#------------------------------------------------------------------------------- # 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 3968 = # 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 restart 10000 2.5.restart dump sci all custom 1000 2.5.xyz id mol type q xs ys zs group rdfgroup_1 union subset_Li_1 subset_Cl_1 403 atoms in group rdfgroup_1 compute rdf_1 rdfgroup_1 rdf 200 4 1 fix rdf_1 rdfgroup_1 ave/time 1 100 100 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector group rdfgroup_3 union subset_Li_1 subset_O(SO4)_1 134 atoms in group rdfgroup_3 compute rdf_3 rdfgroup_3 rdf 200 4 8 fix rdf_3 rdfgroup_3 ave/time 1 100 100 c_rdf_3[*] file 2.5_PairCorrelation_all_3.out mode vector group rdfgroup_4 union subset_Li_1 subset_O(H2O)_1 2778 atoms in group rdfgroup_4 compute rdf_4 rdfgroup_4 rdf 200 4 7 fix rdf_4 rdfgroup_4 ave/time 1 100 100 c_rdf_4[*] file 2.5_PairCorrelation_all_4.out mode vector group rdfgroup_6 union subset_Na_1 subset_Cl_1 395 atoms in group rdfgroup_6 compute rdf_6 rdfgroup_6 rdf 200 6 1 fix rdf_6 rdfgroup_6 ave/time 1 100 100 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector group rdfgroup_9 union subset_Na_1 subset_O(SO4)_1 126 atoms in group rdfgroup_9 compute rdf_9 rdfgroup_9 rdf 200 6 8 fix rdf_9 rdfgroup_9 ave/time 1 100 100 c_rdf_9[*] file 2.5_PairCorrelation_all_9.out mode vector group rdfgroup_10 union subset_Na_1 subset_O(H2O)_1 2770 atoms in group rdfgroup_10 compute rdf_10 rdfgroup_10 rdf 200 6 7 fix rdf_10 rdfgroup_10 ave/time 1 100 100 c_rdf_10[*] file 2.5_PairCorrelation_all_10.out mode vector group rdfgroup_12 union subset_K_1 subset_Cl_1 424 atoms in group rdfgroup_12 compute rdf_12 rdfgroup_12 rdf 200 3 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_14 union subset_K_1 subset_O(SO4)_1 155 atoms in group rdfgroup_14 compute rdf_14 rdfgroup_14 rdf 200 3 8 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_K_1 subset_O(H2O)_1 2799 atoms in group rdfgroup_15 compute rdf_15 rdfgroup_15 rdf 200 3 7 fix rdf_15 rdfgroup_15 ave/time 1 100 100 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector group rdfgroup_19 union subset_Mg_1 subset_Cl_1 599 atoms in group rdfgroup_19 compute rdf_19 rdfgroup_19 rdf 100 5 1 fix rdf_19 rdfgroup_19 ave/time 1 1000 1000 c_rdf_19[*] file 2.5_PairCorrelation_all_19.out mode vector group rdfgroup_20 union subset_Mg_1 subset_O(SO4)_1 330 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 100 5 8 fix rdf_20 rdfgroup_20 ave/time 1 1000 1000 c_rdf_20[*] file 2.5_PairCorrelation_all_20.out mode vector group rdfgroup_21 union subset_Mg_1 subset_O(H2O)_1 2974 atoms in group rdfgroup_21 compute rdf_21 rdfgroup_21 rdf 100 5 7 fix rdf_21 rdfgroup_21 ave/time 1 1000 1000 c_rdf_21[*] file 2.5_PairCorrelation_all_21.out mode vector group rdfgroup_23 union subset_Cl_1 subset_H(H2O)_1 5929 atoms in group rdfgroup_23 compute rdf_23 rdfgroup_23 rdf 100 1 2 fix rdf_23 rdfgroup_23 ave/time 1 1000 1000 c_rdf_23[*] file 2.5_PairCorrelation_all_23.out mode vector group rdfgroup_24 union subset_Cl_1 subset_O(H2O)_1 3161 atoms in group rdfgroup_24 compute rdf_24 rdfgroup_24 rdf 100 1 7 fix rdf_24 rdfgroup_24 ave/time 1 1000 1000 c_rdf_24[*] file 2.5_PairCorrelation_all_24.out mode vector group rdfgroup_25 union subset_Cl_1 subset_O(SO4)_1 517 atoms in group rdfgroup_25 compute rdf_25 rdfgroup_25 rdf 100 1 8 fix rdf_25 rdfgroup_25 ave/time 1 1000 1000 c_rdf_25[*] file 2.5_PairCorrelation_all_25.out mode vector group rdfgroup_26 union subset_S(SO4)_1 subset_H(H2O)_1 5567 atoms in group rdfgroup_26 compute rdf_26 rdfgroup_26 rdf 100 9 2 fix rdf_26 rdfgroup_26 ave/time 1 1000 1000 c_rdf_26[*] file 2.5_PairCorrelation_all_26.out mode vector group rdfgroup_27 union subset_S(SO4)_1 subset_O(H2O)_1 2799 atoms in group rdfgroup_27 compute rdf_27 rdfgroup_27 rdf 100 9 7 fix rdf_27 rdfgroup_27 ave/time 1 1000 1000 c_rdf_27[*] file 2.5_PairCorrelation_all_27.out mode vector group rdfgroup_28 union subset_O(SO4)_1 subset_H(H2O)_1 5660 atoms in group rdfgroup_28 compute rdf_28 rdfgroup_28 rdf 100 8 2 fix rdf_28 rdfgroup_28 ave/time 1 1000 1000 c_rdf_28[*] file 2.5_PairCorrelation_all_28.out mode vector compute group_29 