subset_H(H2O) 5748 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 100 8 2 fix rdf_25 rdfgroup_25 ave/time 1 300000 300000 c_rdf_25[*] file 2.5_PairCorrelation_all_25.out mode vector group rdfgroup_26 union subset_O(SO4) subset_O(H2O) 2936 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 100 8 7 fix rdf_26 rdfgroup_26 ave/time 1 300000 300000 c_rdf_26[*] file 2.5_PairCorrelation_all_26.out mode vector timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25696535 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.002899315 estimated relative force accuracy = 8.7312009e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5852 1800 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 11 19 neighbor lists, perpetual/occasional/extra = 1 18 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri 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 (16) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (17) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (18) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (19) 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 2.66505e-09 8436 2 103.7 2.95379e-07 2812 Per MPI rank memory allocation (min/avg/max) = 14.17 | 14.36 | 14.44 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 -612.58021 97920.754 1.2272094 296.86139 48.690385 75.379795 0 0 18387.611 48516.496 -211.58191 -207881.37 -140853.19 5641.1573 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.18857e-06 8436 2 103.7 9.43844e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.30057e-06 8436 2 103.7 9.38466e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.17132e-06 8436 2 103.7 9.43817e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.86714e-06 8436 2 103.7 0.00012253 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.11074e-06 8436 2 103.7 9.67606e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.11009e-06 8436 2 103.7 9.29925e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.4777e-06 8436 2 103.7 9.98742e-05 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.13029e-06 8436 2 103.7 9.76337e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.42216e-06 8436 2 103.7 0.000114544 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21448e-06 8436 2 103.7 0.000100883 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.51314e-06 8436 2 103.7 0.00010053 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.40996e-06 8436 2 103.7 0.000118429 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.11454e-06 8436 2 103.7 9.47283e-05 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.46066e-06 8436 2 103.7 0.000115187 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.34236e-06 8436 2 103.7 0.000113435 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.14203e-06 8436 2 103.7 9.32278e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.79734e-06 8436 2 103.7 9.84946e-05 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.27148e-06 8436 2 103.7 9.04195e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.31866e-06 8436 2 103.7 0.000100401 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.79651e-06 8436 2 103.7 0.000130312 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.30414e-06 8436 2 103.7 0.00010543 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.96489e-06 8436 2 103.7 0.000135734 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.141e-06 8436 2 103.7 9.95877e-05 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.39506e-06 8436 2 103.7 0.000110583 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.31039e-06 8436 2 103.7 9.45984e-05 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.19997e-06 8436 2 103.7 9.76641e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.13804e-06 8436 2 103.7 0.000107147 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.38316e-06 8436 2 103.7 0.000100116 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.38853e-06 8436 2 103.7 0.000105109 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.24282e-06 8436 2 103.7 9.33735e-05 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.5439e-06 8436 2 103.7 0.000107658 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.22017e-06 8436 2 103.7 0.000117727 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.16927e-06 8436 2 103.7 9.47214e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.1639e-06 8436 2 103.7 0.00011885 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.44638e-06 8436 2 103.7 0.000101499 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.09462e-06 8436 2 103.7 9.24906e-05 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.44043e-06 8436 2 103.7 0.000109587 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.38793e-06 8436 2 103.7 0.000104759 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.40902e-06 8436 2 103.7 0.000103059 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.45094e-06 