#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 10 ps 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 1000 1000 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 1 1 1 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 10000 2.5.restart dump trj all custom 100 2.5.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 100 1 100 v_etotal v_pe v_ke file 2.5.energies.txt dump sci all custom 1000 2.5.xyz id mol type q xs ys zs group rdfgroup_22 union subset_Mg_1 subset_Cl_1 599 atoms in group rdfgroup_22 compute rdf_22 rdfgroup_22 rdf 200 5 1 fix rdf_22 rdfgroup_22 ave/time 1 100 100 c_rdf_22[*] file 2.5_PairCorrelation_all_22.out mode vector group rdfgroup_23 union subset_Mg_1 subset_O(H2O)_1 2974 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 200 5 7 fix rdf_23 rdfgroup_23 ave/time 1 100 100 c_rdf_23[*] file 2.5_PairCorrelation_all_23.out mode vector group rdfgroup_24 union subset_Mg_1 subset_O(SO4)_1 330 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 200 5 8 fix rdf_24 rdfgroup_24 ave/time 1 100 100 c_rdf_24[*] file 2.5_PairCorrelation_all_24.out mode vector group rdfgroup_25 union subset_Cl_1 subset_H(H2O)_1 5929 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 1 2 fix rdf_25 rdfgroup_25 ave/time 1 100 100 c_rdf_25[*] file 2.5_PairCorrelation_all_25.out mode vector group rdfgroup_26 union subset_Cl_1 subset_O(H2O)_1 3161 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 200 1 7 fix rdf_26 rdfgroup_26 ave/time 1 100 100 c_rdf_26[*] file 2.5_PairCorrelation_all_26.out mode vector group rdfgroup_27 union subset_O(SO4)_1 subset_H(H2O)_1 5660 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 200 8 2 fix rdf_27 rdfgroup_27 ave/time 1 100 100 c_rdf_27[*] file 2.5_PairCorrelation_all_27.out mode vector group rdfgroup_28 union subset_S(SO4)_1 subset_O(H2O)_1 2799 atoms in group rdfgroup_28 compute rdf_28 rdfgroup_28 rdf 200 9 7 fix rdf_28 rdfgroup_28 ave/time 1 100 100 c_rdf_28[*] file 2.5_PairCorrelation_all_28.out mode vector group rdfgroup_29 union subset_jiemian-Na subset_jiemian-Cl 10 atoms in group rdfgroup_29 compute rdf_29 rdfgroup_29 rdf 200 6 1 fix rdf_29 rdfgroup_29 ave/time 1 100 100 c_rdf_29[*] file 2.5_PairCorrelation_all_29.out mode vector group rdfgroup_30 union subset_jiemian-Na subset_jiemian-O 107 atoms in group rdfgroup_30 compute rdf_30 rdfgroup_30 rdf 200 6 7 fix rdf_30 rdfgroup_30 ave/time 1 100 100 c_rdf_30[*] file 2.5_PairCorrelation_all_30.out mode vector group rdfgroup_31 union subset_jiemian-K subset_jiemian-Cl 11 atoms in group rdfgroup_31 compute rdf_31 rdfgroup_31 rdf 200 3 1 fix rdf_31 rdfgroup_31 ave/time 1 100 100 c_rdf_31[*] file 2.5_PairCorrelation_all_31.out mode vector group rdfgroup_32 union subset_jiemian-K subset_jiemian-O 108 atoms in group rdfgroup_32 compute rdf_32 rdfgroup_32 rdf 200 3 7 fix rdf_32 rdfgroup_32 ave/time 1 100 100 c_rdf_32[*] file 2.5_PairCorrelation_all_32.out mode vector group rdfgroup_33 union subset_jiemian-mg subset_jiemian-Cl 12 atoms in group rdfgroup_33 compute rdf_33 rdfgroup_33 rdf 200 5 1 fix rdf_33 rdfgroup_33 ave/time 1 100 100 c_rdf_33[*] file 2.5_PairCorrelation_all_33.out mode vector group rdfgroup_34 union subset_jiemian-mg subset_jiemian-O 109 atoms in group rdfgroup_34 compute rdf_34 rdfgroup_34 rdf 200 5 7 fix rdf_34 rdfgroup_34 ave/time 1 100 100 c_rdf_34[*] file 2.5_PairCorrelation_all_34.out mode vector group rdfgroup_35 union subset_jiemian-Cl subset_jiemian-H 220 