#------------------------------------------------------------------------------- # 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 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 403 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) 134 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) 2778 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 395 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) 126 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) 2770 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 424 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) 155 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) 2799 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 599 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) 330 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) 2974 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) 3161 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) 5929 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) 5567 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) 2799 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) 5660 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) 2892 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) = 0.25885735 grid = 30 36 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0026279522 estimated relative force accuracy = 7.9139999e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9900 3240 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 9 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 9.50473e-12 8304 2 103.7 1.07927e-09 2768 Per MPI rank memory allocation (min/avg/max) = 15.36 | 15.67 | 15.75 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-06 171.8434 97500.24 1.2451768 297.58713 47.820637 78.315997 0 0 21344.165 34391.946 -214.90495 -217213.06 -161350.81 5616.805 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.17625e-06 8304 2 103.7 9.13564e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.21389e-06 8304 2 103.7 9.45131e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.1874e-06 8304 2 103.7 0.000101464 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16571e-06 8304 2 103.7 0.000101773 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.30712e-06 8304 2 103.7 9.39883e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.11102e-06 8304 2 103.7 9.11213e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.40395e-06 8304 2 103.7 0.000107963 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.21663e-06 8304 2 103.7 0.000100469 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.13942e-06 8304 2 103.7 9.16911e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.24497e-06 8304 2 103.7 9.56838e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.26272e-06 8304 2 103.7 9.00798e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.14351e-06 8304 2 103.7 0.00010921 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.44949e-06 8304 2 103.7 9.95921e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.24268e-06 8304 2 103.7 0.000116131 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.33408e-06 8304 2 103.7 9.26362e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.65416e-06 8304 2 103.7 0.000117542 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.30822e-06 8304 2 103.7 0.000101196 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.17193e-06 8304 2 103.7 0.000119136 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.3948e-06 8304 2 103.7 0.000102864 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.6343e-06 8304 2 103.7 0.000111184 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.53491e-06 8304 2 103.7 0.000109391 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.23987e-06 8304 2 103.7 9.82098e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.36358e-06 8304 2 103.7 0.000105162 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.19211e-06 8304 2 103.7 9.94988e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.71866e-06 8304 2 103.7 9.95984e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.26089e-06 8304 2 103.7 0.00011312 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.63529e-06 8304 2 103.7 0.000125557 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.31672e-06 8304 2 103.7 9.49723e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.2033e-06 8304 2 103.7 9.83432e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.2355e-06 8304 2 103.7 0.000103012 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.54701e-06 8304 2 103.7 0.000107123 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.32644e-06 8304 2 103.7 9.13092e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.80395e-06 8304 2 103.7 0.000148949 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 2.01018e-06 8304 2 103.7 0.000158408 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.15837e-06 8304 2 103.7 9.26881e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19774e-06 8304 2 103.7 9.47201e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.34282e-06 8304 2 103.7 0.00011244 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.40369e-06 8304 2 103.7 0.000117828 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.57058e-06 8304 2 103.7 9.36075e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.15254e-06 8304 2 103.7 9.31114e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.32268e-06 8304 2 103.7 9.87302e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.73658e-06 8304 2 103.7 0.000111471 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.11248e-06 8304 2 103.7 9.13256e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.40292e-06 8304 2 103.7 9.7392e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.28549e-06 8304 2 103.7 8.9827e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.41716e-06 8304 2 103.7 0.000106279 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.28966e-06 8304 2 103.7 0.000123697 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.06876e-06 8304 2 103.7 9.32689e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.18382e-06 8304 2 103.7 8.6483e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.18657e-06 8304 2 103.7 9.36841e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.31998e-06 8304 2 103.7 9.85336e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.38946e-06 8304 2 103.7 0.000118112 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.11121e-06 8304 2 103.7 9.1659e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.22423e-06 8304 2 103.7 0.000100915 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.26831e-06 8304 2 103.7 0.000108612 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.33384e-06 8304 2 103.7 9.03413e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.20483e-06 8304 2 103.7 0.000100484 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.28662e-06 8304 2 103.7 9.63982e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.13317e-06 8304 2 103.7 0.000118185 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.07173e-06 8304 2 103.7 9.20229e-05 2768 3000000 3000000 31.777052 97500.24 1.2451768 299.12101 48.547683 58.919736 0 0 21298.647 34558.588 -214.90495 -217227.77 -161263.07 5645.7562 Loop time of 79911.9 on 16 procs for 3000000 steps with 9101 atoms Performance: 3.244 ns/day, 7.399 hours/ns, 37.541 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 | 25944 | 27404 | 30819 | 738.2 | 34.29 Bond | 9.8516 | 15.727 | 23.601 | 75.0 | 0.02 Kspace | 7492.3 | 10913 | 12370 |1173.2 | 13.66 Neigh | 2549.6 | 2551.2 | 2552.3 | 1.9 | 3.19 Comm | 994.89 | 1013.8 | 1033.9 | 37.6 | 1.27 Output | 0.1438 | 0.16411 | 0.18294 | 3.1 | 0.00 Modify | 37845 | 37853 | 37862 | 2.7 | 47.37 Other | | 160.9 | | | 0.20 Nlocal: 568.812 ave 594 max 544 min Histogram: 3 0 0 0 2 5 3 2 0 1 Nghost: 8853.94 ave 8914 max 8755 min Histogram: 2 0 0 1 3 2 1 0 3 4 Neighs: 304959 ave 320365 max 288709 min Histogram: 3 0 0 0 3 2 4 3 0 1 Total # of neighbors = 4879347 Ave neighs/atom = 536.13306 Ave special neighs/atom = 1.8929788 Neighbor list builds = 148340 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) = 0.25885735 grid = 30 36 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0026279522 estimated relative force accuracy = 7.9139999e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9900 3240 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.07173e-06 8304 2 103.7 9.20229e-05 2768 Per MPI rank memory allocation (min/avg/max) = 41.73 | 41.9 | 41.93 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 32.651021 97500.24 1.2451768 299.12101 48.547683 58.919736 0 0 21298.647 34558.588 -214.90495 -217227.77 -161263.07 5645.7562 Loop time of 1.40612e-05 on 16 procs for 0 steps with 9101 atoms 105.8% 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 | | 1.406e-05 | | |100.00 Nlocal: 568.812 ave 594 max 544 min Histogram: 3 0 0 0 2 5 3 2 0 1 Nghost: 8853.94 ave 8914 max 8755 min Histogram: 2 0 0 1 3 2 1 0 3 4 Neighs: 304959 ave 320365 max 288709 min Histogram: 3 0 0 0 3 2 4 3 0 1 Total # of neighbors = 4879347 Ave neighs/atom = 536.13306 Ave special neighs/atom = 1.8929788 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: 29:44:56