#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 50 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 5000 5000 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 5 1 5 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 50000 2.5.restart dump sci all custom 5000 2.5.xyz id mol type q xs ys zs group rdfgroup_1 union subset_Li_1 subset_Cl_1 350 atoms in group rdfgroup_1 compute rdf_1 rdfgroup_1 rdf 100 4 1 fix rdf_1 rdfgroup_1 ave/time 1 5000 5000 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector group rdfgroup_2 union subset_Li_1 subset_S(SO4)_1 38 atoms in group rdfgroup_2 compute rdf_2 rdfgroup_2 rdf 100 4 9 fix rdf_2 rdfgroup_2 ave/time 1 5000 5000 c_rdf_2[*] file 2.5_PairCorrelation_all_2.out mode vector group rdfgroup_3 union subset_Li_1 subset_O(H2O)_1 2819 atoms in group rdfgroup_3 compute rdf_3 rdfgroup_3 rdf 100 4 7 fix rdf_3 rdfgroup_3 ave/time 1 5000 5000 c_rdf_3[*] file 2.5_PairCorrelation_all_3.out mode vector group rdfgroup_4 union subset_K_1 subset_Cl_1 383 atoms in group rdfgroup_4 compute rdf_4 rdfgroup_4 rdf 100 3 1 fix rdf_4 rdfgroup_4 ave/time 1 5000 5000 c_rdf_4[*] file 2.5_PairCorrelation_all_4.out mode vector group rdfgroup_5 union subset_K_1 subset_S(SO4)_1 71 atoms in group rdfgroup_5 compute rdf_5 rdfgroup_5 rdf 100 3 9 fix rdf_5 rdfgroup_5 ave/time 1 5000 5000 c_rdf_5[*] file 2.5_PairCorrelation_all_5.out mode vector group rdfgroup_6 union subset_K_1 subset_O(H2O)_1 2852 atoms in group rdfgroup_6 compute rdf_6 rdfgroup_6 rdf 100 3 7 fix rdf_6 rdfgroup_6 ave/time 1 5000 5000 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector group rdfgroup_7 union subset_Na_1 subset_Cl_1 399 atoms in group rdfgroup_7 compute rdf_7 rdfgroup_7 rdf 100 6 1 fix rdf_7 rdfgroup_7 ave/time 1 5000 5000 c_rdf_7[*] file 2.5_PairCorrelation_all_7.out mode vector group rdfgroup_8 union subset_Na_1 subset_S(SO4)_1 87 atoms in group rdfgroup_8 compute rdf_8 rdfgroup_8 rdf 100 6 9 fix rdf_8 rdfgroup_8 ave/time 1 5000 5000 c_rdf_8[*] file 2.5_PairCorrelation_all_8.out mode vector group rdfgroup_9 union subset_Na_1 subset_O(H2O)_1 2868 atoms in group rdfgroup_9 compute rdf_9 rdfgroup_9 rdf 100 6 7 fix rdf_9 rdfgroup_9 ave/time 1 5000 5000 c_rdf_9[*] file 2.5_PairCorrelation_all_9.out mode vector group rdfgroup_10 union subset_Mg_1 subset_Cl_1 494 atoms in group rdfgroup_10 compute rdf_10 rdfgroup_10 rdf 100 5 1 fix rdf_10 rdfgroup_10 ave/time 1 5000 5000 c_rdf_10[*] file 2.5_PairCorrelation_all_10.out mode vector group rdfgroup_11 union subset_Mg_1 subset_S(SO4)_1 182 atoms in group rdfgroup_11 compute rdf_11 rdfgroup_11 rdf 100 5 9 fix rdf_11 rdfgroup_11 ave/time 1 5000 5000 c_rdf_11[*] file 2.5_PairCorrelation_all_11.out mode vector group rdfgroup_12 union subset_Mg_1 subset_O(H2O)_1 2963 atoms in group rdfgroup_12 compute rdf_12 rdfgroup_12 rdf 100 5 7 fix rdf_12 rdfgroup_12 ave/time 1 5000 5000 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector group rdfgroup_13 union subset_Cl_1 subset_O(H2O)_1 3155 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 100 1 7 fix rdf_13 rdfgroup_13 ave/time 1 5000 5000 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector group rdfgroup_14 union subset_S(SO4)_1 subset_O(H2O)_1 2843 atoms in group rdfgroup_14 compute rdf_14 rdfgroup_14 rdf 100 9 7 fix rdf_14 rdfgroup_14 ave/time 1 5000 5000 c_rdf_14[*] file 2.5_PairCorrelation_all_14.out mode vector compute group_15 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_15 all ave/time 1 100 100 c_group_15 file 2.5_GroupInteractions_Layer1_Layer2_15.out compute group_16 subset_Layer1 group/group