#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 5 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 4018 = # 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 500000 500000 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 500 1 500 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 5000000 2.5.restart dump sci all custom 500000 2.5.xyz id mol type q xs ys zs compute group_1 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_1 all ave/time 1 100 100 c_group_1 file 2.5_GroupInteractions_Layer1_Layer2_1.out timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32606129 grid = 45 45 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0031698471 estimated relative force accuracy = 9.5459005e-06 using double precision KISS FFT 3d grid and FFT values/proc = 16200 6348 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 8 8 20 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 6.68075e-09 12054 2 103.7 7.08542e-07 4018 Per MPI rank memory allocation (min/avg/max) = 13.27 | 13.82 | 14.07 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 1048.0154 189229.23 1.419626 297.91409 54.825879 279.92927 0 0 43785.372 71075.914 -862.55543 -497626.56 -382430.52 9863.2971 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.84756e-06 12054 2 103.7 0.000138052 4018 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.33398e-06 12054 2 103.7 8.81988e-05 4018 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.44218e-06 12054 2 103.7 0.000102617 4018 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25899e-06 12054 2 103.7 0.000102693 4018 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.18183e-06 12054 2 103.7 9.2537e-05 4018 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.32586e-06 12054 2 103.7 0.000107121 4018 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.18003e-06 12054 2 103.7 0.000112033 4018 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.21306e-06 12054 2 103.7 0.000112956 4018 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.22958e-06 12054 2 103.7 9.38915e-05 4018 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.12095e-06 12054 2 103.7 9.18251e-05 4018 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.21477e-06 12054 2 103.7 9.57575e-05 4018 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.40684e-06 12054 2 103.7 9.97394e-05 4018 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.26173e-06 12054 2 103.7 9.67708e-05 4018 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.25746e-06 12054 2 103.7 0.000101908 4018 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.12403e-06 12054 2 103.7 9.33782e-05 4018 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.13046e-06 12054 2 103.7 9.77578e-05 4018 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.20807e-06 12054 2 103.7 9.75378e-05 4018 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.2577e-06 12054 2 103.7 0.000101864 4018 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.1531e-06 12054 2 103.7 9.3946e-05 4018 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.35803e-06 12054 2 103.7 9.93789e-05 4018 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.15253e-06 12054 2 103.7 9.30221e-05 4018 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.33051e-06 12054 2 103.7 0.000134047 4018 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.14194e-06 12054 2 103.7 9.69944e-05 4018 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.61278e-06 12054 2 103.7 0.000136039 4018 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.19911e-06 12054 2 103.7 9.87291e-05 4018 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.58658e-06 12054 2 103.7 0.000107583 4018 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.83788e-06 12054 2 103.7 0.000110545 4018 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.29079e-06 12054 2 103.7 9.1248e-05 4018 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.67738e-06 12054 2 103.7 0.000114624 4018 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.47326e-06 12054 2 103.7 9.66449e-05 4018 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.29258e-06 12054 2 103.7 9.76706e-05 4018 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.62238e-06 12054 2 103.7 9.69764e-05 4018 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.24073e-06 12054 2 103.7 9.09609e-05 4018 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.30212e-06 12054 2 103.7 9.35993e-05 4018 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.37006e-06 12054 2 103.7 9.61927e-05 4018 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.62481e-06 12054 2 103.7 0.000112745 4018 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.15511e-06 12054 2 103.7 9.16106e-05 4018 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.19302e-06 12054 2 103.7 9.53696e-05 4018 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.34835e-06 12054 2 103.7 0.000107705 4018 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.11764e-06 12054 2 103.7 0.000104248 4018 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.29118e-06 12054 2 103.7 9.94333e-05 4018 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.32541e-06 12054 2 103.7 9.57409e-05 4018 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.1961e-06 12054 2 103.7 9.12609e-05 4018 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.43682e-06 12054 2 103.7 0.000100735 4018 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.2797e-06 12054 2 103.7 9.60129e-05 4018 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.28688e-06 12054 2 103.7 9.65635e-05 4018 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.24477e-06 12054 2 103.7 9.46828e-05 4018 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.31773e-06 12054 2 103.7 9.34491e-05 4018 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.54157e-06 12054 2 103.7 0.000100983 4018 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.42451e-06 12054 2 103.7 0.000114917 4018 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.34204e-06 12054 2 103.7 9.78483e-05 4018 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.16065e-06 12054 2 103.7 0.000103404 4018 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.14845e-06 12054 2 103.7 9.74136e-05 4018 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.35303e-06 12054 2 103.7 0.000100391 4018 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.32024e-06 12054 2 103.7 9.80725e-05 4018 