#------------------------------------------------------------------------------- # 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 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 compute group_15 subset_layer2 group/group subset_Li_1 pair yes kspace yes fix group_15 all ave/time 1 100 100 c_group_15 file 2.5_GroupInteractions_layer2_Li_1_15.out compute group_16 subset_layer2 group/group subset_Na_1 pair yes kspace yes fix group_16 all ave/time 1 100 100 c_group_16 file 2.5_GroupInteractions_layer2_Na_1_16.out compute group_17 subset_layer2 group/group subset_Cl_1 pair yes kspace yes fix group_17 all ave/time 1 100 100 c_group_17 file 2.5_GroupInteractions_layer2_Cl_1_17.out compute group_18 subset_layer2 group/group subset_K_1 pair yes kspace yes fix group_18 all ave/time 1 100 100 c_group_18 file 2.5_GroupInteractions_layer2_K_1_18.out compute group_19 subset_layer2 group/group subset_Mg_1 pair yes kspace yes fix group_19 all ave/time 1 100 100 c_group_19 file 2.5_GroupInteractions_layer2_Mg_1_19.out compute group_20 subset_layer2 group/group subset_SO4_1 pair yes kspace yes fix group_20 all ave/time 1 100 100 c_group_20 file 2.5_GroupInteractions_layer2_SO4_1_20.out compute group_21 subset_layer2 group/group subset_H2O_1 pair yes kspace yes fix group_21 all ave/time 1 100 100 c_group_21 file 2.5_GroupInteractions_layer2_H2O_1_21.out timestep 1 run 3000000 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 8 neighbor lists, perpetual/occasional/extra = 1 7 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 group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (3) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (4) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (5) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (6) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (7) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (8) 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 6.49147e-13 8436 2 103.7 7.81881e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.73 | 14.43 | 14.93 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 -377.83747 141184.09 1.4079299 296.90938 46.210832 60.947133 0 0 31839.334 -35569.237 -312.04795 -284064.65 -287687.39 6789.0687 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.33877e-06 8436 2 103.7 0.000108892 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.21944e-06 8436 2 103.7 0.000106929 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.27598e-06 8436 2 103.7 0.000102507 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.13036e-06 8436 2 103.7 9.82232e-05 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.21718e-06 8436 2 103.7 9.82146e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.08267e-06 8436 2 103.7 9.25638e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.42067e-06 8436 2 103.7 0.000128056 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.07281e-06 8436 2 103.7 9.18205e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.3517e-06 8436 2 103.7 0.000104118 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.08812e-06 8436 2 103.7 9.44889e-05 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.45176e-06 8436 2 103.7 0.00011316 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.47953e-06 8436 2 103.7 9.89805e-05 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.55717e-06 8436 2 103.7 0.000101865 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.24648e-06 8436 2 103.7 9.80812e-05 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.22424e-06 8436 2 103.7 9.49142e-05 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.46191e-06 8436 2 103.7 0.0001101 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.1751e-06 8436 2 103.7 9.58057e-05 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.22029e-06 8436 2 103.7 9.781e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.18982e-06 8436 2 103.7 9.38088e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.52142e-06 8436 2 103.7 0.000101894 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.06625e-06 8436 2 103.7 9.36462e-05 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.2022e-06 8436 2 103.7 9.37195e-05 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.34147e-06 8436 2 103.7 9.1337e-05 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.34053e-06 8436 2 103.7 0.000100154 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.19024e-06 8436 2 103.7 9.43114e-05 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.29787e-06 8436 2 103.7 9.65109e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.26872e-06 8436 2 103.7 9.49178e-05 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.25268e-06 8436 2 103.7 8.92615e-05 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.11073e-06 8436 2 103.7 9.90655e-05 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.81237e-06 8436 2 103.7 0.000112009 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.22071e-06 