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_29 all ave/time 1 100 100 c_group_29 file 2.5_GroupInteractions_Layer1_Layer2_29.out compute group_30 subset_Layer1 group/group subset_Layer2 pair yes kspace no fix group_30 all ave/time 1 100 100 c_group_30 file 2.5_GroupInteractions_Layer1_Layer2_30.out compute group_31 subset_Layer1 group/group subset_Layer2 pair no kspace yes fix group_31 all ave/time 1 100 100 c_group_31 file 2.5_GroupInteractions_Layer1_Layer2_31.out timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25990968 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028399001 estimated relative force accuracy = 8.5522747e-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 WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) 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 21 neighbor lists, perpetual/occasional/extra = 1 20 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 (20) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (21) compute group/group, 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 1.30657e-10 11904 2 103.7 1.44438e-08 3968 Per MPI rank memory allocation (min/avg/max) = 13.19 | 13.71 | 14.16 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 -973.59726 141607.97 1.3931277 295.54502 309.40186 498.91745 0 0 36939.286 24181.922 -389.38508 -379450.1 -317520.57 8749.73 10000 10000 -573.54435 141607.97 1.3931277 300.2898 345.57328 493.97192 0 0 37282.139 23805.163 -389.38508 -379471.38 -317544.54 8890.2013 Loop time of 298.345 on 32 procs for 10000 steps with 13901 atoms Performance: 2.896 ns/day, 8.287 hours/ns, 33.518 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 | 58.377 | 70.789 | 89.827 | 129.1 | 23.73 Bond | 0.020459 | 0.098902 | 0.21661 | 21.4 | 0.03 Kspace | 20.956 | 40.222 | 52.928 | 174.0 | 13.48 Neigh | 6.7571 | 6.7679 | 6.7808 | 0.2 | 2.27 Comm | 6.1621 | 6.6612 | 7.0776 | 10.8 | 2.23 Output | 0.014124 | 0.017065 | 0.019951 | 1.3 | 0.01 Modify | 172.89 | 173.18 | 173.39 | 1.3 | 58.05 Other | | 0.613 | | | 0.21 Nlocal: 434.406 ave 511 max 388 min Histogram: 7 6 7 2 2 0 0 0 0 8 Nghost: 8283.31 ave 8711 max 7643 min Histogram: 8 0 0 0 0 2 6 6 2 8 Neighs: 246948 ave 328886 max 201934 min Histogram: 7 9 7 1 0 0 0 0 0 8 Total # of neighbors = 7902341 Ave neighs/atom = 568.47284 Ave special neighs/atom = 2.0450327 Neighbor list builds = 522 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) = 0.25990968 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028399001 estimated relative force accuracy = 8.5522747e-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 WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) SHAKE stats (type/ave/delta/count) on step 10000 1 0.97 1.4354e-06 11904 2 103.7 0.00010107 3968 Per MPI rank memory allocation (min/avg/max) = 36.45 | 38.52 | 44.68 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 -572.50123 141607.97 1.3931277 300.2898 345.57328 493.97192 0 0 37282.139 23805.163 -389.38508 -379471.38 -317544.54 8890.2013 Loop time of 1.0943e-05 on 32 procs for 0 steps with 13901 atoms 107.1% 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 | | 1.094e-05 | | |100.00 Nlocal: 434.406 ave 511 max 388 min Histogram: 7 6 7 2 2 0 0 0 0 8 Nghost: 8283.31 ave 8711 max 7643 min Histogram: 8 0 0 0 0 2 6 6 2 8 Neighs: 246948 ave 328886 max 201934 min Histogram: 7 9 7 1 0 0 0 0 0 8 Total # of neighbors = 7902341 Ave neighs/atom = 568.47284 Ave special neighs/atom = 2.0450327 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_1 unfix rdf_1 group rdfgroup_1 delete uncompute rdf_3 unfix rdf_3 group rdfgroup_3 delete uncompute rdf_4 unfix rdf_4 group rdfgroup_4 delete uncompute rdf_6 unfix rdf_6 group rdfgroup_6 delete uncompute rdf_9 unfix rdf_9 group rdfgroup_9 delete uncompute rdf_10 unfix rdf_10 group rdfgroup_10 delete uncompute rdf_12 unfix rdf_12 group rdfgroup_12 delete uncompute rdf_14 unfix rdf_14 group rdfgroup_14 delete uncompute rdf_15 unfix rdf_15 group rdfgroup_15 delete 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 group_29 unfix group_29 uncompute group_30 unfix group_30 uncompute group_31 unfix group_31 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 0:07:24