#------------------------------------------------------------------------------- # 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 2812 = # 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_19 union subset_Mg_1 subset_Cl_1 494 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)_1 275 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 200 5 8 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 2963 atoms in group rdfgroup_21 compute rdf_21 rdfgroup_21 rdf 200 5 7 fix rdf_21 rdfgroup_21 ave/time 1 100 100 c_rdf_21[*] file 2.5_PairCorrelation_all_21.out mode vector group rdfgroup_23 union subset_Cl_1 subset_H(H2O)_1 5967 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_Cl_1 subset_O(H2O)_1 3155 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 200 1 7 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_O(SO4)_1 467 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 200 1 8 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_S(SO4)_1 subset_H(H2O)_1 5655 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 200 9 2 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_S(SO4)_1 subset_O(H2O)_1 2843 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 200 9 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_O(SO4)_1 subset_H(H2O)_1 5748 atoms in group rdfgroup_28 compute rdf_28 rdfgroup_28 rdf 200 8 2 fix rdf_28 rdfgroup_28 ave/time 1 100 100 c_rdf_28[*] file 2.5_PairCorrelation_all_28.out mode vector group rdfgroup_22 union subset_jiemian-Na subset_jiemian-o 100 atoms in group rdfgroup_22 compute rdf_22 rdfgroup_22 rdf 200 6 7 fix rdf_22 rdfgroup_22 ave/time 1 100 100 c_rdf_22[*] file 2.5_PairCorrelation_all_22.out mode vector group rdfgroup_12 union subset_jiemian-Na subset_jiemian-Cl 8 atoms in group rdfgroup_12 compute rdf_12 rdfgroup_12 rdf 200 6 1 fix rdf_12 rdfgroup_12 ave/time 1 100 100 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector group rdfgroup_13 union subset_jiemian-K subset_jiemian-o 99 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 200 3 7 fix rdf_13 rdfgroup_13 ave/time 1 100 100 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector group rdfgroup_14 union subset_jiemian-Cl subset_jiemian-o 102 atoms in group rdfgroup_14 compute rdf_14 rdfgroup_14 rdf 200 1 7 fix rdf_14 rdfgroup_14 ave/time 1 100 100 c_rdf_14[*] file 2.5_PairCorrelation_all_14.out mode vector group rdfgroup_15 union subset_jiemian-K subset_jiemian-Cl 7 atoms in group rdfgroup_15 compute rdf_15 rdfgroup_15 rdf 200 3 1 fix rdf_15 rdfgroup_15 ave/time 1 100 100 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-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 15 neighbor lists, perpetual/occasional/extra = 1 14 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 SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.48037e-13 8436 2 103.7 7.71223e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.73 | 14.45 | 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 -79.123805 141184.09 1.4079299 294.32343 41.895329 79.032406 0 0 32157.224 -35746.762 -312.04795 -284049.43 -287518.04 6729.939 10000 10000 -131.42785 141184.09 1.4079299 298.63458 48.196594 76.721877 0 0 32049.708 -35714.676 -312.04795 -284059.96 -287600 6828.5166 Loop time of 155.97 on 32 procs for 10000 steps with 10808 atoms Performance: 5.540 ns/day, 4.332 hours/ns, 64.115 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.29 | 45.676 | 65.858 | 283.6 | 29.29 Bond | 0.012304 | 0.031518 | 0.071148 | 9.9 | 0.02 Kspace | 17.054 | 37.337 | 69.978 | 315.3 | 23.94 Neigh | 4.3968 | 4.4156 | 4.4379 | 0.6 | 2.83 Comm | 4.1302 | 5.369 | 5.8631 | 24.2 | 3.44 Output | 0.11339 | 0.13811 | 0.16334 | 3.9 | 0.09 Modify | 62.25 | 62.666 | 63.606 | 5.6 | 40.18 Other | | 0.3365 | | | 0.22 Nlocal: 337.75 ave 429 max 160 min Histogram: 4 4 0 0 0 0 0 7 9 8 Nghost: 6424.38 ave 7710 max 4734 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 158559 ave 231599 max 43058 min Histogram: 8 0 0 0 0 4 1 3 12 4 Total # of neighbors = 5073881 Ave neighs/atom = 469.45605 Ave special neighs/atom = 1.6184308 Neighbor list builds = 493 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-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 1.24334e-06 8436 2 103.7 9.12659e-05 2812 Per MPI rank memory allocation (min/avg/max) = 17.8 | 25.19 | 29.67 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 -130.88791 141184.09 1.4079299 298.63458 48.196594 76.721877 0 0 32049.708 -35714.676 -312.04795 -284059.96 -287600 6828.5166 Loop time of 1.24015e-05 on 32 procs for 0 steps with 10808 atoms 105.6% 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 | | 1.24e-05 | | |100.00 Nlocal: 337.75 ave 429 max 160 min Histogram: 4 4 0 0 0 0 0 7 9 8 Nghost: 6424.38 ave 7710 max 4734 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 158559 ave 231599 max 43058 min Histogram: 8 0 0 0 0 4 1 3 12 4 Total # of neighbors = 5073881 Ave neighs/atom = 469.45605 Ave special neighs/atom = 1.6184308 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_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_22 unfix rdf_22 group rdfgroup_22 delete uncompute rdf_12 unfix rdf_12 group rdfgroup_12 delete uncompute rdf_13 unfix rdf_13 group rdfgroup_13 delete uncompute rdf_14 unfix rdf_14 group rdfgroup_14 delete uncompute rdf_15 unfix rdf_15 group rdfgroup_15 delete unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 0:05:01