#------------------------------------------------------------------------------- # 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 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 200 4 1 fix rdf_1 rdfgroup_1 ave/time 1 30000 30000 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 200 4 8 fix rdf_2 rdfgroup_2 ave/time 1 30000 30000 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 200 4 7 fix rdf_5 rdfgroup_5 ave/time 1 30000 30000 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 200 6 1 fix rdf_6 rdfgroup_6 ave/time 1 30000 30000 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 200 6 8 fix rdf_7 rdfgroup_7 ave/time 1 30000 30000 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 200 6 7 fix rdf_9 rdfgroup_9 ave/time 1 30000 30000 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 200 3 1 fix rdf_11 rdfgroup_11 ave/time 1 30000 30000 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 200 3 8 fix rdf_12 rdfgroup_12 ave/time 1 30000 30000 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 200 3 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_15 union subset_Mg subset_Cl 599 atoms in group rdfgroup_15 compute rdf_15 rdfgroup_15 rdf 200 5 1 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_Mg subset_O(SO4) 330 atoms in group rdfgroup_16 compute rdf_16 rdfgroup_16 rdf 200 5 8 fix rdf_16 rdfgroup_16 ave/time 1 30000 30000 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 200 5 7 fix rdf_18 rdfgroup_18 ave/time 1 30000 30000 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 200 1 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_Cl subset_H(H2O) 5929 atoms in group rdfgroup_21 compute rdf_21 rdfgroup_21 rdf 200 1 2 fix rdf_21 rdfgroup_21 ave/time 1 30000 30000 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 200 9 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) subset_O(H2O) 2799 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 200 9 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_O(SO4) subset_H(H2O) 5660 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 8 2 fix rdf_25 rdfgroup_25 ave/time 1 30000 30000 c_rdf_25[*] file 2.5_PairCorrelation_all_25.out mode vector timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2571449 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0029930625 estimated relative force accuracy = 9.0135189e-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 18 neighbor lists, perpetual/occasional/extra = 1 17 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 SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.34578e-08 8304 2 103.7 1.06188e-06 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13.07 | 13.17 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 -102.13476 97258.15 1.2482762 292.55143 39.214126 89.770846 0 0 21395.801 32803.597 -215.43988 -215815.74 -161487.36 5521.7589 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.41452e-06 8304 2 103.7 0.000100614 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.5045e-06 8304 2 103.7 0.000100156 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.58829e-06 8304 2 103.7 0.000106675 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.58578e-06 8304 2 103.7 0.000104509 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.17001e-06 8304 2 103.7 9.2114e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.66071e-06 8304 2 103.7 0.000134369 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.12154e-06 8304 2 103.7 0.00010189 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.32294e-06 8304 2 103.7 9.83926e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.15799e-06 8304 2 103.7 0.000103645 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21593e-06 8304 2 103.7 8.85452e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.25596e-06 8304 2 103.7 0.000105808 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.285e-06 8304 2 103.7 9.49898e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.17315e-06 8304 2 103.7 0.000108298 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20025e-06 8304 2 103.7 9.4914e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.31461e-06 8304 2 103.7 9.46352e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.6253e-06 8304 2 103.7 9.03897e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.30665e-06 8304 2 103.7 0.000112647 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.46004e-06 8304 2 103.7 0.000111712 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.72474e-06 8304 2 103.7 0.000112378 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.21181e-06 8304 2 103.7 0.000103083 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.16324e-06 8304 2 103.7 9.87466e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.15623e-06 8304 2 103.7 9.14067e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.09497e-06 8304 2 103.7 8.87854e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.65887e-06 8304 2 103.7 9.0379e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.07594e-06 8304 2 103.7 9.77543e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.07355e-06 