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.35412e-06 12054 2 103.7 0.000106683 4018 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.3716e-06 12054 2 103.7 0.000104703 4018 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.08963e-06 12054 2 103.7 9.77297e-05 4018 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.10409e-06 12054 2 103.7 9.47068e-05 4018 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.38566e-06 12054 2 103.7 0.000101273 4018 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.26636e-06 12054 2 103.7 0.000100876 4018 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.14643e-06 12054 2 103.7 0.000102635 4018 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.36124e-06 12054 2 103.7 9.85711e-05 4018 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.43617e-06 12054 2 103.7 9.83631e-05 4018 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.25809e-06 12054 2 103.7 9.67315e-05 4018 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.21359e-06 12054 2 103.7 9.51296e-05 4018 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.52915e-06 12054 2 103.7 9.52694e-05 4018 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.24352e-06 12054 2 103.7 9.95409e-05 4018 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.23892e-06 12054 2 103.7 0.000103443 4018 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.18158e-06 12054 2 103.7 9.29108e-05 4018 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.36572e-06 12054 2 103.7 9.4919e-05 4018 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.26452e-06 12054 2 103.7 9.92323e-05 4018 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.77502e-06 12054 2 103.7 0.000107004 4018 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.29985e-06 12054 2 103.7 8.73442e-05 4018 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.39421e-06 12054 2 103.7 0.0001002 4018 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.22311e-06 12054 2 103.7 0.000112301 4018 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.1672e-06 12054 2 103.7 8.89322e-05 4018 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.36566e-06 12054 2 103.7 0.000102977 4018 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.27089e-06 12054 2 103.7 9.41375e-05 4018 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.35817e-06 12054 2 103.7 0.000109246 4018 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.16364e-06 12054 2 103.7 9.19914e-05 4018 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.29963e-06 12054 2 103.7 9.16372e-05 4018 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.13269e-06 12054 2 103.7 9.96675e-05 4018 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.27351e-06 12054 2 103.7 0.000106934 4018 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.3246e-06 12054 2 103.7 9.22116e-05 4018 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.21748e-06 12054 2 103.7 9.95101e-05 4018 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.22135e-06 12054 2 103.7 0.000110022 4018 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.20623e-06 12054 2 103.7 0.000102976 4018 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.37845e-06 12054 2 103.7 0.000109065 4018 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.22849e-06 12054 2 103.7 0.000104034 4018 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.4401e-06 12054 2 103.7 0.000109622 4018 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.12538e-06 12054 2 103.7 9.45904e-05 4018 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.29459e-06 12054 2 103.7 0.000104818 4018 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.29905e-06 12054 2 103.7 0.000101544 4018 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.21143e-06 12054 2 103.7 9.4201e-05 4018 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.47727e-06 12054 2 103.7 0.000122525 4018 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.32383e-06 12054 2 103.7 0.000100456 4018 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.13296e-06 12054 2 103.7 9.70613e-05 4018 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.31928e-06 12054 2 103.7 0.000102689 4018 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.38696e-06 12054 2 103.7 9.73101e-05 4018 5000000 5000000 886.55446 189229.23 1.419626 301.8897 60.66952 272.91884 0 0 43777.179 71050.01 -862.55543 -497607.78 -382447 9994.9211 Loop time of 80658.2 on 32 procs for 5000000 steps with 15126 atoms Performance: 5.356 ns/day, 4.481 hours/ns, 61.990 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4457 | 17986 | 23964 |5480.8 | 22.30 Bond | 6.421 | 19.004 | 31.535 | 174.6 | 0.02 Kspace | 21401 | 27360 | 41000 |4487.2 | 33.92 Neigh | 1885.1 | 1893.4 | 1919.2 | 23.0 | 2.35 Comm | 1826.7 | 2453.9 | 2653.1 | 597.9 | 3.04 Output | 0.016896 | 0.02011 | 0.02317 | 1.3 | 0.00 Modify | 30625 | 30758 | 31189 | 114.3 | 38.13 Other | | 187.2 | | | 0.23 Nlocal: 472.688 ave 586 max 200 min Histogram: 4 4 0 0 0 0 0 0 9 15 Nghost: 5138.94 ave 6171 max 3503 min Histogram: 6 2 0 0 4 4 0 0 0 16 Neighs: 128358 ave 177928 max 25090 min Histogram: 4 4 0 0 0 0 4 0 6 14 Total # of neighbors = 4107448 Ave neighs/atom = 271.54886 Ave special neighs/atom = 1.65199 Neighbor list builds = 255471 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 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) = 0.32606129 grid = 45 45 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0031698471 estimated relative force accuracy = 9.5459005e-06 using double precision KISS FFT 3d grid and FFT values/proc = 16200 6348 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.38696e-06 12054 2 103.7 9.73101e-05 4018 Per MPI rank memory allocation (min/avg/max) = 13.65 | 14.5 | 14.83 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 5000000 5000000 887.15463 189229.23 1.419626 301.8897 60.66952 272.91884 0 0 43777.179 71050.01 -862.55543 -497607.78 -382447 9994.9211 Loop time of 9.37481e-06 on 32 procs for 0 steps with 15126 atoms 109.7% 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 | | 9.375e-06 | | |100.00 Nlocal: 472.688 ave 586 max 200 min Histogram: 4 4 0 0 0 0 0 0 9 15 Nghost: 5138.94 ave 6171 max 3503 min Histogram: 6 2 0 0 4 4 0 0 0 16 Neighs: 128358 ave 177928 max 25090 min Histogram: 4 4 0 0 0 0 4 0 6 14 Total # of neighbors = 4107448 Ave neighs/atom = 271.54886 Ave special neighs/atom = 1.65199 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: 38:41:06