#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3275 = # 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 3000000 2.5.restart dump trj all custom 30000 2.5.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 30000 1 30000 v_etotal v_pe v_ke file 2.5.energies.txt dump sci all custom 300000 2.5.xyz id mol type q xs ys zs compute group_29 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_29 all ave/time 1 100 100 c_group_29 file 2.5_GroupInteractions_Layer1_Layer2_29.out compute group_30 subset_Layer1 group/group subset_Layer2 pair yes kspace no fix group_30 all ave/time 1 100 100 c_group_30 file 2.5_GroupInteractions_Layer1_Layer2_30.out compute group_31 subset_Layer1 group/group subset_Layer2 pair no kspace yes fix group_31 all ave/time 1 100 100 c_group_31 file 2.5_GroupInteractions_Layer1_Layer2_31.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25493894 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0037055622 estimated relative force accuracy = 1.115919e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 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) 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 = 7 5 15 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard (2) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (3) 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 1 0.97 9.07829e-13 9825 1 103.7 7.58149e-11 3275 Per MPI rank memory allocation (min/avg/max) = 14.24 | 14.54 | 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 0 1e-06 -7298.1718 143778.81 1.3074423 301.7083 47.728228 60.779262 0 0 36858.051 -72958.74 -318.5841 -317338.32 -353330.5 7120.9356 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.26393e-06 9825 1 103.7 9.76995e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.35953e-06 9825 1 103.7 0.000104717 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.12605e-06 9825 1 103.7 9.42691e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.45353e-06 9825 1 103.7 9.81273e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.18284e-06 9825 1 103.7 0.000102558 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.12297e-06 9825 1 103.7 8.73017e-05 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.24079e-06 9825 1 103.7 8.84821e-05 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.44428e-06 9825 1 103.7 0.000109966 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.07975e-06 9825 1 103.7 8.95344e-05 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.23787e-06 9825 1 103.7 0.000109423 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.65776e-06 9825 1 103.7 0.000125715 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.15894e-06 9825 1 103.7 9.3908e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.26562e-06 9825 1 103.7 9.48274e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.24565e-06 9825 1 103.7 9.94321e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.30388e-06 9825 1 103.7 0.000106596 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.64539e-06 9825 1 103.7 0.000127986 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.15626e-06 9825 1 103.7 9.58664e-05 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.14823e-06 9825 1 103.7 9.73445e-05 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.23619e-06 9825 1 103.7 0.000120964 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.13794e-06 9825 1 103.7 0.000102305 3275 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.2275e-06 9825 1 103.7 9.60262e-05 3275 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.26429e-06 9825 1 103.7 8.80556e-05 3275 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.16771e-06 9825 1 103.7 9.01071e-05 3275 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.09721e-06 9825 1 103.7 0.000102397 3275 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.24353e-06 9825 1 103.7 0.000103659 3275 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.16196e-06 9825 1 103.7 0.000103499 3275 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.10393e-06 9825 1 103.7 8.89259e-05 3275 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.5113e-06 9825 1 103.7 0.000101058 3275 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.38312e-06 9825 1 103.7 0.000103583 3275 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.21835e-06 9825 1 103.7 9.22294e-05 3275 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.15961e-06 9825 1 103.7 0.000102755 3275 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.39158e-06 9825 1 103.7 0.000121276 3275 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.43083e-06 9825 1 103.7 9.86526e-05 3275 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.45243e-06 9825 1 103.7 0.000110759 3275 