#------------------------------------------------------------------------------- # 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 2768 = # 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 sci all custom 300000 2.5.xyz id mol type q xs ys zs compute group_1 subset_solution2 group/group subset_NaCl pair yes kspace yes fix group_1 all ave/time 1 100 100 c_group_1 file 2.5_GroupInteractions_solution2_NaCl_1.out compute group_2 subset_solution2 group/group subset_NaCl pair yes kspace no fix group_2 all ave/time 1 100 100 c_group_2 file 2.5_GroupInteractions_solution2_NaCl_2.out compute group_3 subset_solution2 group/group subset_NaCl pair no kspace yes fix group_3 all ave/time 1 100 100 c_group_3 file 2.5_GroupInteractions_solution2_NaCl_3.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25914364 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028379227 estimated relative force accuracy = 8.5463198e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 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 16 3 neighbor lists, perpetual/occasional/extra = 1 2 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 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 SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.9474e-09 8304 2 103.7 2.16182e-07 2768 Per MPI rank memory allocation (min/avg/max) = 12.71 | 13.46 | 14.42 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 2000.6481 186830.8 1.5848005 301.43157 44.987807 53.952563 0 0 52383.25 -148557.32 -454.31456 -392169.73 -488244.86 8924.0038 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.16489e-06 8304 2 103.7 9.38442e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.09953e-06 8304 2 103.7 9.20339e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.16671e-06 8304 2 103.7 9.98777e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.27841e-06 8304 2 103.7 9.86358e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.45443e-06 8304 2 103.7 9.034e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.27236e-06 8304 2 103.7 9.79704e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.23907e-06 8304 2 103.7 9.20188e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1195e-06 8304 2 103.7 0.000110103 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.13733e-06 8304 2 103.7 9.81594e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15049e-06 8304 2 103.7 9.38335e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.33632e-06 8304 2 103.7 0.000104649 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.28022e-06 8304 2 103.7 0.000104225 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.3123e-06 8304 2 103.7 9.22927e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.36748e-06 8304 2 103.7 0.000124686 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.13625e-06 8304 2 103.7 9.09922e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.63003e-06 8304 2 103.7 0.00010884 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.16247e-06 8304 2 103.7 9.59993e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.65839e-06 8304 2 103.7 0.000104274 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.74344e-06 8304 2 103.7 0.000114532 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.40547e-06 8304 2 103.7 8.96225e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.49104e-06 8304 2 103.7 9.58119e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.11348e-06 8304 2 103.7 9.38976e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.36887e-06 8304 2 103.7 9.14683e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.37196e-06 8304 2 103.7 0.000103526 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.34754e-06 8304 2 103.7 0.000102015 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.26139e-06 8304 2 103.7 9.57844e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.17167e-06 8304 2 103.7 0.000104972 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.42214e-06 8304 2 103.7 9.14843e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.25115e-06 8304 2 103.7 0.000101208 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.34607e-06 8304 2 103.7 0.00010068 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.2732e-06 8304 2 103.7 9.58466e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.91114e-06 8304 2 103.7 0.000104031 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.06142e-06 8304 2 103.7 0.000109036 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.04247e-06 8304 2 103.7 9.06245e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.47235e-06 8304 2 103.7 0.000120832 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.37531e-06 8304 2 103.7 0.000110704 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.24738e-06 8304 2 103.7 0.000101715 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.4865e-06 8304 2 103.7 0.000113133 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.19053e-06 8304 2 103.7 9.1538e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.15978e-06 8304 2 103.7 9.73955e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.25998e-06 8304 2 103.7 8.81154e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.09739e-06 8304 2 103.7 9.86839e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.54411e-06 8304 2 103.7 0.000106736 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.14369e-06 8304 2 103.7 9.67334e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.25485e-06 8304 2 103.7 9.04417e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.22163e-06 8304 2 103.7 9.27577e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.31166e-06 8304 2 103.7 0.000105605 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.35243e-06 8304 2 103.7 0.000101475 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.26198e-06 8304 2 103.7 9.99467e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.2854e-06 8304 2 103.7 9.42544e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.21694e-06 8304 2 103.7 0.000103238 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.2139e-06 8304 2 103.7 0.00010598 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.05557e-06 8304 2 103.7 9.23231e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.21143e-06 8304 2 103.7 9.29898e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.11237e-06 8304 2 103.7 0.000106354 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.07633e-06 8304 2 103.7 9.47512e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.4144e-06 8304 2 103.7 0.000108299 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.11807e-06 8304 2 103.7 9.26559e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.45804e-06 8304 2 103.7 0.00011946 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.18778e-06 8304 2 103.7 9.32622e-05 2768 3000000 3000000 2021.5512 186830.8 1.5848005 299.37761 49.590135 47.849581 0 0 52434.746 -148641.56 -454.31456 -392163.7 -488273.08 8863.1955 Loop time of 67482.4 on 32 procs for 3000000 steps with 12701 atoms Performance: 3.841 ns/day, 6.248 hours/ns, 44.456 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4442.3 | 15361 | 26365 |7241.2 | 22.76 Bond | 3.5152 | 9.1171 | 20.817 | 181.6 | 0.01 Kspace | 7570.4 | 18599 | 29529 |6607.8 | 27.56 Neigh | 2081.1 | 2087.2 | 2095.9 | 9.0 | 3.09 Comm | 1011.8 | 1325.7 | 1498.3 | 440.6 | 1.96 Output | 0.013742 | 0.016377 | 0.019064 | 1.2 | 0.00 Modify | 29856 | 29988 | 30202 | 74.8 | 44.44 Other | | 112.7 | | | 0.17 Nlocal: 396.906 ave 564 max 202 min Histogram: 4 8 0 4 0 0 0 0 5 11 Nghost: 6331.12 ave 8660 max 3804 min Histogram: 4 4 0 4 4 4 0 4 0 8 Neighs: 173484 ave 306545 max 46849 min Histogram: 12 0 0 2 2 3 1 0 3 9 Total # of neighbors = 5551492 Ave neighs/atom = 437.09094 Ave special neighs/atom = 1.3564286 Neighbor list builds = 148358 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) = 0.25914364 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028379227 estimated relative force accuracy = 8.5463198e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.18778e-06 8304 2 103.7 9.32622e-05 2768 Per MPI rank memory allocation (min/avg/max) = 13.47 | 15.52 | 17.47 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 2022.0297 186830.8 1.5848005 299.37761 49.590135 47.849581 0 0 52434.746 -148641.56 -454.31456 -392163.7 -488273.08 8863.1955 Loop time of 7.56134e-06 on 32 procs for 0 steps with 12701 atoms 109.9% 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 | | 7.561e-06 | | |100.00 Nlocal: 396.906 ave 564 max 202 min Histogram: 4 8 0 4 0 0 0 0 5 11 Nghost: 6331.12 ave 8660 max 3804 min Histogram: 4 4 0 4 4 4 0 4 0 8 Neighs: 173484 ave 306545 max 46849 min Histogram: 12 0 0 2 2 3 1 0 3 9 Total # of neighbors = 5551492 Ave neighs/atom = 437.09094 Ave special neighs/atom = 1.3564286 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_1 unfix group_1 uncompute group_2 unfix group_2 uncompute group_3 unfix group_3 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 30:13:07