#------------------------------------------------------------------------------- # 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 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 7.1132e-13 9825 1 103.7 8.24087e-11 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.26 | 13.64 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 -7562.0612 143778.81 1.3074423 301.09108 33.545652 62.832036 0 0 36721.171 -72798.823 -318.5841 -317330.15 -353311.42 7106.3679 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.21831e-06 9825 1 103.7 9.22822e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.18387e-06 9825 1 103.7 9.35869e-05 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.06292e-06 9825 1 103.7 9.06155e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.37893e-06 9825 1 103.7 9.41635e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.08846e-06 9825 1 103.7 9.17771e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.28636e-06 9825 1 103.7 0.00010075 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.30071e-06 9825 1 103.7 9.79433e-05 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.28524e-06 9825 1 103.7 9.44212e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.19389e-06 9825 1 103.7 9.32293e-05 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.19391e-06 9825 1 103.7 9.38701e-05 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.12172e-06 9825 1 103.7 9.74301e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.2586e-06 9825 1 103.7 9.28025e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.4768e-06 9825 1 103.7 0.000118787 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.17702e-06 9825 1 103.7 9.03539e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.12062e-06 9825 1 103.7 9.59692e-05 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.54669e-06 9825 1 103.7 0.000106697 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.30175e-06 9825 1 103.7 0.000103581 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.17311e-06 9825 1 103.7 9.21302e-05 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.26519e-06 9825 1 103.7 0.000101263 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.27397e-06 9825 1 103.7 9.63448e-05 3275 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.31752e-06 9825 1 103.7 8.95117e-05 3275 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.49646e-06 9825 1 103.7 0.000107378 3275 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.2835e-06 9825 1 103.7 0.00010176 3275 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.28213e-06 9825 1 103.7 8.96848e-05 3275 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.24299e-06 9825 1 103.7 0.000100562 3275 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.18981e-06 9825 1 103.7 9.38307e-05 3275 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.74104e-06 9825 1 103.7 0.000105039 3275 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.36093e-06 9825 1 103.7 9.14269e-05 3275 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.59275e-06 9825 1 103.7 0.000113566 3275 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.23225e-06 9825 1 103.7 8.99363e-05 3275 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.44414e-06 9825 1 103.7 0.000103712 3275 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.32949e-06 9825 1 103.7 9.97385e-05 3275 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.16068e-06 9825 1 103.7 9.33789e-05 3275 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.29545e-06 9825 1 103.7 9.36186e-05 3275 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.3082e-06 9825 1 103.7 9.48168e-05 3275 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.36836e-06 9825 1 103.7 9.44374e-05 3275 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.32201e-06 9825 1 103.7 9.61507e-05 3275 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.25479e-06 9825 1 103.7 9.20411e-05 3275 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.37114e-06 9825 1 103.7 9.80624e-05 3275 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.14828e-06 9825 1 103.7 9.42864e-05 3275 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.26592e-06 9825 1 103.7 0.000101699 3275 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.17396e-06 9825 1 103.7 9.79427e-05 3275 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.2723e-06 9825 1 103.7 9.8353e-05 3275 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.29276e-06 9825 1 103.7 9.5729e-05 3275 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.16748e-06 9825 1 103.7 9.15045e-05 3275 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.37646e-06 9825 1 103.7 0.000104525 3275 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.50061e-06 9825 1 103.7 0.000104732 3275 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.48935e-06 9825 1 103.7 0.000113581 3275 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.39956e-06 9825 1 103.7 9.11926e-05 3275 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.17104e-06 9825 1 103.7 8.89849e-05 3275 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.14779e-06 9825 1 103.7 9.25586e-05 3275 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.22865e-06 9825 1 103.7 0.000102564 3275 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.28003e-06 9825 1 103.7 0.000116106 3275 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.13046e-06 9825 1 103.7 0.000104747 3275 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.17563e-06 9825 1 103.7 8.98985e-05 3275 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.63687e-06 9825 1 103.7 0.000119151 3275 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.12028e-06 9825 1 103.7 0.000103144 3275 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.2692e-06 9825 1 103.7 9.2697e-05 3275 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.15636e-06 9825 1 103.7 0.000101611 3275 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.20435e-06 9825 1 103.7 9.02386e-05 3275 3000000 3000000 -7431.6721 143778.81 1.3074423 301.64504 36.232165 51.00201 0 0 36907.608 -73172.054 -318.5841 -317345.24 -353522.45 7119.4425 Loop time of 53535.4 on 32 procs for 3000000 steps with 12250 atoms Performance: 4.842 ns/day, 4.957 hours/ns, 56.038 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 | 12812 | 15500 | 17155 |1032.8 | 28.95 Bond | 4.0381 | 9.1713 | 16.915 | 128.5 | 0.02 Kspace | 5942.1 | 7622.8 | 10334 |1492.8 | 14.24 Neigh | 922.31 | 924.04 | 926.11 | 3.4 | 1.73 Comm | 1830.6 | 1921.3 | 1971.3 | 107.0 | 3.59 Output | 0.011176 | 0.013919 | 0.016574 | 1.4 | 0.00 Modify | 27418 | 27450 | 27504 | 18.2 | 51.27 Other | | 108.3 | | | 0.20 Nlocal: 382.812 ave 414 max 353 min Histogram: 3 3 3 3 3 5 4 4 1 3 Nghost: 7253.72 ave 7507 max 6965 min Histogram: 4 3 5 0 1 2 3 6 3 5 Neighs: 187524 ave 213807 max 155661 min Histogram: 3 2 3 1 1 3 7 8 3 1 Total # of neighbors = 6000753 Ave neighs/atom = 489.85739 Ave special neighs/atom = 1.6481633 Neighbor list builds = 149527 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) = 0.25493894 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 1.20435e-06 9825 1 103.7 9.02386e-05 3275 Per MPI rank memory allocation (min/avg/max) = 14.5 | 15.52 | 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 -7430.8557 143778.81 1.3074423 301.64504 36.232165 51.00201 0 0 36907.608 -73172.054 -318.5841 -317345.24 -353522.45 7119.4425 Loop time of 1.4506e-05 on 32 procs for 0 steps with 12250 atoms 110.5% 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 | | 1.451e-05 | | |100.00 Nlocal: 382.812 ave 414 max 353 min Histogram: 3 3 3 3 3 5 4 4 1 3 Nghost: 7253.72 ave 7507 max 6965 min Histogram: 4 3 5 0 1 2 3 6 3 5 Neighs: 187524 ave 213807 max 155661 min Histogram: 3 2 3 1 1 3 7 8 3 1 Total # of neighbors = 6000753 Ave neighs/atom = 489.85739 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: 17:25:41