#------------------------------------------------------------------------------- # 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 1937 = # 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) = 0.25681581 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0032470589 estimated relative force accuracy = 9.7784213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5600 1568 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 = 5 5 14 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 1.64217e-09 5811 2 103.7 1.81757e-07 1937 Per MPI rank memory allocation (min/avg/max) = 12.31 | 12.8 | 13.1 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-06 905.48142 100321.18 1.466808 294.98512 31.776601 41.259748 0 0 25798.666 -42598.561 -234.85282 -212476.74 -229203.6 5023.4102 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.25141e-06 5811 2 103.7 0.000115599 1937 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.11133e-06 5811 2 103.7 9.02439e-05 1937 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.30779e-06 5811 2 103.7 0.000105853 1937 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.09199e-06 5811 2 103.7 9.49275e-05 1937 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.04838e-06 5811 2 103.7 9.12981e-05 1937 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.65393e-06 5811 2 103.7 0.000115795 1937 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.26553e-06 5811 2 103.7 0.000110359 1937 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.09351e-06 5811 2 103.7 9.16242e-05 1937 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.11326e-06 5811 2 103.7 9.10789e-05 1937 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.27851e-06 5811 2 103.7 9.98497e-05 1937 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.1883e-06 5811 2 103.7 8.88107e-05 1937 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.31321e-06 5811 2 103.7 9.21939e-05 1937 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.02649e-06 5811 2 103.7 8.72111e-05 1937 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20191e-06 5811 2 103.7 9.92936e-05 1937 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.43191e-06 5811 2 103.7 9.71123e-05 1937 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.13722e-06 5811 2 103.7 9.9589e-05 1937 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.42609e-06 5811 2 103.7 0.00010014 1937 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.17575e-06 5811 2 103.7 9.11991e-05 1937 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.19529e-06 5811 2 103.7 0.000102952 1937 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.93228e-06 5811 2 103.7 0.000129755 1937 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.1978e-06 5811 2 103.7 8.95648e-05 1937 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.56004e-06 5811 2 103.7 0.000106287 1937 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.32271e-06 5811 2 103.7 0.000102141 1937 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.18463e-06 5811 2 103.7 8.82419e-05 1937 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17861e-06 5811 2 103.7 0.000112218 1937 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.15909e-06 5811 2 103.7 8.93305e-05 1937 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.38164e-06 5811 2 103.7 9.09648e-05 1937 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.56014e-06 5811 2 103.7 0.000125577 1937 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.0411e-06 5811 2 103.7 9.67337e-05 1937 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.14166e-06 5811 2 103.7 0.00010509 1937 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.15849e-06 5811 2 103.7 0.000100315 1937 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.40413e-06 5811 2 103.7 0.000156901 1937 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.27059e-06 5811 2 103.7 9.74332e-05 1937 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.19681e-06 5811 2 103.7 9.05529e-05 1937 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.40135e-06 5811 2 103.7 0.000112083 1937 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10653e-06 5811 2 103.7 9.49402e-05 1937 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.3419e-06 5811 2 103.7 9.76916e-05 1937 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.01242e-06 5811 2 103.7 9.50908e-05 1937 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.24776e-06 5811 2 103.7 8.80485e-05 1937 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.46623e-06 5811 2 103.7 0.000109335 1937 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.40041e-06 5811 2 103.7 9.2693e-05 1937 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.17178e-06 5811 2 103.7 9.07932e-05 1937 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.54029e-06 5811 2 103.7 0.000119001 1937 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.15247e-06 5811 2 103.7 9.28057e-05 1937 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.10541e-06 5811 2 103.7 9.22132e-05 1937 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.07075e-06 5811 2 103.7 8.94726e-05 1937 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.36667e-06 5811 2 103.7 0.000100817 1937 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.2144e-06 5811 2 103.7 0.000102447 1937 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.18684e-06 5811 2 103.7 9.0917e-05 1937 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.30645e-06 5811 2 103.7 9.18705e-05 1937 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.34185e-06 5811 2 103.7 9.63258e-05 1937 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.47106e-06 5811 2 103.7 0.000118368 1937 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.05755e-06 5811 2 103.7 9.7103e-05 1937 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.81481e-06 5811 2 103.7 0.000167841 1937 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.34573e-06 5811 2 103.7 9.42096e-05 1937 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.21908e-06 5811 2 103.7 0.000100639 1937 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.62813e-06 5811 2 103.7 0.000109064 1937 