#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3275 = # 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_19 union subset_Mg_1 subset_Cl_1 686 atoms in group rdfgroup_19 compute rdf_19 rdfgroup_19 rdf 200 5 1 fix rdf_19 rdfgroup_19 ave/time 1 100 100 c_rdf_19[*] file 2.5_PairCorrelation_all_19.out mode vector group rdfgroup_20 union subset_Mg_1 subset_O(SO4)_1 348 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 200 5 7 fix rdf_20 rdfgroup_20 ave/time 1 100 100 c_rdf_20[*] file 2.5_PairCorrelation_all_20.out mode vector group rdfgroup_21 union subset_Mg_1 subset_O(H2O)_1 2939 atoms in group rdfgroup_21 compute rdf_21 rdfgroup_21 rdf 200 5 6 fix rdf_21 rdfgroup_21 ave/time 1 100 100 c_rdf_21[*] file 2.5_PairCorrelation_all_21.out mode vector group rdfgroup_22 union subset_Cl_1 subset_O(H2O)_1 3145 atoms in group rdfgroup_22 compute rdf_22 rdfgroup_22 rdf 200 1 6 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_Cl_1 subset_H(H2O)_1 5844 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 200 1 2 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_S(SO4)_1 subset_O(H2O)_1 2726 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 200 8 6 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_O(SO4)_1 subset_H(H2O)_1 5506 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 7 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_jiemian-Mg subset_jiemian-Cl 35 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 200 5 1 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_jiemian-Mg subset_jiemian-OS 18 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 200 5 7 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_jiemian-Mg subset_jiemian-OH 120 atoms in group rdfgroup_28 compute rdf_28 rdfgroup_28 rdf 200 5 6 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-Cl subset_jiemian-H 241 atoms in group rdfgroup_29 compute rdf_29 rdfgroup_29 rdf 200 1 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_32 union subset_jiemian-OS subset_jiemian-H 224 atoms in group rdfgroup_32 compute rdf_32 rdfgroup_32 rdf 200 7 2 fix rdf_32 rdfgroup_32 ave/time 1 100 100 c_rdf_32[*] file 2.5_PairCorrelation_all_32.out mode vector timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 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 15 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 6.91891e-13 9825 1 103.7 7.61986e-11 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.31 | 13.65 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 -7264.2677 143340.91 1.3114365 297.04057 44.393748 69.392569 0 0 36933.282 -72546.665 -319.55737 -317415.75 -352915.35 7010.7677 10000 10000 -7094.9282 143340.91 1.3114365 291.14626 31.39117 70.411861 0 0 37242.336 -73151.783 -319.55737 -317422.88 -353230.52 6871.6497 Loop time of 145.489 on 32 procs for 10000 steps with 12250 atoms Performance: 5.939 ns/day, 4.041 hours/ns, 68.734 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42.491 | 52.902 | 61.575 | 72.7 | 36.36 Bond | 0.013857 | 0.033259 | 0.059091 | 8.0 | 0.02 Kspace | 20.138 | 28.786 | 39.207 | 99.0 | 19.79 Neigh | 3.2182 | 3.224 | 3.2295 | 0.2 | 2.22 Comm | 5.7717 | 6.1274 | 6.3628 | 8.2 | 4.21 Output | 0.013297 | 0.015812 | 0.018356 | 1.2 | 0.01 Modify | 53.835 | 54.045 | 54.297 | 2.2 | 37.15 Other | | 0.3556 | | | 0.24 Nlocal: 382.812 ave 415 max 344 min Histogram: 3 1 4 5 0 5 2 2 6 4 Nghost: 7286.94 ave 7682 max 6833 min Histogram: 4 0 8 0 4 2 2 0 6 6 Neighs: 188235 ave 214966 max 151427 min Histogram: 3 2 3 1 1 5 1 6 7 3 Total # of neighbors = 6023507 Ave neighs/atom = 491.71486 Ave special neighs/atom = 1.6481633 Neighbor list builds = 500 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 1 0.97 1.19927e-06 9825 1 103.7 0.000109765 3275 Per MPI rank memory allocation (min/avg/max) = 22.13 | 25.36 | 27.38 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 -7094.0429 143340.91 1.3114365 291.14626 31.39117 70.411861 0 0 37242.336 -73151.783 -319.55737 -317422.88 -353230.52 6871.6497 Loop time of 1.31857e-05 on 32 procs for 0 steps with 12250 atoms 102.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.319e-05 | | |100.00 Nlocal: 382.812 ave 415 max 344 min Histogram: 3 1 4 5 0 5 2 2 6 4 Nghost: 7286.94 ave 7682 max 6833 min Histogram: 4 0 8 0 4 2 2 0 6 6 Neighs: 188235 ave 214966 max 151427 min Histogram: 3 2 3 1 1 5 1 6 7 3 Total # of neighbors = 6023507 Ave neighs/atom = 491.71486 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_19 unfix rdf_19 group rdfgroup_19 delete uncompute rdf_20 unfix rdf_20 group rdfgroup_20 delete uncompute rdf_21 unfix rdf_21 group rdfgroup_21 delete 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_32 unfix rdf_32 group rdfgroup_32 delete unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 0:04:39