#------------------------------------------------------------------------------- # 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 3472 = # 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_kainite pair yes kspace yes fix group_1 all ave/time 1 100 100 c_group_1 file 2.5_GroupInteractions_solution2_kainite_1.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25978169 grid = 36 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030652478 estimated relative force accuracy = 9.2309027e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8800 3240 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) 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 5 17 2 neighbor lists, perpetual/occasional/extra = 1 1 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 SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.70816e-09 10416 2 103.7 1.86915e-07 3472 Per MPI rank memory allocation (min/avg/max) = 13.35 | 13.62 | 13.78 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 -290.22541 148206.07 1.5203572 295.23424 431.35722 616.44291 0 0 39690.516 -34299.143 -439.56021 -404773.66 -398334.49 8613.8039 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.27027e-06 10416 2 103.7 9.95807e-05 3472 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.62985e-06 10416 2 103.7 0.000128963 3472 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.34287e-06 10416 2 103.7 0.000101284 3472 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.18701e-06 10416 2 103.7 9.38063e-05 3472 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.14151e-06 10416 2 103.7 9.27517e-05 3472 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.46739e-06 10416 2 103.7 0.00011281 3472 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.28059e-06 10416 2 103.7 9.57808e-05 3472 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.30803e-06 10416 2 103.7 9.52543e-05 3472 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.09002e-06 10416 2 103.7 0.000106198 3472 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.22742e-06 10416 2 103.7 9.53635e-05 3472 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.09682e-06 10416 2 103.7 9.48892e-05 3472 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21839e-06 10416 2 103.7 0.000101262 3472 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.17423e-06 10416 2 103.7 9.14503e-05 3472 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.19641e-06 10416 2 103.7 9.04538e-05 3472 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.18945e-06 10416 2 103.7 9.69537e-05 3472 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.2523e-06 10416 2 103.7 9.94492e-05 3472 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.52622e-06 10416 2 103.7 9.13819e-05 3472 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.17565e-06 10416 2 103.7 9.80474e-05 3472 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.41336e-06 10416 2 103.7 0.000106778 3472 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.13133e-06 10416 2 103.7 0.00010151 3472 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.17398e-06 10416 2 103.7 9.88973e-05 3472 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.67146e-06 10416 2 103.7 0.000120349 3472 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.40113e-06 10416 2 103.7 0.000105519 3472 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.89123e-06 10416 2 103.7 0.000117627 3472 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.11532e-06 10416 2 103.7 9.67191e-05 3472 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.50862e-06 10416 2 103.7 0.000104823 3472 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.30332e-06 10416 2 103.7 9.05966e-05 3472 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.21605e-06 10416 2 103.7 0.00011978 3472 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.19339e-06 10416 2 103.7 9.1438e-05 3472 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.64089e-06 10416 2 103.7 0.000131481 3472 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.3251e-06 10416 2 103.7 9.48019e-05 3472 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.45249e-06 10416 2 103.7 9.40709e-05 3472 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.26011e-06 10416 2 103.7 0.000122605 3472 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.17868e-06 10416 2 103.7 8.93334e-05 3472 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.1236e-06 10416 2 103.7 9.48762e-05 3472 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.23016e-06 10416 2 103.7 9.4983e-05 3472 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.12794e-06 10416 2 103.7 0.000100166 3472 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.40028e-06 10416 2 103.7 9.38187e-05 3472 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.48482e-06 10416 2 103.7 0.000103692 3472 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.71929e-06 10416 2 103.7 0.000109472 3472 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.4882e-06 10416 2 103.7 0.000112209 3472 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.20814e-06 10416 2 103.7 0.000102711 3472 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.65484e-06 10416 2 103.7 0.000114978 3472 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.24982e-06 10416 2 103.7 9.95675e-05 3472 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.16186e-06 10416 2 103.7 8.99049e-05 3472 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.25709e-06 10416 2 103.7 9.34577e-05 3472 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.27624e-06 10416 2 103.7 9.27807e-05 3472 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.10689e-06 10416 2 103.7 9.40755e-05 3472 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.25491e-06 10416 2 103.7 9.93367e-05 3472 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.30352e-06 10416 2 103.7 8.83836e-05 3472 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.21842e-06 10416 2 103.7 9.4675e-05 3472 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.44748e-06 10416 2 103.7 9.78943e-05 3472 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.26335e-06 10416 2 103.7 9.45794e-05 3472 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.15553e-06 10416 2 103.7 9.06249e-05 3472 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.34069e-06 10416 2 103.7 9.59356e-05 3472 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.13737e-06 10416 2 103.7 0.000122025 3472 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.17847e-06 10416 2 103.7 9.72176e-05 3472 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.38571e-06 10416 2 103.7 0.000111764 3472 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.26838e-06 10416 2 103.7 0.000100034 3472 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.24444e-06 10416 2 103.7 0.00010098 3472 3000000 3000000 343.7049 148206.07 1.5203572 299.41249 449.2298 624.50707 0 0 40042.47 -34679.856 -439.56021 -404765.48 -398329.13 8735.7092 Loop time of 49219.2 on 32 procs for 3000000 steps with 13261 atoms Performance: 5.266 ns/day, 4.557 hours/ns, 60.952 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 | 14607 | 18578 | 20766 |1477.7 | 37.75 Bond | 6.5199 | 29.976 | 70.466 | 445.2 | 0.06 Kspace | 6819.5 | 9011.4 | 12972 |2112.0 | 18.31 Neigh | 1604 | 1606.2 | 1609.6 | 3.8 | 3.26 Comm | 1357.6 | 1511.3 | 1579 | 161.9 | 3.07 Output | 0.013476 | 0.016345 | 0.019061 | 1.3 | 0.00 Modify | 18319 | 18374 | 18469 | 34.8 | 37.33 Other | | 108.2 | | | 0.22 Nlocal: 414.406 ave 453 max 354 min Histogram: 3 1 0 3 4 0 7 4 6 4 Nghost: 7634.72 ave 8007 max 7193 min Histogram: 6 4 2 0 0 3 3 3 4 7 Neighs: 213746 ave 246118 max 168508 min Histogram: 4 1 3 1 2 3 3 6 5 4 Total # of neighbors = 6839886 Ave neighs/atom = 515.78961 Ave special neighs/atom = 2.0037705 Neighbor list builds = 149687 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) = 0.25978169 grid = 36 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030652478 estimated relative force accuracy = 9.2309027e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8800 3240 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) SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.24444e-06 10416 2 103.7 0.00010098 3472 Per MPI rank memory allocation (min/avg/max) = 14.11 | 14.74 | 14.92 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 344.47713 148206.07 1.5203572 299.41249 449.2298 624.50707 0 0 40042.47 -34679.856 -439.56021 -404765.48 -398329.13 8735.7092 Loop time of 7.89144e-06 on 32 procs for 0 steps with 13261 atoms 114.4% 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 | | 7.891e-06 | | |100.00 Nlocal: 414.406 ave 453 max 354 min Histogram: 3 1 0 3 4 0 7 4 6 4 Nghost: 7634.72 ave 8007 max 7193 min Histogram: 6 4 2 0 0 3 3 3 4 7 Neighs: 213746 ave 246118 max 168508 min Histogram: 4 1 3 1 2 3 3 6 5 4 Total # of neighbors = 6839886 Ave neighs/atom = 515.78961 Ave special neighs/atom = 2.0037705 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_1 unfix group_1 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 23:19:45