8304 2 103.7 8.91203e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.38223e-06 8304 2 103.7 9.7436e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.1766e-06 8304 2 103.7 0.000107696 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.17343e-06 8304 2 103.7 8.92258e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.33017e-06 8304 2 103.7 0.000108813 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.40299e-06 8304 2 103.7 0.000109726 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.25658e-06 8304 2 103.7 0.000101254 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.30763e-06 8304 2 103.7 0.000103865 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.14681e-06 8304 2 103.7 9.48661e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.30342e-06 8304 2 103.7 0.000103548 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.21829e-06 8304 2 103.7 9.61222e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.15252e-06 8304 2 103.7 9.66574e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.40205e-06 8304 2 103.7 0.000110383 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.13932e-06 8304 2 103.7 0.000104529 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26475e-06 8304 2 103.7 9.66524e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.08206e-06 8304 2 103.7 8.7912e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.58888e-06 8304 2 103.7 0.000109304 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.22647e-06 8304 2 103.7 9.21058e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.44812e-06 8304 2 103.7 0.000116555 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.39589e-06 8304 2 103.7 0.000117481 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.15307e-06 8304 2 103.7 9.20259e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.29665e-06 8304 2 103.7 9.2437e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.35524e-06 8304 2 103.7 9.24745e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.20158e-06 8304 2 103.7 0.000122637 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.28214e-06 8304 2 103.7 9.74864e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.12547e-06 8304 2 103.7 0.000100382 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.46182e-06 8304 2 103.7 0.000110978 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.10523e-06 8304 2 103.7 9.41869e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.25331e-06 8304 2 103.7 8.82581e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.58489e-06 8304 2 103.7 9.66154e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.54855e-06 8304 2 103.7 9.99434e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.61717e-06 8304 2 103.7 0.000131253 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.13447e-06 8304 2 103.7 8.97882e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.41779e-06 8304 2 103.7 9.19452e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.56272e-06 8304 2 103.7 0.000132002 2768 3000000 3000000 14.825141 97258.15 1.2482762 304.52494 39.611597 72.386927 0 0 21204.288 33095.272 -215.43988 -215787.37 -161375.81 5747.7527 Loop time of 41394.4 on 32 procs for 3000000 steps with 9101 atoms Performance: 6.262 ns/day, 3.833 hours/ns, 72.473 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 | 12779 | 13483 | 14177 | 254.0 | 32.57 Bond | 4.0447 | 9.4194 | 16.414 | 125.6 | 0.02 Kspace | 5181.1 | 5873.8 | 6586.7 | 388.3 | 14.19 Neigh | 977.8 | 979.61 | 981.62 | 4.3 | 2.37 Comm | 1639.9 | 1659.9 | 1675.1 | 23.1 | 4.01 Output | 0.011505 | 0.013757 | 0.016004 | 1.1 | 0.00 Modify | 19243 | 19258 | 19291 | 9.1 | 46.52 Other | | 130.2 | | | 0.31 Nlocal: 284.406 ave 311 max 256 min Histogram: 1 1 1 7 5 6 5 3 1 2 Nghost: 7160.53 ave 7210 max 7099 min Histogram: 3 1 1 4 4 4 5 4 3 3 Neighs: 152844 ave 168236 max 137058 min Histogram: 1 1 1 10 2 8 3 3 1 2 Total # of neighbors = 4891000 Ave neighs/atom = 537.41347 Ave special neighs/atom = 1.8929788 Neighbor list builds = 148273 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) = 0.2571449 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0029930625 estimated relative force accuracy = 9.0135189e-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 1.56272e-06 8304 2 103.7 0.000132002 2768 Per MPI rank memory allocation (min/avg/max) = 25.87 | 26.07 | 26.14 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 15.548823 97258.15 1.2482762 304.52494 39.611597 72.386927 0 0 21204.288 33095.272 -215.43988 -215787.37 -161375.81 5747.7527 Loop time of 1.15327e-05 on 32 procs for 0 steps with 9101 atoms 115.4% 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 | | 1.153e-05 | | |100.00 Nlocal: 284.406 ave 311 max 256 min Histogram: 1 1 1 7 5 6 5 3 1 2 Nghost: 7160.53 ave 7210 max 7099 min Histogram: 3 1 1 4 4 4 5 4 3 3 Neighs: 152844 ave 168236 max 137058 min Histogram: 1 1 1 10 2 8 3 3 1 2 Total # of neighbors = 4891000 Ave neighs/atom = 537.41347 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 unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_Custom.out