8436 2 103.7 9.49944e-05 2812 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.28311e-06 8436 2 103.7 9.3048e-05 2812 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.24651e-06 8436 2 103.7 9.51417e-05 2812 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.28121e-06 8436 2 103.7 0.000101028 2812 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.17006e-06 8436 2 103.7 9.37394e-05 2812 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.49149e-06 8436 2 103.7 0.000111178 2812 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.10542e-06 8436 2 103.7 0.000103375 2812 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.50488e-06 8436 2 103.7 0.00010838 2812 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.10212e-06 8436 2 103.7 0.000110447 2812 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.15079e-06 8436 2 103.7 9.75239e-05 2812 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.11499e-06 8436 2 103.7 9.03021e-05 2812 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.16784e-06 8436 2 103.7 8.74181e-05 2812 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.88129e-06 8436 2 103.7 0.000131755 2812 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.28889e-06 8436 2 103.7 9.54186e-05 2812 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.4651e-06 8436 2 103.7 0.000109484 2812 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.42221e-06 8436 2 103.7 0.000105492 2812 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.46972e-06 8436 2 103.7 9.28592e-05 2812 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.26261e-06 8436 2 103.7 0.000101229 2812 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.34153e-06 8436 2 103.7 0.00010509 2812 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.66451e-06 8436 2 103.7 0.00010382 2812 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.13928e-06 8436 2 103.7 9.44581e-05 2812 3000000 3000000 382.22721 97920.754 1.2272094 300.04821 44.294299 78.879296 0 0 18841.732 48198.698 -211.58191 -207913.86 -140750.26 5701.7153 Loop time of 43554.5 on 32 procs for 3000000 steps with 9188 atoms Performance: 5.951 ns/day, 4.033 hours/ns, 68.879 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13287 | 13660 | 14402 | 202.7 | 31.36 Bond | 4.4245 | 9.4348 | 17.837 | 109.9 | 0.02 Kspace | 5571.9 | 6313.8 | 6687.6 | 300.1 | 14.50 Neigh | 1013.3 | 1015.2 | 1017.2 | 4.0 | 2.33 Comm | 1663.4 | 1681.4 | 1696.2 | 17.7 | 3.86 Output | 0.082491 | 0.1083 | 0.13202 | 4.6 | 0.00 Modify | 20769 | 20779 | 20792 | 4.0 | 47.71 Other | | 95.79 | | | 0.22 Nlocal: 287.125 ave 306 max 262 min Histogram: 1 2 0 5 4 4 7 3 4 2 Nghost: 7198.09 ave 7279 max 7156 min Histogram: 9 2 4 7 1 0 3 4 1 1 Neighs: 154717 ave 166083 max 140694 min Histogram: 2 1 2 4 4 6 4 3 4 2 Total # of neighbors = 4950948 Ave neighs/atom = 538.84937 Ave special neighs/atom = 1.9037875 Neighbor list builds = 148918 Dangerous builds = 0 undump trj unfix trjE 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) = 0.25696535 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.002899315 estimated relative force accuracy = 8.7312009e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5852 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.13928e-06 8436 2 103.7 9.44581e-05 2812 Per MPI rank memory allocation (min/avg/max) = 26.64 | 26.85 | 26.9 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 383.04938 97920.754 1.2272094 300.04821 44.294299 78.879296 0 0 18841.732 48198.698 -211.58191 -207913.86 -140750.26 5701.7153 Loop time of 7.13872e-06 on 32 procs for 0 steps with 9188 atoms 124.3% 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 | | 7.139e-06 | | |100.00 Nlocal: 287.125 ave 306 max 262 min Histogram: 1 2 0 5 4 4 7 3 4 2 Nghost: 7198.09 ave 7279 max 7156 min Histogram: 9 2 4 7 1 0 3 4 1 1 Neighs: 154717 ave 166083 max 140694 min Histogram: 2 1 2 4 4 6 4 3 4 2 Total # of neighbors = 4950948 Ave neighs/atom = 538.84937 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_1 unfix rdf_1 group rdfgroup_1 delete uncompute rdf_2 unfix rdf_2 group rdfgroup_2 delete uncompute rdf_5 unfix rdf_5 group rdfgroup_5 delete uncompute rdf_6 unfix rdf_6 group rdfgroup_6 delete uncompute rdf_7 unfix rdf_7 group rdfgroup_7 delete uncompute rdf_9 unfix rdf_9 group rdfgroup_9 delete uncompute rdf_11 unfix rdf_11 group rdfgroup_11 delete uncompute rdf_12 unfix rdf_12 group rdfgroup_12 delete uncompute rdf_13 unfix rdf_13 group rdfgroup_13 delete uncompute rdf_15 unfix rdf_15 group rdfgroup_15 delete uncompute rdf_16 unfix rdf_16 group rdfgroup_16 delete uncompute rdf_18 unfix rdf_18 group rdfgroup_18 delete uncompute rdf_20 unfix rdf_20 group rdfgroup_20 delete uncompute rdf_21 unfix rdf_21 group rdfgroup_21 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 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 16:45:59