#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 ns 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump trj all custom 30000 2.5.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 30000 1 30000 v_etotal v_pe v_ke file 2.5.energies.txt dump sci all custom 300000 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 30000 30000 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector group rdfgroup_2 union subset_Li_1 subset_S(SO4)_1 41 atoms in group rdfgroup_2 compute rdf_2 rdfgroup_2 rdf 200 4 9 fix rdf_2 rdfgroup_2 ave/time 1 30000 30000 c_rdf_2[*] file 2.5_PairCorrelation_all_2.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 30000 30000 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 30000 30000 c_rdf_4[*] file 2.5_PairCorrelation_all_4.out mode vector group rdfgroup_5 union subset_Li_1 subset_H(H2O)_1 5546 atoms in group rdfgroup_5 compute rdf_5 rdfgroup_5 rdf 200 4 2 fix rdf_5 rdfgroup_5 ave/time 1 30000 30000 c_rdf_5[*] file 2.5_PairCorrelation_all_5.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 30000 30000 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector group rdfgroup_8 union subset_Na_1 subset_S(SO4)_1 33 atoms in group rdfgroup_8 compute rdf_8 rdfgroup_8 rdf 200 6 9 fix rdf_8 rdfgroup_8 ave/time 1 30000 30000 c_rdf_8[*] file 2.5_PairCorrelation_all_8.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 30000 30000 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 30000 30000 c_rdf_10[*] file 2.5_PairCorrelation_all_10.out mode vector group rdfgroup_11 union subset_Na_1 subset_H(H2O)_1 5538 atoms in group rdfgroup_11 compute rdf_11 rdfgroup_11 rdf 200 6 2 fix rdf_11 rdfgroup_11 ave/time 1 30000 30000 c_rdf_11[*] file 2.5_PairCorrelation_all_11.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 30000 30000 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector group rdfgroup_13 union subset_K_1 subset_S(SO4)_1 62 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 200 3 9 fix rdf_13 rdfgroup_13 ave/time 1 30000 30000 c_rdf_13[*] file 2.5_PairCorrelation_all_13.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 30000 30000 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 30000 30000 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector group rdfgroup_16 union subset_K_1 subset_H(H2O)_1 5567 atoms in group rdfgroup_16 compute rdf_16 rdfgroup_16 rdf 200 3 2 fix rdf_16 rdfgroup_16 ave/time 1 30000 30000 c_rdf_16[*] file 2.5_PairCorrelation_all_16.out mode vector compute group_22 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_22 all ave/time 1 100 100 c_group_22 file 2.5_GroupInteractions_Layer1_Layer2_22.out compute group_23 subset_Layer1 group/group subset_Layer2 pair yes kspace no fix group_23 all ave/time 1 100 100 c_group_23 file 2.5_GroupInteractions_Layer1_Layer2_23.out compute group_24 subset_Layer1 group/group subset_Layer2 pair no kspace yes fix group_24 all ave/time 1 100 100 c_group_24 file 2.5_GroupInteractions_Layer1_Layer2_24.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 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 18 neighbor lists, perpetual/occasional/extra = 1 17 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 (17) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (18) 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 1.58784e-12 11904 2 103.7 1.13261e-10 3968 Per MPI rank memory allocation (min/avg/max) = 16.17 | 16.44 | 17.16 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 -119.88029 139006.3 1.4192018 295.57401 343.75006 654.49337 0 0 37647.163 22777.662 -396.67289 -380037.19 -318614.12 8750.5883 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.21488e-06 11904 2 103.7 9.20628e-05 3968 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.20359e-06 11904 2 103.7 0.00010361 3968 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.43677e-06 11904 2 103.7 0.000115169 3968 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.2544e-06 11904 2 103.7 9.35368e-05 3968 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.44522e-06 11904 2 103.7 9.45696e-05 3968 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.20817e-06 11904 2 103.7 9.23794e-05 3968 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.14523e-06 11904 2 103.7 9.44759e-05 3968 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.43841e-06 11904 2 103.7 9.95665e-05 3968 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.18755e-06 11904 2 103.7 9.32086e-05 3968 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.43375e-06 11904 2 103.7 0.000114794 3968 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.20768e-06 11904 2 103.7 9.17813e-05 3968 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.33438e-06 11904 2 103.7 0.000108882 3968 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.22179e-06 11904 2 103.7 9.05405e-05 3968 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.18653e-06 11904 2 103.7 9.28368e-05 3968 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.4163e-06 11904 2 103.7 0.000108295 3968 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.58682e-06 11904 2 103.7 8.98806e-05 3968 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.1319e-06 11904 2 103.7 9.83334e-05 3968 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.26959e-06 11904 2 103.7 9.06968e-05 3968 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.43962e-06 11904 2 103.7 0.000105554 3968 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.33601e-06 11904 2 103.7 0.000110637 3968 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.2295e-06 11904 2 103.7 0.00010404 3968 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.18132e-06 11904 2 103.7 9.35949e-05 3968 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.38147e-06 11904 2 103.7 0.000114084 3968 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.35329e-06 11904 2 103.7 9.55896e-05 3968 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.26506e-06 11904 2 103.7 0.000109237 3968 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.23145e-06 11904 2 103.7 