#------------------------------------------------------------------------------- # 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 2297 = # 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) = 0.25671212 grid = 25 24 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0033834134 estimated relative force accuracy = 1.0189049e-05 using double precision KISS FFT 3d grid and FFT values/proc = 5415 1248 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 = 5 4 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 8.69467e-10 6891 2 103.7 9.6397e-08 2297 Per MPI rank memory allocation (min/avg/max) = 12.83 | 12.93 | 13.07 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 -233.6695 80485.548 1.3394174 297.90367 123.30642 145.14562 0 0 19690.525 18411.799 -204.83328 -198685.98 -160315.2 4895.5123 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.22957e-06 6891 2 103.7 8.74245e-05 2297 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.74061e-06 6891 2 103.7 9.71603e-05 2297 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.52365e-06 6891 2 103.7 0.000108481 2297 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.74709e-06 6891 2 103.7 0.000124564 2297 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.41166e-06 6891 2 103.7 0.000111953 2297 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.58269e-06 6891 2 103.7 8.56051e-05 2297 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 9.22751e-07 6891 2 103.7 9.07875e-05 2297 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.18407e-06 6891 2 103.7 9.44297e-05 2297 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.17458e-06 6891 2 103.7 9.1142e-05 2297 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.19482e-06 6891 2 103.7 9.55847e-05 2297 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.25037e-06 6891 2 103.7 9.43914e-05 2297 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21359e-06 6891 2 103.7 0.000111184 2297 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 2.0939e-06 6891 2 103.7 0.000172783 2297 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.11083e-06 6891 2 103.7 9.36186e-05 2297 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.1817e-06 6891 2 103.7 9.69701e-05 2297 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.85359e-06 6891 2 103.7 0.000103526 2297 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.35774e-06 6891 2 103.7 9.89917e-05 2297 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.09878e-06 6891 2 103.7 8.9816e-05 2297 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.34047e-06 6891 2 103.7 9.27199e-05 2297 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.11166e-06 6891 2 103.7 9.90722e-05 2297 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.17894e-06 6891 2 103.7 0.00010463 2297 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.07811e-06 6891 2 103.7 8.85777e-05 2297 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.22566e-06 6891 2 103.7 9.86654e-05 2297 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.3689e-06 6891 2 103.7 0.000105225 2297 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.35598e-06 6891 2 103.7 9.65858e-05 2297 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.42394e-06 6891 2 103.7 9.60139e-05 2297 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.1116e-06 6891 2 103.7 0.000103963 2297 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.84154e-06 6891 2 103.7 0.000121042 2297 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.27924e-06 6891 2 103.7 9.92782e-05 2297 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.30366e-06 6891 2 103.7 0.00014649 2297 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.57637e-06 6891 2 103.7 0.000101274 2297 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.48756e-06 6891 2 103.7 0.000102039 2297 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.32078e-06 6891 2 103.7 9.56466e-05 2297 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.27164e-06 6891 2 103.7 9.85599e-05 2297 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.2321e-06 6891 2 103.7 9.477e-05 2297 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.66335e-06 6891 2 103.7 0.000115209 2297 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.26696e-06 6891 2 103.7 0.000101947 2297 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.05022e-06 6891 2 103.7 9.47042e-05 2297 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.61654e-06 6891 2 103.7 0.00012148 2297 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.10025e-06 6891 2 103.7 9.24615e-05 2297 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.17839e-06 6891 2 103.7 9.82668e-05 2297 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.25263e-06 6891 2 103.7 9.425e-05 2297 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.24484e-06 6891 2 103.7 0.000103954 2297 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.24511e-06 6891 2 103.7 9.61157e-05 2297 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.19442e-06 6891 2 103.7 0.000108531 2297 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.86726e-06 6891 2 103.7 0.000132182 2297 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.29045e-06 6891 2 103.7 0.000111566 2297 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.25749e-06 6891 2 103.7 0.000102063 2297 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.80958e-06 6891 2 103.7 0.000150587 2297 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.21753e-06 6891 2 103.7 9.05299e-05 2297 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.54611e-06 6891 2 103.7 0.000122005 2297 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.34723e-06 6891 2 103.7 0.00010589 2297 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.42518e-06 6891 2 103.7 9.83587e-05 2297 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.22549e-06 6891 2 103.7 9.29711e-05 2297 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.27032e-06 6891 2 103.7 9.3032e-05 2297 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.09316e-06 6891 2 103.7 0.000110957 2297 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.42797e-06 6891 2 103.7 0.000103407 2297 