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.47003e-06 9825 1 103.7 0.000107619 3275 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.35839e-06 9825 1 103.7 0.000108366 3275 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.21205e-06 9825 1 103.7 9.32022e-05 3275 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.11696e-06 9825 1 103.7 9.60634e-05 3275 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.19963e-06 9825 1 103.7 9.95046e-05 3275 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.43318e-06 9825 1 103.7 0.000117171 3275 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.39415e-06 9825 1 103.7 0.000110861 3275 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.64942e-06 9825 1 103.7 0.000146167 3275 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.10128e-06 9825 1 103.7 9.12744e-05 3275 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.5143e-06 9825 1 103.7 0.00011491 3275 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.10279e-06 9825 1 103.7 9.61266e-05 3275 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.15932e-06 9825 1 103.7 9.93859e-05 3275 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.10325e-06 9825 1 103.7 9.9031e-05 3275 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.41715e-06 9825 1 103.7 0.000101792 3275 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.34301e-06 9825 1 103.7 9.52603e-05 3275 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.28949e-06 9825 1 103.7 8.99125e-05 3275 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.12596e-06 9825 1 103.7 0.000102683 3275 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.31408e-06 9825 1 103.7 0.000100097 3275 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.37753e-06 9825 1 103.7 0.000104677 3275 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.39489e-06 9825 1 103.7 0.000100152 3275 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.1784e-06 9825 1 103.7 9.17964e-05 3275 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.13308e-06 9825 1 103.7 0.000105059 3275 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.10614e-06 9825 1 103.7 9.87077e-05 3275 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.32841e-06 9825 1 103.7 0.000124623 3275 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.16159e-06 9825 1 103.7 9.94782e-05 3275 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.09311e-06 9825 1 103.7 9.4396e-05 3275 3000000 3000000 -7295.268 143778.81 1.3074423 299.3624 35.91463 55.153252 0 0 37080.463 -73381.013 -318.5841 -317340.62 -353550.1 7065.5676 Loop time of 53462.4 on 32 procs for 3000000 steps with 12250 atoms Performance: 4.848 ns/day, 4.950 hours/ns, 56.114 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 | 12958 | 15493 | 17231 |1037.4 | 28.98 Bond | 4.1036 | 9.1838 | 18.672 | 124.5 | 0.02 Kspace | 5914.1 | 7670.3 | 10218 |1492.4 | 14.35 Neigh | 928.02 | 929.14 | 930.69 | 2.0 | 1.74 Comm | 1819.9 | 1918.7 | 1980.9 | 117.7 | 3.59 Output | 0.099145 | 0.12859 | 0.15729 | 4.9 | 0.00 Modify | 27296 | 27335 | 27399 | 20.9 | 51.13 Other | | 107 | | | 0.20 Nlocal: 382.812 ave 415 max 345 min Histogram: 1 2 4 3 1 7 4 4 5 1 Nghost: 7264.84 ave 7525 max 6956 min Histogram: 4 4 0 2 4 2 0 6 6 4 Neighs: 187544 ave 209861 max 152527 min Histogram: 3 1 4 0 1 4 2 7 6 4 Total # of neighbors = 6001407 Ave neighs/atom = 489.91078 Ave special neighs/atom = 1.6481633 Neighbor list builds = 149691 Dangerous builds = 0 undump trj unfix trjE 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) = 0.25493894 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0037055622 estimated relative force accuracy = 1.115919e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 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) 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 1 0.97 1.09311e-06 9825 1 103.7 9.4396e-05 3275 Per MPI rank memory allocation (min/avg/max) = 14.5 | 15.55 | 15.94 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 -7294.4425 143778.81 1.3074423 299.3624 35.91463 55.153252 0 0 37080.463 -73381.013 -318.5841 -317340.62 -353550.1 7065.5676 Loop time of 1.19176e-05 on 32 procs for 0 steps with 12250 atoms 108.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.192e-05 | | |100.00 Nlocal: 382.812 ave 415 max 345 min Histogram: 1 2 4 3 1 7 4 4 5 1 Nghost: 7264.84 ave 7525 max 6956 min Histogram: 4 4 0 2 4 2 0 6 6 4 Neighs: 187544 ave 209861 max 152527 min Histogram: 3 1 4 0 1 4 2 7 6 4 Total # of neighbors = 6001407 Ave neighs/atom = 489.91078 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_29 unfix group_29 uncompute group_30 unfix group_30 uncompute group_31 unfix group_31 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 17:25:23