#------------------------------------------------------------------------------- # 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 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_23 union subset_Li_1 subset_S(SO4)_1 41 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 200 4 9 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_Na_1 subset_S(SO4)_1 33 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 200 6 9 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_K_1 subset_S(SO4)_1 62 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 3 9 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_Mg_1 subset_S(SO4)_1 237 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 200 5 9 fix rdf_26 rdfgroup_26 ave/time 1 30000 30000 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 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 15 5 neighbor lists, perpetual/occasional/extra = 1 4 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 SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.13964e-12 8304 2 103.7 8.38298e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.15 | 13.64 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 -432.49142 140505.98 1.42352 295.63473 42.814832 76.967432 0 0 34342.415 -50741.99 -315.99625 -291935.36 -308215.15 6722.0299 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.39679e-06 8304 2 103.7 0.00010915 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.17137e-06 8304 2 103.7 9.39913e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.36088e-06 8304 2 103.7 9.87978e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.12957e-06 8304 2 103.7 9.2132e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.17057e-06 8304 2 103.7 9.16134e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.48299e-06 8304 2 103.7 0.000102035 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.61673e-06 8304 2 103.7 0.000127624 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.29888e-06 8304 2 103.7 0.000111487 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.26894e-06 8304 2 103.7 9.48752e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15197e-06 8304 2 103.7 9.2705e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.34333e-06 8304 2 103.7 9.1546e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.46257e-06 8304 2 103.7 0.000102006 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.37436e-06 8304 2 103.7 9.3951e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20087e-06 8304 2 103.7 0.000106665 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.51397e-06 8304 2 103.7 0.000104941 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.42925e-06 8304 2 103.7 0.000120402 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.24372e-06 8304 2 103.7 0.000112282 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.22748e-06 8304 2 103.7 9.39084e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.37132e-06 8304 2 103.7 0.000107394 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.33835e-06 8304 2 103.7 9.2862e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.18637e-06 8304 2 103.7 8.85002e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.00645e-06 8304 2 103.7 9.12527e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.17603e-06 8304 2 103.7 9.34847e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.1902e-06 8304 2 103.7 0.000108503 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.14096e-06 8304 2 103.7 9.04057e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.71575e-06 8304 2 103.7 0.000118344 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.11598e-06 8304 2 103.7 0.000103766 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.12548e-06 8304 2 103.7 9.27298e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.7113e-06 8304 2 103.7 0.000113546 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.19952e-06 8304 2 103.7 9.10263e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.21199e-06 8304 2 103.7 9.7638e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.14923e-06 8304 2 103.7 0.000104624 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.30792e-06 8304 2 103.7 0.000110672 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.25819e-06 8304 2 103.7 9.47201e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.29866e-06 8304 2 103.7 9.8636e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.57659e-06 8304 2 103.7 0.000123787 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.66609e-06 8304 2 103.7 0.000102292 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.29655e-06 8304 2 103.7 9.81251e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.05683e-06 8304 2 103.7 8.99587e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.15531e-06 8304 2 103.7 9.82331e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.39438e-06 8304 2 103.7 0.000104337 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.17449e-06 8304 2 103.7 9.0526e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.24202e-06 8304 2 103.7 9.52804e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.22756e-06 8304 2 103.7 8.72683e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.26354e-06 8304 2 103.7 9.14669e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.16269e-06 8304 2 103.7 0.000101521 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.0869e-06 8304 2 103.7 8.95955e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.32197e-06 8304 2 103.7 0.000103858 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.49474e-06 8304 2 103.7 0.000101886 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.34793e-06 8304 2 103.7 9.4802e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.12642e-06 8304 2 103.7 9.17607e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.14137e-06 8304 2 103.7 9.00164e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.29156e-06 8304 2 103.7 9.88671e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.45838e-06 8304 2 103.7 0.000103344 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.25509e-06 8304 2 103.7 0.000106273 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.64074e-06 8304 2 103.7 0.000121873 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.15498e-06 8304 2 103.7 9.536e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.26589e-06 8304 2 103.7 0.000115652 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.30827e-06 8304 2 103.7 0.000108312 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.12599e-06 8304 2 103.7 8.83652e-05 2768 3000000 3000000 -362.98541 140505.98 1.42352 299.87853 36.004119 63.381029 0 0 34319.656 -50723.562 -315.99625 -291929.61 -308234.13 6818.5239 Loop time of 29499 on 32 procs for 3000000 steps with 10721 atoms Performance: 8.787 ns/day, 2.731 hours/ns, 101.698 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3898.4 | 13203 | 18302 |4803.0 | 44.76 Bond | 2.8938 | 8.0312 | 17.206 | 138.9 | 0.03 Kspace | 6274.3 | 11385 | 20753 |5192.4 | 38.60 Neigh | 1347 | 1349.5 | 1353.7 | 4.9 | 4.57 Comm | 1119.7 | 1454.1 | 1589.7 | 402.1 | 4.93 Output | 0.012488 | 0.014828 | 0.017223 | 1.1 | 0.00 Modify | 1906.4 | 2023 | 2296.5 | 291.6 | 6.86 Other | | 75.64 | | | 0.26 Nlocal: 335.031 ave 412 max 160 min Histogram: 4 4 0 0 0 0 0 4 5 15 Nghost: 6414.47 ave 7682 max 4680 min Histogram: 8 0 0 0 8 0 0 1 3 12 Neighs: 156632 ave 223340 max 43515 min Histogram: 8 0 0 0 0 4 1 3 5 11 Total # of neighbors = 5012240 Ave neighs/atom = 467.51609 Ave special neighs/atom = 1.6069397 Neighbor list builds = 148754 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 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 1.12599e-06 8304 2 103.7 8.83652e-05 2768 Per MPI rank memory allocation (min/avg/max) = 13.97 | 16.87 | 18.22 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 -362.39099 140505.98 1.42352 299.87853 36.004119 63.381029 0 0 34319.656 -50723.562 -315.99625 -291929.61 -308234.13 6818.5239 Loop time of 6.82884e-06 on 32 procs for 0 steps with 10721 atoms 123.6% 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 | | 6.829e-06 | | |100.00 Nlocal: 335.031 ave 412 max 160 min Histogram: 4 4 0 0 0 0 0 4 5 15 Nghost: 6414.47 ave 7682 max 4680 min Histogram: 8 0 0 0 8 0 0 1 3 12 Neighs: 156632 ave 223340 max 43515 min Histogram: 8 0 0 0 0 4 1 3 5 11 Total # of neighbors = 5012240 Ave neighs/atom = 467.51609 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci 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 4 unfix shaken Total wall time: 10:54:51