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.52882e-06 6891 2 103.7 0.000105769 2297 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.066e-06 6891 2 103.7 9.65111e-05 2297 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10582e-06 6891 2 103.7 8.85838e-05 2297 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.07688e-06 6891 2 103.7 0.000119765 2297 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.49947e-06 6891 2 103.7 0.000108471 2297 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.13041e-06 6891 2 103.7 9.0778e-05 2297 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.24324e-06 6891 2 103.7 8.96111e-05 2297 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.24368e-06 6891 2 103.7 0.000104049 2297 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.216e-06 6891 2 103.7 9.32288e-05 2297 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.39794e-06 6891 2 103.7 0.000101743 2297 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.1724e-06 6891 2 103.7 9.24683e-05 2297 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.33239e-06 6891 2 103.7 0.000101391 2297 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.16307e-06 6891 2 103.7 0.00011132 2297 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.21952e-06 6891 2 103.7 9.53433e-05 2297 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.1428e-06 6891 2 103.7 9.14061e-05 2297 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.00133e-06 6891 2 103.7 9.56167e-05 2297 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.50976e-06 6891 2 103.7 0.000109155 2297 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.24849e-06 6891 2 103.7 0.000101485 2297 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.38693e-06 6891 2 103.7 0.000111339 2297 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.27089e-06 6891 2 103.7 0.000105188 2297 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.39928e-06 6891 2 103.7 9.29269e-05 2297 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.48207e-06 6891 2 103.7 0.00010875 2297 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.30792e-06 6891 2 103.7 9.50276e-05 2297 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.28345e-06 6891 2 103.7 9.97185e-05 2297 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.17733e-06 6891 2 103.7 9.92835e-05 2297 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.16281e-06 6891 2 103.7 9.10269e-05 2297 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.15131e-06 6891 2 103.7 9.48698e-05 2297 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.35619e-06 6891 2 103.7 9.75638e-05 2297 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.54391e-06 6891 2 103.7 0.000116512 2297 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.44326e-06 6891 2 103.7 9.79871e-05 2297 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.47065e-06 6891 2 103.7 0.000110893 2297 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.23177e-06 6891 2 103.7 9.3725e-05 2297 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.19991e-06 6891 2 103.7 9.68431e-05 2297 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.4943e-06 6891 2 103.7 0.0001168 2297 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.19227e-06 6891 2 103.7 9.57758e-05 2297 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.30555e-06 6891 2 103.7 0.000112922 2297 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.62908e-06 6891 2 103.7 0.000106366 2297 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.26006e-06 6891 2 103.7 0.000113557 2297 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.2099e-06 6891 2 103.7 9.31472e-05 2297 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.45183e-06 6891 2 103.7 0.000142885 2297 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.10652e-06 6891 2 103.7 9.75412e-05 2297 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.24102e-06 6891 2 103.7 0.000109471 2297 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.21605e-06 6891 2 103.7 9.47169e-05 2297 5000000 5000000 -233.4298 80485.548 1.3394174 297.2542 120.48503 135.66175 0 0 19701.828 18239.791 -204.83328 -198689.57 -160491.81 4884.8394 Loop time of 56418.6 on 32 procs for 5000000 steps with 7811 atoms Performance: 7.657 ns/day, 3.134 hours/ns, 88.623 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18092 | 20002 | 25719 |1580.4 | 35.45 Bond | 8.8432 | 22.345 | 66.477 | 332.3 | 0.04 Kspace | 6358.2 | 12110 | 14061 |2050.0 | 21.47 Neigh | 1770.9 | 1775.8 | 1780 | 6.1 | 3.15 Comm | 2418.4 | 2486.3 | 2623 | 120.4 | 4.41 Output | 0.009454 | 0.011523 | 0.013423 | 1.1 | 0.00 Modify | 19792 | 19889 | 19942 | 32.6 | 35.25 Other | | 132.7 | | | 0.24 Nlocal: 244.094 ave 286 max 221 min Histogram: 6 4 6 5 4 2 1 0 1 3 Nghost: 6750.16 ave 7168 max 6450 min Histogram: 9 6 4 1 0 0 0 1 6 5 Neighs: 136516 ave 179742 max 117619 min Histogram: 7 6 7 5 3 0 0 0 0 4 Total # of neighbors = 4368511 Ave neighs/atom = 559.27679 Ave special neighs/atom = 1.9743951 Neighbor list builds = 240945 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) = 0.25671212 grid = 25 24 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0033834134 estimated relative force accuracy = 1.0189049e-05 using double precision KISS FFT 3d grid and FFT values/proc = 5415 1248 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 5000000 2 0.97 1.21605e-06 6891 2 103.7 9.47169e-05 2297 Per MPI rank memory allocation (min/avg/max) = 13.59 | 13.73 | 14.57 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 -232.46735 80485.548 1.3394174 297.2542 120.48503 135.66175 0 0 19701.828 18239.791 -204.83328 -198689.57 -160491.81 4884.8394 Loop time of 8.74209e-06 on 32 procs for 0 steps with 7811 atoms 113.3% 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 | | 8.742e-06 | | |100.00 Nlocal: 244.094 ave 286 max 221 min Histogram: 6 4 6 5 4 2 1 0 1 3 Nghost: 6750.16 ave 7168 max 6450 min Histogram: 9 6 4 1 0 0 0 1 6 5 Neighs: 136516 ave 179742 max 117619 min Histogram: 7 6 7 5 3 0 0 0 0 4 Total # of neighbors = 4368511 Ave neighs/atom = 559.27679 Ave special neighs/atom = 1.9743951 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: 27:12:28