#------------------------------------------------------------------------------- # 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 2699 = # 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 460 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) 122 atoms in group rdfgroup_2 compute rdf_2 rdfgroup_2 rdf 100 4 7 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) 2713 atoms in group rdfgroup_5 compute rdf_5 rdfgroup_5 rdf 100 4 6 fix rdf_5 rdfgroup_5 ave/time 1 300000 300000 c_rdf_5[*] file 2.5_PairCorrelation_all_5.out mode vector group rdfgroup_11 union subset_K subset_Cl 452 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) 114 atoms in group rdfgroup_12 compute rdf_12 rdfgroup_12 rdf 100 3 7 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) 2705 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 100 3 6 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 686 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) 348 atoms in group rdfgroup_16 compute rdf_16 rdfgroup_16 rdf 100 5 7 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) 2939 atoms in group rdfgroup_18 compute rdf_18 rdfgroup_18 rdf 100 5 6 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) 3145 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 100 1 6 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) 5844 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) 5425 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 100 8 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) 2726 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 100 8 6 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) 5506 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 100 7 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) 2807 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 100 7 6 fix rdf_26 rdfgroup_26 ave/time 1 300000 300000 c_rdf_26[*] file 2.5_PairCorrelation_all_26.out mode vector group rdfgroup_27 union subset_Li subset_H(H2O) 5412 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 100 4 2 fix rdf_27 rdfgroup_27 ave/time 1 300000 300000 c_rdf_27[*] file 2.5_PairCorrelation_all_27.out mode vector group rdfgroup_28 union subset_K subset_H(H2O) 5404 atoms in group rdfgroup_28 compute rdf_28 rdfgroup_28 rdf 100 3 2 fix rdf_28 rdfgroup_28 ave/time 1 300000 300000 c_rdf_28[*] file 2.5_PairCorrelation_all_28.out mode vector group rdfgroup_29 union subset_Mg subset_H(H2O) 5638 atoms in group rdfgroup_29 compute rdf_29 rdfgroup_29 rdf 100 5 2 fix rdf_29 rdfgroup_29 ave/time 1 300000 300000 c_rdf_29[*] file 2.5_PairCorrelation_all_29.out mode vector timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25725581 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030423457 estimated relative force accuracy = 9.1619338e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 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 10 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 3.03395e-09 8097 2 103.7 3.37987e-07 2699 Per MPI rank memory allocation (min/avg/max) = 15 | 15.38 | 15.64 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 -139.98457 97112.971 1.2515496 295.96398 43.466844 82.376858 0 0 22827.512 20321.458 -213.18523 -219072.63 -175797.81 5503.2409 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.53919e-06 8097 2 103.7 0.000114352 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.29639e-06 8097 2 103.7 0.000105723 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.63094e-06 8097 2 103.7 0.000118232 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.28531e-06 8097 2 103.7 9.03491e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 9.97105e-07 8097 2 103.7 9.90048e-05 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.13316e-06 8097 2 103.7 9.08722e-05 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.55553e-06 8097 2 103.7 0.000102397 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.4334e-06 8097 2 103.7 0.000113423 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.25805e-06 8097 2 103.7 0.000111179 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.41583e-06 8097 2 103.7 9.85522e-05 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.64024e-06 8097 2 103.7 0.000111029 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.15428e-06 8097 2 103.7 9.389e-05 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.05378e-06 8097 2 103.7 0.000116888 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.19614e-06 8097 2 103.7 0.000105967 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.33367e-06 8097 2 103.7 9.31712e-05 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.12228e-06 8097 2 103.7 9.70591e-05 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.10949e-06 8097 2 103.7 0.00010576 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.40691e-06 8097 2 103.7 0.000106644 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.1798e-06 8097 2 103.7 0.000101026 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.5039e-06 8097 2 103.7 0.00011136 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.16178e-06 8097 2 103.7 9.09204e-05 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.03976e-06 8097 2 103.7 9.28308e-05 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.56795e-06 8097 2 103.7 0.000111633 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.12894e-06 8097 2 103.7 0.000119755 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.31291e-06 8097 