#------------------------------------------------------------------------------- # 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 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 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_19 union subset_Mg_1 subset_Cl_1 686 atoms in group rdfgroup_19 compute rdf_19 rdfgroup_19 rdf 200 5 1 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_Mg_1 subset_O(SO4)_1 348 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 200 5 7 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_Mg_1 subset_O(H2O)_1 2939 atoms in group rdfgroup_21 compute rdf_21 rdfgroup_21 rdf 200 5 6 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_Cl_1 subset_O(H2O)_1 3145 atoms in group rdfgroup_22 compute rdf_22 rdfgroup_22 rdf 200 1 6 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_Cl_1 subset_H(H2O)_1 5844 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 200 1 2 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_S(SO4)_1 subset_O(H2O)_1 2726 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 200 8 6 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_O(SO4)_1 subset_H(H2O)_1 5506 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 7 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_jiemian-Mg subset_jiemian-Cl 35 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 200 5 1 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_jiemian-Mg subset_jiemian-OS 18 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 200 5 7 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-OH 120 atoms in group rdfgroup_28 compute rdf_28 rdfgroup_28 rdf 200 5 6 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-Cl subset_jiemian-H 241 atoms in group rdfgroup_29 compute rdf_29 rdfgroup_29 rdf 200 1 2 fix rdf_29 rdfgroup_29 ave/time 1 30000 30000 c_rdf_29[*] file 2.5_PairCorrelation_all_29.out mode vector group rdfgroup_32 union subset_jiemian-OS subset_jiemian-H 224 atoms in group rdfgroup_32 compute rdf_32 rdfgroup_32 rdf 200 7 2 fix rdf_32 rdfgroup_32 ave/time 1 30000 30000 c_rdf_32[*] file 2.5_PairCorrelation_all_32.out mode vector timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2550303 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 = 7000 2016 generated 0 of 28 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 = 7 5 15 13 neighbor lists, perpetual/occasional/extra = 1 12 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 SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.25611e-13 9825 1 103.7 8.20535e-11 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.3 | 13.65 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 -7071.4331 143340.91 1.3114365 297.88406 43.773539 70.988266 0 0 37155.357 -73116.302 -319.55737 -317448.18 -353294.36 7030.6757 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.04524e-06 9825 1 103.7 9.31898e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.29514e-06 9825 1 103.7 9.73497e-05 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.23693e-06 9825 1 103.7 9.01902e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.17912e-06 9825 1 103.7 9.23242e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.11246e-06 9825 1 103.7 8.79344e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.19762e-06 9825 1 103.7 9.49275e-05 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.47509e-06 9825 1 103.7 0.000109127 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.24816e-06 9825 1 103.7 9.26218e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.6374e-06 9825 1 103.7 0.000120119 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.28572e-06 9825 1 103.7 0.000113205 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 2.08118e-06 9825 1 103.7 0.000109846 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.36917e-06 9825 1 103.7 9.94881e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.62848e-06 9825 1 103.7 0.000117823 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.47848e-06 9825 1 103.7 9.70713e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.40492e-06 9825 1 103.7 0.000104397 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.45571e-06 9825 1 103.7 0.00010429 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.58389e-06 9825 1 103.7 0.000132284 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.54839e-06 9825 1 103.7 0.000102131 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.33447e-06 9825 1 103.7 0.000102374 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.0769e-06 9825 1 103.7 9.33328e-05 3275 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.17247e-06 9825 1 103.7 9.98683e-05 3275 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.439e-06 9825 1 103.7 9.17892e-05 3275 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.33856e-06 9825 1 103.7 9.71827e-05 3275 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.25417e-06 9825 1 103.7 0.000100266 3275 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.21789e-06 9825 1 103.7 0.000104721 3275 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.11976e-06 9825 1 103.7 0.000106887 3275 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.60432e-06 9825 1 103.7 0.000107223 3275 