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.04362e-06 5811 2 103.7 8.96889e-05 1937 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.08397e-06 5811 2 103.7 0.000104223 1937 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.15517e-06 5811 2 103.7 0.000104253 1937 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.22471e-06 5811 2 103.7 8.98159e-05 1937 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.24235e-06 5811 2 103.7 8.97593e-05 1937 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.14861e-06 5811 2 103.7 9.86826e-05 1937 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.66365e-06 5811 2 103.7 0.000118733 1937 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.25554e-06 5811 2 103.7 8.41491e-05 1937 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.12063e-06 5811 2 103.7 9.05672e-05 1937 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.51431e-06 5811 2 103.7 9.67579e-05 1937 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.24925e-06 5811 2 103.7 0.000102846 1937 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.09757e-06 5811 2 103.7 9.16247e-05 1937 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.38371e-06 5811 2 103.7 0.0001168 1937 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.25976e-06 5811 2 103.7 9.66747e-05 1937 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.255e-06 5811 2 103.7 0.000130792 1937 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.37884e-06 5811 2 103.7 9.46326e-05 1937 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.19652e-06 5811 2 103.7 9.53434e-05 1937 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.07332e-06 5811 2 103.7 0.000108185 1937 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.52101e-06 5811 2 103.7 8.79666e-05 1937 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.41594e-06 5811 2 103.7 0.000103743 1937 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.10384e-06 5811 2 103.7 8.6222e-05 1937 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 2.21021e-06 5811 2 103.7 0.000141347 1937 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.18865e-06 5811 2 103.7 0.000100104 1937 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.52521e-06 5811 2 103.7 0.00013576 1937 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.31835e-06 5811 2 103.7 0.000104133 1937 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.10473e-06 5811 2 103.7 8.70149e-05 1937 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.11826e-06 5811 2 103.7 8.67441e-05 1937 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.18247e-06 5811 2 103.7 0.000124141 1937 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.32421e-06 5811 2 103.7 8.97103e-05 1937 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.29343e-06 5811 2 103.7 8.84495e-05 1937 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.28428e-06 5811 2 103.7 9.71885e-05 1937 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.15209e-06 5811 2 103.7 0.000102886 1937 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.53732e-06 5811 2 103.7 9.78811e-05 1937 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.27678e-06 5811 2 103.7 9.86564e-05 1937 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.87092e-06 5811 2 103.7 0.000139826 1937 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.22901e-06 5811 2 103.7 9.40557e-05 1937 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.22458e-06 5811 2 103.7 0.000102448 1937 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.2462e-06 5811 2 103.7 8.97647e-05 1937 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.11487e-06 5811 2 103.7 9.64722e-05 1937 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.40882e-06 5811 2 103.7 0.000113994 1937 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.2534e-06 5811 2 103.7 9.24682e-05 1937 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.39792e-06 5811 2 103.7 0.000103639 1937 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.63656e-06 5811 2 103.7 0.000113941 1937 5000000 5000000 642.90492 100321.18 1.466808 297.04497 24.031695 49.267906 0 0 25664.208 -42494.038 -234.85282 -212466.33 -229222.86 5058.4881 Loop time of 51354.9 on 32 procs for 5000000 steps with 7651 atoms Performance: 8.412 ns/day, 2.853 hours/ns, 97.362 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 | 4893.3 | 16748 | 23644 |5595.2 | 32.61 Bond | 5.4007 | 12.303 | 25.406 | 168.9 | 0.02 Kspace | 7372.2 | 14318 | 26220 |6093.0 | 27.88 Neigh | 1747.5 | 1753.1 | 1763.8 | 12.4 | 3.41 Comm | 1650.1 | 2113.5 | 2340.6 | 508.4 | 4.12 Output | 0.0085633 | 0.010597 | 0.01251 | 1.1 | 0.00 Modify | 16133 | 16308 | 16654 | 141.9 | 31.76 Other | | 102.5 | | | 0.20 Nlocal: 239.094 ave 310 max 114 min Histogram: 8 0 0 0 0 2 2 3 7 10 Nghost: 5659.28 ave 7047 max 4117 min Histogram: 8 0 0 8 0 0 0 8 0 8 Neighs: 112595 ave 161929 max 29222 min Histogram: 8 0 0 0 3 1 2 2 3 13 Total # of neighbors = 3603027 Ave neighs/atom = 470.92236 Ave special neighs/atom = 1.5765259 Neighbor list builds = 239830 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) = 0.25681581 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0032470589 estimated relative force accuracy = 9.7784213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5600 1568 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.63656e-06 5811 2 103.7 0.000113941 1937 Per MPI rank memory allocation (min/avg/max) = 12.69 | 13.51 | 13.86 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 643.3877 100321.18 1.466808 297.04497 24.031695 49.267906 0 0 25664.208 -42494.038 -234.85282 -212466.33 -229222.86 5058.4881 Loop time of 7.18472e-06 on 32 procs for 0 steps with 7651 atoms 119.6% 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 | | 7.185e-06 | | |100.00 Nlocal: 239.094 ave 310 max 114 min Histogram: 8 0 0 0 0 2 2 3 7 10 Nghost: 5659.28 ave 7047 max 4117 min Histogram: 8 0 0 8 0 0 0 8 0 8 Neighs: 112595 ave 161929 max 29222 min Histogram: 8 0 0 0 3 1 2 2 3 13 Total # of neighbors = 3603027 Ave neighs/atom = 470.92236 Ave special neighs/atom = 1.5765259 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: 25:02:01