#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3728 = # 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 sci all custom 1000 2.5.xyz id mol type q xs ys zs group rdfgroup_23 union subset_Mg_1 subset_Cl_1 599 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 200 5 1 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_Mg_1 subset_O(H2O)_1 2974 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 5 7 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_Cl_1 subset_H(H2O)_1 5929 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 200 1 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_O(SO4)_1 subset_H(H2O)_1 5660 atoms in group rdfgroup_29 compute rdf_29 rdfgroup_29 rdf 200 8 2 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-K subset_jiemian-Cl 17 atoms in group rdfgroup_30 compute rdf_30 rdfgroup_30 rdf 200 3 1 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-O 142 atoms in group rdfgroup_31 compute rdf_31 rdfgroup_31 rdf 200 3 7 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-mg subset_jiemian-Cl 17 atoms in group rdfgroup_32 compute rdf_32 rdfgroup_32 rdf 200 5 1 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-O 142 atoms in group rdfgroup_33 compute rdf_33 rdfgroup_33 rdf 200 5 7 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-Cl subset_jiemian-H 283 atoms in group rdfgroup_34 compute rdf_34 rdfgroup_34 rdf 200 1 2 fix rdf_34 rdfgroup_34 ave/time 1 100 100 c_rdf_34[*] file 2.5_PairCorrelation_all_34.out mode vector timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 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 = 5 7 13 13 neighbor lists, perpetual/occasional/extra = 1 12 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 SHAKE stats (type/ave/delta/count) on step 0 1 0.97 7.92921e-13 11184 2 103.7 7.5886e-11 3728 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.11 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 334798.69 143799.62 1.371895 295.63016 307.6218 383.01447 0 0 270925.67 -51492.735 -383.45046 -378976.63 -158853.06 8117.7741 10000 10000 335941.39 143799.62 1.371895 297.19356 281.6988 402.49295 0 0 271557.66 -52355.183 -383.45046 -378971.94 -159085.27 8160.7039 Loop time of 178.822 on 32 procs for 10000 steps with 13901 atoms Performance: 4.832 ns/day, 4.967 hours/ns, 55.921 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 55.351 | 67.301 | 93.029 | 162.2 | 37.64 Bond | 0.016962 | 0.084346 | 0.19102 | 19.4 | 0.05 Kspace | 20.191 | 46.047 | 57.845 | 197.6 | 25.75 Neigh | 4.5938 | 4.6143 | 4.6356 | 0.6 | 2.58 Comm | 6.0409 | 6.4585 | 6.9355 | 11.1 | 3.61 Output | 0.016191 | 0.018992 | 0.021816 | 1.2 | 0.01 Modify | 53.598 | 53.892 | 54.078 | 2.3 | 30.14 Other | | 0.4066 | | | 0.23 Nlocal: 434.406 ave 522 max 392 min Histogram: 12 8 3 1 0 0 0 0 0 8 Nghost: 8193.88 ave 8637 max 7480 min Histogram: 7 1 0 0 0 0 3 13 0 8 Neighs: 243744 ave 345184 max 195903 min Histogram: 10 11 2 1 0 0 0 0 3 5 Total # of neighbors = 7799815 Ave neighs/atom = 561.0974 Ave special neighs/atom = 1.8838932 Neighbor list builds = 495 Dangerous builds = 0 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 1 0.97 1.53716e-06 11184 2 103.7 9.91589e-05 3728 Per MPI rank memory allocation (min/avg/max) = 27.2 | 28.53 | 32.42 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 335942.34 143799.62 1.371895 297.19356 281.6988 402.49295 0 0 271557.66 -52355.183 -383.45046 -378971.94 -159085.27 8160.7039 Loop time of 8.63384e-06 on 32 procs for 0 steps with 13901 atoms 111.1% 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 | | 8.634e-06 | | |100.00 Nlocal: 434.406 ave 522 max 392 min Histogram: 12 8 3 1 0 0 0 0 0 8 Nghost: 8193.88 ave 8637 max 7480 min Histogram: 7 1 0 0 0 0 3 13 0 8 Neighs: 243744 ave 345184 max 195903 min Histogram: 10 11 2 1 0 0 0 0 3 5 Total # of neighbors = 7799815 Ave neighs/atom = 561.0974 Ave special neighs/atom = 1.8838932 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 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 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out