#------------------------------------------------------------------------------- # 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 3728 = # 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_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 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25822755 grid = 32 40 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0031888792 estimated relative force accuracy = 9.6032151e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7429 2560 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 7 10 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 2.13148e-09 11184 2 103.7 2.3671e-07 3728 Per MPI rank memory allocation (min/avg/max) = 13.1 | 13.61 | 14.08 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-06 346.45168 130061.67 1.4001311 299.49429 295.56647 375.58239 0 0 34739.812 22310.997 -361.40299 -344972.21 -287250.25 8223.8803 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.42633e-06 11184 2 103.7 0.000111013 3728 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.18089e-06 11184 2 103.7 9.33699e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.43963e-06 11184 2 103.7 9.91268e-05 3728 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16009e-06 11184 2 103.7 0.000104562 3728 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.41641e-06 11184 2 103.7 0.000103154 3728 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.32776e-06 11184 2 103.7 9.11996e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.67458e-06 11184 2 103.7 0.000133321 3728 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.17087e-06 11184 2 103.7 9.91875e-05 3728 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.33331e-06 11184 2 103.7 0.000104692 3728 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.26214e-06 11184 2 103.7 9.98918e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.16463e-06 11184 2 103.7 9.64774e-05 3728 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.80313e-06 11184 2 103.7 0.000124748 3728 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.40994e-06 11184 2 103.7 0.000106515 3728 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.27024e-06 11184 2 103.7 0.000117982 3728 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.26544e-06 11184 2 103.7 9.32536e-05 3728 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.61851e-06 11184 2 103.7 0.000121378 3728 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.39613e-06 11184 2 103.7 9.60285e-05 3728 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.26135e-06 11184 2 103.7 8.84727e-05 3728 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.30748e-06 11184 2 103.7 0.000100053 3728 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.21738e-06 11184 2 103.7 9.05943e-05 3728 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.13324e-06 11184 2 103.7 8.8559e-05 3728 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.25395e-06 11184 2 103.7 9.4167e-05 3728 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.37987e-06 11184 2 103.7 8.74427e-05 3728 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.43597e-06 11184 2 103.7 0.000102425 3728 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.18968e-06 11184 2 103.7 9.16841e-05 3728 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.34427e-06 11184 2 103.7 0.000105207 3728 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.15049e-06 11184 2 103.7 9.5221e-05 3728 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.28667e-06 11184 2 103.7 9.87506e-05 3728 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.05246e-06 11184 2 103.7 9.20104e-05 3728 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26646e-06 11184 2 103.7 0.000119865 3728 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.34301e-06 11184 2 103.7 0.000108301 3728 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.32848e-06 11184 2 103.7 0.000104014 3728 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.22177e-06 11184 2 103.7 0.000100907 3728 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.09051e-06 11184 2 103.7 0.000103457 3728 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.33655e-06 11184 2 103.7 9.15498e-05 3728 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.23916e-06 11184 2 103.7 9.66421e-05 3728 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.39381e-06 11184 2 103.7 9.95394e-05 3728 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.60113e-06 11184 2 103.7 0.00010472 3728 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.12901e-06 11184 2 103.7 0.000113583 3728 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.51362e-06 11184 2 103.7 0.000112707 3728 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.27388e-06 11184 2 103.7 9.21785e-05 3728 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.3727e-06 11184 2 103.7 0.000112634 3728 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.41372e-06 11184 2 103.7 0.00010121 3728 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.21102e-06 11184 2 103.7 9.94351e-05 3728 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.33344e-06 11184 2 103.7 9.219e-05 3728 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.31545e-06 11184 2 103.7 9.8385e-05 3728 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.4768e-06 11184 2 103.7 0.000119372 3728 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.06842e-06 11184 2 103.7 8.84839e-05 3728 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.27299e-06 11184 2 103.7 9.01683e-05 3728 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.45793e-06 11184 2 103.7 0.000117187 3728 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.48738e-06 11184 2 103.7 0.000124046 3728 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.23494e-06 11184 2 103.7 9.30575e-05 3728 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.2671e-06 11184 2 103.7 0.000102858 3728 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.35926e-06 11184 2 103.7 9.3428e-05 3728 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.22219e-06 11184 2 103.7 8.95396e-05 3728 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.33804e-06 11184 2 103.7 9.80122e-05 3728 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.22006e-06 11184 2 103.7 9.65542e-05 3728 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.16842e-06 11184 2 103.7 0.000102475 3728 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.25392e-06 11184 2 103.7 9.0106e-05 3728 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.4424e-06 11184 2 103.7 0.000106258 3728 3000000 3000000 902.24016 130061.67 1.4001311 296.44905 279.69716 368.86739 0 0 35210.324 21840.742 -361.40299 -344943.21 -287243.58 8140.2604 Loop time of 52134.8 on 32 procs for 3000000 steps with 12941 atoms Performance: 4.972 ns/day, 4.827 hours/ns, 57.543 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17454 | 19992 | 24994 |1985.4 | 38.35 Bond | 5.5245 | 23.056 | 58.011 | 400.0 | 0.04 Kspace | 5701.6 | 10753 | 13332 |2732.4 | 20.62 Neigh | 1858.9 | 1862.7 | 1866.9 | 4.9 | 3.57 Comm | 1732.1 | 1820.6 | 1920.1 | 136.7 | 3.49 Output | 0.013038 | 0.015862 | 0.018495 | 1.3 | 0.00 Modify | 17496 | 17571 | 17630 | 36.5 | 33.70 Other | | 112.6 | | | 0.22 Nlocal: 404.406 ave 474 max 361 min Histogram: 5 6 7 6 0 0 0 0 3 5 Nghost: 8167.72 ave 8403 max 7599 min Histogram: 5 3 0 0 0 0 0 0 11 13 Neighs: 232249 ave 296774 max 193017 min Histogram: 6 9 3 6 0 0 0 0 1 7 Total # of neighbors = 7431973 Ave neighs/atom = 574.29665 Ave special neighs/atom = 2.0236458 Neighbor list builds = 149239 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) = 0.25822755 grid = 32 40 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0031888792 estimated relative force accuracy = 9.6032151e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7429 2560 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 1.4424e-06 11184 2 103.7 0.000106258 3728 Per MPI rank memory allocation (min/avg/max) = 14.63 | 14.91 | 15.6 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 903.27527 130061.67 1.4001311 296.44905 279.69716 368.86739 0 0 35210.324 21840.742 -361.40299 -344943.21 -287243.58 8140.2604 Loop time of 1.2534e-05 on 32 procs for 0 steps with 12941 atoms 114.7% 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 | | 1.253e-05 | | |100.00 Nlocal: 404.406 ave 474 max 361 min Histogram: 5 6 7 6 0 0 0 0 3 5 Nghost: 8167.72 ave 8403 max 7599 min Histogram: 5 3 0 0 0 0 0 0 11 13 Neighs: 232249 ave 296774 max 193017 min Histogram: 6 9 3 6 0 0 0 0 1 7 Total # of neighbors = 7431973 Ave neighs/atom = 574.29665 Ave special neighs/atom = 2.0236458 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: 25:11:54