#------------------------------------------------------------------------------- # 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 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 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs group rdfgroup_1 union subset_Li_1 subset_Cl_1 350 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_1 38 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 38 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 2819 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_1 2819 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_1 399 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_1 87 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 87 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 2868 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_1 2868 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_1 383 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_1 71 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 71 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 2852 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_1 2852 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) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-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 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 2 0.97 1.09879e-12 8436 2 103.7 7.72502e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.13 | 14.69 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-06 119.19045 130091.43 1.4011632 297.38395 49.381797 237.30931 0 0 29348.851 -19074.638 -295.4552 -267614.11 -257053.2 6331.8771 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.25861e-06 8436 2 103.7 0.000101496 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.30939e-06 8436 2 103.7 0.000110884 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.82155e-06 8436 2 103.7 0.000115979 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.26866e-06 8436 2 103.7 0.000107043 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.12492e-06 8436 2 103.7 9.30349e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.13481e-06 8436 2 103.7 8.91823e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.29245e-06 8436 2 103.7 9.306e-05 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.46116e-06 8436 2 103.7 9.17292e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.77309e-06 8436 2 103.7 0.000120851 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.18789e-06 8436 2 103.7 0.000106515 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.17772e-06 8436 2 103.7 9.93152e-05 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.68272e-06 8436 2 103.7 9.38256e-05 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.22267e-06 8436 2 103.7 0.000112488 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.43199e-06 8436 2 103.7 0.000100826 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.26943e-06 8436 2 103.7 0.000100393 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.14636e-06 8436 2 103.7 9.01113e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21213e-06 8436 2 103.7 9.37637e-05 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.12006e-06 8436 2 103.7 9.77887e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.42016e-06 8436 2 103.7 0.000105269 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17465e-06 8436 2 103.7 9.41729e-05 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.11278e-06 8436 2 103.7 9.95222e-05 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.17021e-06 8436 2 103.7 0.000100243 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.33944e-06 8436 2 103.7 0.000112354 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.16122e-06 8436 2 103.7 9.80058e-05 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.24205e-06 8436 2 103.7 0.000111559 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.36045e-06 8436 2 103.7 0.00011322 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.1375e-06 8436 2 103.7 0.000100827 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.42113e-06 8436 2 103.7 0.000103448 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 2.24755e-06 8436 2 103.7 0.000174974 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.2543e-06 8436 2 103.7 9.58408e-05 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.30569e-06 8436 2 103.7 0.000105544 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.22719e-06 8436 2 103.7 0.000106515 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.58108e-06 8436 2 103.7 0.000123894 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.09827e-06 8436 2 103.7 0.000101872 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.79087e-06 8436 2 103.7 0.000146969 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.25553e-06 8436 2 103.7 0.000100602 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.22336e-06 8436 2 103.7 9.1181e-05 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.20378e-06 8436 2 103.7 9.31689e-05 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.17452e-06 8436 2 103.7 9.11571e-05 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.22746e-06 8436 2 103.7 9.73684e-05 2812 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.08098e-06 8436 2 103.7 9.69313e-05 2812 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.47648e-06 8436 2 103.7 9.77261e-05 2812 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.32612e-06 8436 2 103.7 9.70004e-05 2812 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.49762e-06 8436 2 103.7 9.85469e-05 2812 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.41538e-06 8436 2 103.7 9.24092e-05 2812 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.26457e-06 8436 2 103.7 0.000101108 2812 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.29629e-06 8436 2 103.7 9.83669e-05 2812 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.08971e-06 8436 2 103.7 9.41946e-05 2812 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.19275e-06 8436 2 103.7 0.000100543 2812 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.28986e-06 8436 2 103.7 0.000103001 2812 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.10933e-06 8436 2 103.7 9.62622e-05 2812 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.18216e-06 8436 2 103.7 9.80055e-05 2812 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.18588e-06 8436 2 103.7 9.99976e-05 2812 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.21632e-06 8436 2 103.7 8.67981e-05 2812 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.19537e-06 8436 2 103.7 0.000118458 2812 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.44487e-06 8436 2 103.7 9.78165e-05 2812 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.2223e-06 8436 2 103.7 9.30868e-05 2812 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.13256e-06 8436 2 103.7 0.000101887 2812 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.69637e-06 8436 2 103.7 0.000103537 2812 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.26746e-06 8436 2 103.7 0.000108306 2812 3000000 3000000 290.47734 130091.43 1.4011632 300.68089 49.683317 254.54407 0 0 29436.34 -19140.519 -295.4552 -267591.98 -256991.93 6402.0753 Loop time of 88501.1 on 16 procs for 3000000 steps with 10468 atoms Performance: 2.929 ns/day, 8.195 hours/ns, 33.898 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 | 9313 | 25670 | 33645 |5996.8 | 29.00 Bond | 4.5761 | 13.425 | 27.092 | 191.6 | 0.02 Kspace | 7141.6 | 15166 | 31584 |7826.2 | 17.14 Neigh | 1859.2 | 1862.2 | 1866.2 | 5.1 | 2.10 Comm | 1145.9 | 1356.4 | 1449.8 | 326.2 | 1.53 Output | 0.017816 | 0.019813 | 0.021749 | 0.9 | 0.00 Modify | 44235 | 44292 | 44448 | 42.0 | 50.05 Other | | 141 | | | 0.16 Nlocal: 654.25 ave 779 max 373 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8583.88 ave 9956 max 7306 min Histogram: 4 0 0 3 1 4 0 0 0 4 Neighs: 320414 ave 421381 max 113335 min Histogram: 4 0 0 0 0 0 0 4 0 8 Total # of neighbors = 5126619 Ave neighs/atom = 489.74198 Ave special neighs/atom = 1.6709973 Neighbor list builds = 149036 Dangerous builds = 0 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) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-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 3000000 2 0.97 1.26746e-06 8436 2 103.7 0.000108306 2812 Per MPI rank memory allocation (min/avg/max) = 26.1 | 40.12 | 47.14 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 291.1694 130091.43 1.4011632 300.68089 49.683317 254.54407 0 0 29436.34 -19140.519 -295.4552 -267591.98 -256991.93 6402.0753 Loop time of 4.30425e-06 on 16 procs for 0 steps with 10468 atoms 126.3% 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 | | 4.304e-06 | | |100.00 Nlocal: 654.25 ave 779 max 373 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8583.88 ave 9956 max 7306 min Histogram: 4 0 0 3 1 4 0 0 0 4 Neighs: 320414 ave 421381 max 113335 min Histogram: 4 0 0 0 0 0 0 4 0 8 Total # of neighbors = 5126619 Ave neighs/atom = 489.74198 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_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 4 unfix shaken Total wall time: 33:05:58