#------------------------------------------------------------------------------- # 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) = 0.25757539 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0028859317 estimated relative force accuracy = 8.6908976e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9196 3600 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 5.97041e-10 8304 2 103.7 6.78773e-08 2768 Per MPI rank memory allocation (min/avg/max) = 15.03 | 15.5 | 15.69 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 -615.84117 98081.663 1.2377954 300.68015 37.707015 70.103397 0 0 21028.11 33768.279 -213.63101 -216143.27 -161239.07 5675.1842 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.78273e-06 8304 2 103.7 0.00011622 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.10485e-06 8304 2 103.7 9.40848e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.22082e-06 8304 2 103.7 9.58837e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.18723e-06 8304 2 103.7 9.74697e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.59491e-06 8304 2 103.7 9.74202e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.46072e-06 8304 2 103.7 0.000105226 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.72946e-06 8304 2 103.7 0.000106261 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.44914e-06 8304 2 103.7 0.0001132 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.37688e-06 8304 2 103.7 0.000115863 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.27608e-06 8304 2 103.7 9.5428e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.44715e-06 8304 2 103.7 9.90395e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.35348e-06 8304 2 103.7 0.000105183 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.55138e-06 8304 2 103.7 0.000146041 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.17668e-06 8304 2 103.7 0.000111021 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.13837e-06 8304 2 103.7 0.000102756 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.90765e-06 8304 2 103.7 0.000128023 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.55043e-06 8304 2 103.7 0.000109167 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.084e-06 8304 2 103.7 9.29019e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.98587e-06 8304 2 103.7 0.000119553 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.46387e-06 8304 2 103.7 9.99574e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.2534e-06 8304 2 103.7 9.47863e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.38573e-06 8304 2 103.7 0.000100672 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.18118e-06 8304 2 103.7 9.2045e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.53439e-06 8304 2 103.7 0.000102794 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.45449e-06 8304 2 103.7 9.46017e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.57444e-06 8304 2 103.7 0.000132019 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.29437e-06 8304 2 103.7 9.44064e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.18165e-06 8304 2 103.7 0.0001002 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.20311e-06 8304 2 103.7 0.000102047 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.56653e-06 8304 2 103.7 0.000109183 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.27336e-06 8304 2 103.7 9.02306e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.51386e-06 8304 2 103.7 0.000112568 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.28601e-06 8304 2 103.7 9.1528e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.48705e-06 8304 2 103.7 9.82173e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.23224e-06 8304 2 103.7 9.29588e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.17159e-06 8304 2 103.7 9.02634e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.29837e-06 8304 2 103.7 0.00010131 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.28321e-06 8304 2 103.7 9.7148e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.31059e-06 8304 2 103.7 9.99578e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.19331e-06 8304 2 103.7 9.03624e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.49886e-06 8304 2 103.7 0.000102889 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.29081e-06 8304 2 103.7 9.90041e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.15446e-06 8304 2 103.7 0.000118178 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.30901e-06 8304 2 103.7 0.0001063 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.0374e-06 8304 2 103.7 9.58129e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.48028e-06 8304 2 103.7 0.000104965 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.13231e-06 8304 2 103.7 9.42812e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.32777e-06 8304 2 103.7 0.000120131 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.37385e-06 8304 2 103.7 0.0001042 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.43812e-06 8304 2 103.7 9.48888e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.20756e-06 8304 2 103.7 8.91278e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.44145e-06 8304 2 103.7 9.96368e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.51126e-06 8304 2 103.7 9.99907e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.19776e-06 8304 2 103.7 9.4109e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.22221e-06 8304 2 103.7 9.94906e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.29254e-06 8304 2 103.7 9.19593e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.3369e-06 8304 2 103.7 0.000100345 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.2471e-06 8304 2 103.7 0.000101232 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.22631e-06 8304 2 103.7 9.83314e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.59501e-06 8304 2 103.7 0.000104975 2768 3000000 3000000 -317.70163 98081.663 1.2377954 299.51169 38.803553 65.268087 0 0 21133.997 33651.505 -213.63101 -216175.07 -161285.5 5653.1302 Loop time of 79253.1 on 16 procs for 3000000 steps with 9101 atoms Performance: 3.271 ns/day, 7.338 hours/ns, 37.853 timesteps/s 99.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25414 | 27004 | 31212 | 872.5 | 34.07 Bond | 6.6467 | 15.461 | 21.42 | 92.3 | 0.02 Kspace | 6732.4 | 10963 | 12564 |1376.3 | 13.83 Neigh | 2198.5 | 2201.4 | 2203.2 | 3.4 | 2.78 Comm | 1077.8 | 1109.3 | 1135.7 | 48.9 | 1.40 Output | 0.1455 | 0.16561 | 0.18426 | 3.0 | 0.00 Modify | 37773 | 37799 | 37822 | 7.3 | 47.69 Other | | 161.1 | | | 0.20 Nlocal: 568.812 ave 584 max 551 min Histogram: 3 0 2 0 1 2 2 2 2 2 Nghost: 8637.06 ave 8727 max 8520 min Histogram: 1 1 1 1 2 4 2 0 2 2 Neighs: 303122 ave 313969 max 288864 min Histogram: 1 1 0 1 3 4 0 2 3 1 Total # of neighbors = 4849958 Ave neighs/atom = 532.90386 Ave special neighs/atom = 1.8929788 Neighbor list builds = 148551 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) = 0.25757539 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0028859317 estimated relative force accuracy = 8.6908976e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9196 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.59501e-06 8304 2 103.7 0.000104975 2768 Per MPI rank memory allocation (min/avg/max) = 41.6 | 41.77 | 41.87 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 -316.92137 98081.663 1.2377954 299.51169 38.803553 65.268087 0 0 21133.997 33651.505 -213.63101 -216175.07 -161285.5 5653.1302 Loop time of 5.09831e-06 on 16 procs for 0 steps with 9101 atoms 114.0% 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 | | 5.098e-06 | | |100.00 Nlocal: 568.812 ave 584 max 551 min Histogram: 3 0 2 0 1 2 2 2 2 2 Nghost: 8637.06 ave 8727 max 8520 min Histogram: 1 1 1 1 2 4 2 0 2 2 Neighs: 303122 ave 313969 max 288864 min Histogram: 1 1 0 1 3 4 0 2 3 1 Total # of neighbors = 4849958 Ave neighs/atom = 532.90386 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: 29:28:56