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.45332e-06 9825 1 103.7 0.000109372 3275 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.28461e-06 9825 1 103.7 0.000101022 3275 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.44644e-06 9825 1 103.7 9.74626e-05 3275 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.1921e-06 9825 1 103.7 0.000109176 3275 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.13691e-06 9825 1 103.7 0.000103525 3275 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.38204e-06 9825 1 103.7 0.000102629 3275 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.07328e-06 9825 1 103.7 8.98846e-05 3275 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.47895e-06 9825 1 103.7 9.09415e-05 3275 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.39585e-06 9825 1 103.7 9.50394e-05 3275 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.22905e-06 9825 1 103.7 9.67581e-05 3275 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.34643e-06 9825 1 103.7 0.000123824 3275 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.32449e-06 9825 1 103.7 0.00011698 3275 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 9.77693e-07 9825 1 103.7 8.91677e-05 3275 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.32015e-06 9825 1 103.7 0.000102976 3275 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.29114e-06 9825 1 103.7 9.71444e-05 3275 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.42041e-06 9825 1 103.7 0.000117405 3275 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.10719e-06 9825 1 103.7 8.93908e-05 3275 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.36801e-06 9825 1 103.7 0.00010938 3275 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.27751e-06 9825 1 103.7 9.3497e-05 3275 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.26528e-06 9825 1 103.7 9.77992e-05 3275 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.15966e-06 9825 1 103.7 0.000123576 3275 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.33583e-06 9825 1 103.7 0.000111549 3275 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.54084e-06 9825 1 103.7 9.74248e-05 3275 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.4615e-06 9825 1 103.7 0.000115722 3275 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.08451e-06 9825 1 103.7 9.39493e-05 3275 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.31442e-06 9825 1 103.7 9.67915e-05 3275 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.31014e-06 9825 1 103.7 0.000101652 3275 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.33636e-06 9825 1 103.7 9.39555e-05 3275 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.28843e-06 9825 1 103.7 9.51653e-05 3275 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.31511e-06 9825 1 103.7 9.65148e-05 3275 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.53464e-06 9825 1 103.7 9.33387e-05 3275 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.26001e-06 9825 1 103.7 9.21089e-05 3275 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.19152e-06 9825 1 103.7 0.000113811 3275 3000000 3000000 -7400.0869 143340.91 1.3114365 297.09869 38.784906 60.379503 0 0 36907.473 -72906.738 -319.55737 -317452.94 -353353.04 7012.1392 Loop time of 42094.8 on 32 procs for 3000000 steps with 12250 atoms Performance: 6.158 ns/day, 3.898 hours/ns, 71.268 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12762 | 15610 | 17312 |1091.9 | 37.08 Bond | 3.5398 | 8.9092 | 15.464 | 118.2 | 0.02 Kspace | 6212.3 | 7907.5 | 10754 |1537.4 | 18.78 Neigh | 931 | 932.49 | 934.04 | 2.9 | 2.22 Comm | 1754.8 | 1842.4 | 1898.4 | 108.7 | 4.38 Output | 0.013503 | 0.016148 | 0.018814 | 1.2 | 0.00 Modify | 15638 | 15695 | 15765 | 30.9 | 37.28 Other | | 98.86 | | | 0.23 Nlocal: 382.812 ave 423 max 345 min Histogram: 2 2 5 2 6 4 4 3 2 2 Nghost: 7274.25 ave 7594 max 6915 min Histogram: 4 4 1 3 2 3 3 4 2 6 Neighs: 188126 ave 223578 max 152136 min Histogram: 3 3 2 2 4 4 8 2 2 2 Total # of neighbors = 6020027 Ave neighs/atom = 491.43078 Ave special neighs/atom = 1.6481633 Neighbor list builds = 149506 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) = 0.2550303 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 = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.19152e-06 9825 1 103.7 0.000113811 3275 Per MPI rank memory allocation (min/avg/max) = 22.13 | 26.03 | 27.38 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 -7399.1902 143340.91 1.3114365 297.09869 38.784906 60.379503 0 0 36907.473 -72906.738 -319.55737 -317452.94 -353353.04 7012.1392 Loop time of 8.8015e-06 on 32 procs for 0 steps with 12250 atoms 119.3% 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 | | 8.802e-06 | | |100.00 Nlocal: 382.812 ave 423 max 345 min Histogram: 2 2 5 2 6 4 4 3 2 2 Nghost: 7274.25 ave 7594 max 6915 min Histogram: 4 4 1 3 2 3 3 4 2 6 Neighs: 188126 ave 223578 max 152136 min Histogram: 3 3 2 2 4 4 8 2 2 2 Total # of neighbors = 6020027 Ave neighs/atom = 491.43078 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci 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_32 unfix rdf_32 group rdfgroup_32 delete unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 14:16:04