subset_Layer2 pair yes kspace no fix group_16 all ave/time 1 100 100 c_group_16 file 2.5_GroupInteractions_Layer1_Layer2_16.out compute group_17 subset_Layer1 group/group subset_Layer2 pair no kspace yes fix group_17 all ave/time 1 100 100 c_group_17 file 2.5_GroupInteractions_Layer1_Layer2_17.out timestep 1 run 50000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25553612 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034265209 estimated relative force accuracy = 1.0318866e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 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 5 18 17 neighbor lists, perpetual/occasional/extra = 1 16 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 group/group, 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 SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.91891e-13 8436 2 103.7 7.77192e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.12 | 14.14 | 14.71 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-06 978.68993 127841.08 1.4258274 293.38804 54.665233 109.89479 0 0 29684.934 -18968.918 -300.656 -268002.52 -257121.94 6246.7964 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.26513e-06 8436 2 103.7 0.000126672 2812 50000 50000 1078.4828 127841.08 1.4258274 297.75646 52.69621 84.151735 0 0 29780.367 -19158.855 -300.656 -267986.88 -257228.52 6339.8086 Loop time of 1520.35 on 16 procs for 50000 steps with 10468 atoms Performance: 2.841 ns/day, 8.446 hours/ns, 32.887 timesteps/s 99.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 148.4 | 440.74 | 582.49 | 815.2 | 28.99 Bond | 0.075451 | 0.23492 | 0.36317 | 20.5 | 0.02 Kspace | 109.57 | 251.91 | 545.36 |1081.5 | 16.57 Neigh | 31.025 | 31.07 | 31.133 | 0.7 | 2.04 Comm | 19.614 | 23.338 | 25.184 | 43.5 | 1.54 Output | 0.016738 | 0.018886 | 0.020828 | 0.9 | 0.00 Modify | 769.5 | 770.65 | 773.44 | 5.6 | 50.69 Other | | 2.395 | | | 0.16 Nlocal: 654.25 ave 775 max 356 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8681.38 ave 10141 max 7371 min Histogram: 4 0 0 2 4 2 0 0 0 4 Neighs: 326818 ave 427203 max 106071 min Histogram: 4 0 0 0 0 0 0 2 2 8 Total # of neighbors = 5229091 Ave neighs/atom = 499.53105 Ave special neighs/atom = 1.6709973 Neighbor list builds = 2476 Dangerous builds = 0 undump sci restart 0 dump sci all custom 50000 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) = 0.25553612 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034265209 estimated relative force accuracy = 1.0318866e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.26513e-06 8436 2 103.7 0.000126672 2812 Per MPI rank memory allocation (min/avg/max) = 25.33 | 38.96 | 45.22 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 50000 50000 1079.2582 127841.08 1.4258274 297.75646 52.69621 84.151735 0 0 29780.367 -19158.855 -300.656 -267986.88 -257228.52 6339.8086 Loop time of 4.24231e-06 on 16 procs for 0 steps with 10468 atoms 117.9% 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 | | 4.242e-06 | | |100.00 Nlocal: 654.25 ave 775 max 356 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8681.38 ave 10141 max 7371 min Histogram: 4 0 0 2 4 2 0 0 0 4 Neighs: 326818 ave 427203 max 106071 min Histogram: 4 0 0 0 0 0 0 2 2 8 Total # of neighbors = 5229091 Ave neighs/atom = 499.53105 Ave special neighs/atom = 1.6709973 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_7 unfix rdf_7 group rdfgroup_7 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 group_15 unfix group_15 uncompute group_16 unfix group_16 uncompute group_17 unfix group_17 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 0:38:58