2 103.7 0.000136161 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.0624e-06 8097 2 103.7 9.03977e-05 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.85458e-06 8097 2 103.7 0.000131376 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.31223e-06 8097 2 103.7 9.48603e-05 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.49461e-06 8097 2 103.7 0.000102638 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.1075e-06 8097 2 103.7 9.00255e-05 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.21378e-06 8097 2 103.7 0.000104609 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.16826e-06 8097 2 103.7 0.000111329 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.55511e-06 8097 2 103.7 0.000109108 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.16514e-06 8097 2 103.7 0.00010815 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.19864e-06 8097 2 103.7 0.000102426 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.41115e-06 8097 2 103.7 0.000116896 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.07151e-06 8097 2 103.7 8.88298e-05 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.04577e-06 8097 2 103.7 8.97628e-05 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.24971e-06 8097 2 103.7 8.8306e-05 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26244e-06 8097 2 103.7 8.72219e-05 2699 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.43312e-06 8097 2 103.7 0.000107645 2699 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.02647e-06 8097 2 103.7 9.67332e-05 2699 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 2.22048e-06 8097 2 103.7 0.000148117 2699 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.35475e-06 8097 2 103.7 0.000106831 2699 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.14202e-06 8097 2 103.7 0.000100186 2699 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.77913e-06 8097 2 103.7 0.000128045 2699 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.56595e-06 8097 2 103.7 0.00010222 2699 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.59651e-06 8097 2 103.7 0.000109472 2699 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.45296e-06 8097 2 103.7 0.000105914 2699 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.97123e-06 8097 2 103.7 0.000135539 2699 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.23273e-06 8097 2 103.7 0.000107481 2699 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.19646e-06 8097 2 103.7 9.62634e-05 2699 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.35288e-06 8097 2 103.7 0.000104138 2699 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.14135e-06 8097 2 103.7 8.93078e-05 2699 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.17919e-06 8097 2 103.7 0.000105467 2699 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.42596e-06 8097 2 103.7 0.000112982 2699 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.30799e-06 8097 2 103.7 9.8296e-05 2699 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.13128e-06 8097 2 103.7 0.000113048 2699 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.25353e-06 8097 2 103.7 0.000101093 2699 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.14165e-06 8097 2 103.7 9.67914e-05 2699 3000000 3000000 -224.50093 97112.971 1.2515496 292.16974 27.00398 65.97194 0 0 23034.543 19959.404 -213.18523 -219081.31 -175994.39 5432.6898 Loop time of 80743.5 on 16 procs for 3000000 steps with 8938 atoms Performance: 3.210 ns/day, 7.476 hours/ns, 37.155 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 | 23221 | 24523 | 25344 | 389.8 | 30.37 Bond | 7.7007 | 13.275 | 19.24 | 84.2 | 0.02 Kspace | 7155.8 | 7969.2 | 9260.6 | 679.3 | 9.87 Neigh | 1978.6 | 1979.5 | 1980.7 | 1.4 | 2.45 Comm | 875.81 | 891.18 | 908.01 | 33.2 | 1.10 Output | 0.12743 | 0.14644 | 0.16391 | 3.0 | 0.00 Modify | 45219 | 45223 | 45226 | 1.1 | 56.01 Other | | 144.1 | | | 0.18 Nlocal: 558.625 ave 587 max 533 min Histogram: 1 2 0 2 4 4 0 0 1 2 Nghost: 8641.38 ave 8742 max 8502 min Histogram: 1 0 1 2 0 3 4 2 2 1 Neighs: 295220 ave 312321 max 275643 min Histogram: 1 1 1 2 3 2 2 1 1 2 Total # of neighbors = 4723515 Ave neighs/atom = 528.47561 Ave special neighs/atom = 1.8722309 Neighbor list builds = 147871 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) = 0.25725581 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030423457 estimated relative force accuracy = 9.1619338e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.14165e-06 8097 2 103.7 9.67914e-05 2699 Per MPI rank memory allocation (min/avg/max) = 41.55 | 41.75 | 41.83 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 -223.53239 97112.971 1.2515496 292.16974 27.00398 65.97194 0 0 23034.543 19959.404 -213.18523 -219081.31 -175994.39 5432.6898 Loop time of 3.62275e-06 on 16 procs for 0 steps with 8938 atoms 139.7% 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 | | 3.623e-06 | | |100.00 Nlocal: 558.625 ave 587 max 533 min Histogram: 1 2 0 2 4 4 0 0 1 2 Nghost: 8641.38 ave 8742 max 8502 min Histogram: 1 0 1 2 0 3 4 2 2 1 Neighs: 295220 ave 312321 max 275643 min Histogram: 1 1 1 2 3 2 2 1 1 2 Total # of neighbors = 4723515 Ave neighs/atom = 528.47561 Ave special neighs/atom = 1.8722309 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_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 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 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 28:43:21