8436 2 103.7 9.4252e-05 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.42506e-06 8436 2 103.7 0.000100846 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.33492e-06 8436 2 103.7 9.43486e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.06441e-06 8436 2 103.7 8.85635e-05 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.60129e-06 8436 2 103.7 0.000102587 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.22024e-06 8436 2 103.7 9.29317e-05 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.33263e-06 8436 2 103.7 0.000111177 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.55632e-06 8436 2 103.7 0.000116516 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.38042e-06 8436 2 103.7 0.000111625 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.27947e-06 8436 2 103.7 0.000104186 2812 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.45567e-06 8436 2 103.7 0.000101577 2812 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.1388e-06 8436 2 103.7 8.98568e-05 2812 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.13101e-06 8436 2 103.7 9.30584e-05 2812 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.30244e-06 8436 2 103.7 9.88514e-05 2812 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.12049e-06 8436 2 103.7 9.21442e-05 2812 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.6264e-06 8436 2 103.7 0.000116641 2812 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.10793e-06 8436 2 103.7 9.44918e-05 2812 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.1361e-06 8436 2 103.7 9.00537e-05 2812 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.26644e-06 8436 2 103.7 8.91034e-05 2812 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.06033e-06 8436 2 103.7 8.7665e-05 2812 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.71953e-06 8436 2 103.7 0.000131406 2812 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.11492e-06 8436 2 103.7 9.97737e-05 2812 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.30757e-06 8436 2 103.7 0.000118206 2812 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.25069e-06 8436 2 103.7 9.10123e-05 2812 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.02946e-06 8436 2 103.7 0.000105738 2812 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.34238e-06 8436 2 103.7 9.71036e-05 2812 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.31493e-06 8436 2 103.7 9.42841e-05 2812 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.11881e-06 8436 2 103.7 9.66575e-05 2812 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.14145e-06 8436 2 103.7 9.20665e-05 2812 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.14681e-06 8436 2 103.7 9.91541e-05 2812 3000000 3000000 -105.82944 141184.09 1.4079299 296.50385 31.454292 74.50599 0 0 32041.685 -35693.982 -312.04795 -284080.19 -287626.52 6779.7959 Loop time of 70864.6 on 32 procs for 3000000 steps with 10808 atoms Performance: 3.658 ns/day, 6.562 hours/ns, 42.334 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3854 | 13410 | 18536 |4848.7 | 18.92 Bond | 3.5459 | 9.1772 | 17.827 | 131.5 | 0.01 Kspace | 5958.7 | 11119 | 20776 |5356.6 | 15.69 Neigh | 1344.9 | 1347.1 | 1351.4 | 5.7 | 1.90 Comm | 1177.3 | 1570 | 1718.6 | 436.0 | 2.22 Output | 0.10001 | 0.12742 | 0.15436 | 4.5 | 0.00 Modify | 43200 | 43324 | 43624 | 67.3 | 61.14 Other | | 85.25 | | | 0.12 Nlocal: 337.75 ave 419 max 160 min Histogram: 4 4 0 0 0 0 0 3 8 13 Nghost: 6438.38 ave 7730 max 4759 min Histogram: 8 0 0 5 3 0 0 0 5 11 Neighs: 158185 ave 227136 max 43887 min Histogram: 8 0 0 0 0 1 3 4 10 6 Total # of neighbors = 5061929 Ave neighs/atom = 468.3502 Ave special neighs/atom = 1.6184308 Neighbor list builds = 149343 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) = 0.25537807 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 3000000 2 0.97 1.14681e-06 8436 2 103.7 9.91541e-05 2812 Per MPI rank memory allocation (min/avg/max) = 15.13 | 19.61 | 21.67 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 3000000 3000000 -105.24407 141184.09 1.4079299 296.50385 31.454292 74.50599 0 0 32041.685 -35693.982 -312.04795 -284080.19 -287626.52 6779.7959 Loop time of 7.23119e-06 on 32 procs for 0 steps with 10808 atoms 121.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.231e-06 | | |100.00 Nlocal: 337.75 ave 419 max 160 min Histogram: 4 4 0 0 0 0 0 3 8 13 Nghost: 6438.38 ave 7730 max 4759 min Histogram: 8 0 0 5 3 0 0 0 5 11 Neighs: 158185 ave 227136 max 43887 min Histogram: 8 0 0 0 0 1 3 4 10 6 Total # of neighbors = 5061929 Ave neighs/atom = 468.3502 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_15 unfix group_15 uncompute group_16 unfix group_16 uncompute group_17 unfix group_17 uncompute group_18 unfix group_18 uncompute group_19 unfix group_19 uncompute group_20 unfix group_20 uncompute group_21 unfix group_21 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out