atoms in group rdfgroup_35 compute rdf_35 rdfgroup_35 rdf 200 1 2 fix rdf_35 rdfgroup_35 ave/time 1 100 100 c_rdf_35[*] file 2.5_PairCorrelation_all_35.out mode vector group rdfgroup_36 union subset_jiemian-Cl subset_jiemian-O 115 atoms in group rdfgroup_36 compute rdf_36 rdfgroup_36 rdf 200 1 7 fix rdf_36 rdfgroup_36 ave/time 1 100 100 c_rdf_36[*] file 2.5_PairCorrelation_all_36.out mode vector timestep 1 run 10000 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 16 neighbor lists, perpetual/occasional/extra = 1 15 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 (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 SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.74825e-13 8304 2 103.7 7.75486e-11 2768 Per MPI rank memory allocation (min/avg/max) = 13.72 | 14.42 | 14.92 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 -466.98413 140505.98 1.42352 303.8401 39.016667 64.876186 0 0 34214.997 -50323.836 -315.99625 -291890.34 -307895.29 6908.6005 10000 10000 -79.011641 140505.98 1.42352 293.73143 44.133757 71.211794 0 0 34431.916 -50503.685 -315.99625 -291911.13 -307867.56 6678.7533 Loop time of 150.615 on 32 procs for 10000 steps with 10721 atoms Performance: 5.736 ns/day, 4.184 hours/ns, 66.394 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.281 | 45.242 | 66.264 | 286.4 | 30.04 Bond | 0.012147 | 0.032826 | 0.0647 | 8.9 | 0.02 Kspace | 18.908 | 40.018 | 72.212 | 305.7 | 26.57 Neigh | 4.4161 | 4.4266 | 4.4428 | 0.3 | 2.94 Comm | 4.2706 | 5.4915 | 6.0691 | 25.0 | 3.65 Output | 0.12198 | 0.14709 | 0.17262 | 3.9 | 0.10 Modify | 54.428 | 54.911 | 55.877 | 6.5 | 36.46 Other | | 0.3468 | | | 0.23 Nlocal: 335.031 ave 423 max 160 min Histogram: 5 3 0 0 0 0 1 6 4 13 Nghost: 6446.09 ave 7724 max 4735 min Histogram: 8 0 0 0 8 0 0 0 8 8 Neighs: 157094 ave 228755 max 41434 min Histogram: 8 0 0 0 0 4 0 3 8 9 Total # of neighbors = 5027023 Ave neighs/atom = 468.89497 Ave special neighs/atom = 1.6069397 Neighbor list builds = 495 Dangerous builds = 0 undump trj unfix trjE undump sci restart 0 dump sci all custom 10000 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 10000 2 0.97 1.3502e-06 8304 2 103.7 9.63036e-05 2768 Per MPI rank memory allocation (min/avg/max) = 18.17 | 26.23 | 30.81 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 10000 10000 -78.460956 140505.98 1.42352 293.73143 44.133757 71.211794 0 0 34431.916 -50503.685 -315.99625 -291911.13 -307867.56 6678.7533 Loop time of 8.06131e-06 on 32 procs for 0 steps with 10721 atoms 117.8% 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 | | 8.061e-06 | | |100.00 Nlocal: 335.031 ave 423 max 160 min Histogram: 5 3 0 0 0 0 1 6 4 13 Nghost: 6446.09 ave 7724 max 4735 min Histogram: 8 0 0 0 8 0 0 0 8 8 Neighs: 157094 ave 228755 max 41434 min Histogram: 8 0 0 0 0 4 0 3 8 9 Total # of neighbors = 5027023 Ave neighs/atom = 468.89497 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_22 unfix rdf_22 group rdfgroup_22 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 uncompute rdf_30 unfix rdf_30 group rdfgroup_30 delete uncompute rdf_31 unfix rdf_31 group rdfgroup_31 delete uncompute rdf_32 unfix rdf_32 group rdfgroup_32 delete uncompute rdf_33 unfix rdf_33 group rdfgroup_33 delete uncompute rdf_34 unfix rdf_34 group rdfgroup_34 delete uncompute rdf_35 unfix rdf_35 group rdfgroup_35 delete uncompute rdf_36 unfix rdf_36 group rdfgroup_36 delete unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 0:04:47