9.83222e-05 3968 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.3024e-06 11904 2 103.7 0.000112589 3968 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.8356e-06 11904 2 103.7 0.000142211 3968 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.54559e-06 11904 2 103.7 0.000112049 3968 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.10041e-06 11904 2 103.7 9.97356e-05 3968 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.44254e-06 11904 2 103.7 0.000111784 3968 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.35418e-06 11904 2 103.7 8.97862e-05 3968 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.29917e-06 11904 2 103.7 0.000106062 3968 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.17939e-06 11904 2 103.7 9.7363e-05 3968 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.33863e-06 11904 2 103.7 0.000109438 3968 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.20898e-06 11904 2 103.7 0.000101387 3968 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.21166e-06 11904 2 103.7 9.99732e-05 3968 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.47954e-06 11904 2 103.7 0.000107142 3968 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.46391e-06 11904 2 103.7 0.000101028 3968 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.41711e-06 11904 2 103.7 0.000106297 3968 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.49873e-06 11904 2 103.7 0.000137741 3968 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.54583e-06 11904 2 103.7 9.95223e-05 3968 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.10469e-06 11904 2 103.7 9.23115e-05 3968 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.33775e-06 11904 2 103.7 9.10024e-05 3968 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.34189e-06 11904 2 103.7 0.000105292 3968 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.53725e-06 11904 2 103.7 0.000103311 3968 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.22926e-06 11904 2 103.7 0.00010066 3968 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.2631e-06 11904 2 103.7 9.63841e-05 3968 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.16273e-06 11904 2 103.7 0.000107076 3968 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.5434e-06 11904 2 103.7 0.000103057 3968 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.42694e-06 11904 2 103.7 0.000100289 3968 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.29324e-06 11904 2 103.7 9.54645e-05 3968 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.4956e-06 11904 2 103.7 0.000115035 3968 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.46594e-06 11904 2 103.7 0.000110756 3968 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.37149e-06 11904 2 103.7 0.000100134 3968 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.23614e-06 11904 2 103.7 0.000100156 3968 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.05188e-06 11904 2 103.7 9.15722e-05 3968 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.28748e-06 11904 2 103.7 0.00010253 3968 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.17063e-06 11904 2 103.7 9.23981e-05 3968 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.29784e-06 11904 2 103.7 0.000121921 3968 3000000 3000000 270.38631 139006.3 1.4192018 300.25199 356.08406 644.83959 0 0 38038.681 22339.039 -396.67289 -380047.58 -318668.94 8889.0818 Loop time of 144058 on 16 procs for 3000000 steps with 13901 atoms Performance: 1.799 ns/day, 13.339 hours/ns, 20.825 timesteps/s 98.7% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33284 | 40031 | 51099 |3174.8 | 27.79 Bond | 15.901 | 47.986 | 109.01 | 521.1 | 0.03 Kspace | 10030 | 21163 | 27947 |4396.1 | 14.69 Neigh | 2823.4 | 2825.5 | 2828.5 | 3.0 | 1.96 Comm | 1305.6 | 1364.2 | 1422.9 | 97.4 | 0.95 Output | 0.20014 | 0.22744 | 0.25354 | 3.6 | 0.00 Modify | 78409 | 78447 | 78487 | 9.1 | 54.46 Other | | 178.5 | | | 0.12 Nlocal: 868.812 ave 1007 max 783 min Histogram: 3 4 3 1 1 0 0 0 0 4 Nghost: 10665.1 ave 11130 max 9930 min Histogram: 4 0 0 0 0 1 3 1 3 4 Neighs: 502441 ave 652576 max 417656 min Histogram: 2 6 4 0 0 0 0 0 0 4 Total # of neighbors = 8039057 Ave neighs/atom = 578.30782 Ave special neighs/atom = 2.0450327 Neighbor list builds = 149634 Dangerous builds = 0 undump trj unfix trjE undump sci restart 0 dump sci all custom 3000000 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) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 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 3000000 1 0.97 1.29784e-06 11904 2 103.7 0.000121921 3968 Per MPI rank memory allocation (min/avg/max) = 47.31 | 54.23 | 61.25 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 3000000 3000000 271.66952 139006.3 1.4192018 300.25199 356.08406 644.83959 0 0 38038.681 22339.039 -396.67289 -380047.58 -318668.94 8889.0818 Loop time of 1.10081e-05 on 16 procs for 0 steps with 13901 atoms 112.4% CPU use with 16 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 | | 1.101e-05 | | |100.00 Nlocal: 868.812 ave 1007 max 783 min Histogram: 3 4 3 1 1 0 0 0 0 4 Nghost: 10665.1 ave 11130 max 9930 min Histogram: 4 0 0 0 0 1 3 1 3 4 Neighs: 502441 ave 652576 max 417656 min Histogram: 2 6 4 0 0 0 0 0 0 4 Total # of neighbors = 8039057 Ave neighs/atom = 578.30782 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_2 unfix rdf_2 group rdfgroup_2 delete uncompute rdf_3 unfix rdf_3 group rdfgroup_3 delete uncompute rdf_4 unfix rdf_4 group rdfgroup_4 delete uncompute rdf_5 unfix rdf_5 group rdfgroup_5 delete uncompute rdf_6 unfix rdf_6 group rdfgroup_6 delete uncompute rdf_8 unfix rdf_8 group rdfgroup_8 delete uncompute rdf_9 unfix rdf_9 group rdfgroup_9 delete uncompute rdf_10 unfix rdf_10 group rdfgroup_10 delete uncompute rdf_11 unfix rdf_11 group rdfgroup_11 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 uncompute rdf_16 unfix rdf_16 group rdfgroup_16 delete uncompute group_22 unfix group_22 uncompute group_23 unfix group_23 uncompute group_24 unfix group_24 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 52:13:38