#------------------------------------------------------------------------------- # Stage 2.6: NVT integration for 2 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3488 = # 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 200000 200000 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 2.6_averages.txt off 1 fix 3 movable ave/time 200 1 200 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 2.6_instantaneous.txt restart 2000000 2.6.restart dump sci all custom 200000 2.6.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 2.6_GroupInteractions_Layer1_Layer2_1.out timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32529392 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0036767963 estimated relative force accuracy = 1.1072563e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 9 9 9 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 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 SHAKE stats (type/ave/delta/count) on step 0 1 0.97 1.36757e-12 10464 2 103.7 7.91118e-11 3488 Per MPI rank memory allocation (min/avg/max) = 12.91 | 13.29 | 13.35 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 -7.4108666 122022.49 1.3680167 297.26602 239.97773 287.77678 0 0 31467.828 105044.76 -644.18917 -392883.92 -255843.57 7524.7063 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.16284e-06 10464 2 103.7 0.000100828 3488 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.13921e-06 10464 2 103.7 9.44572e-05 3488 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.36229e-06 10464 2 103.7 0.000107311 3488 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.07226e-06 10464 2 103.7 9.19437e-05 3488 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.55221e-06 10464 2 103.7 0.000113102 3488 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.38778e-06 10464 2 103.7 9.40113e-05 3488 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.24201e-06 10464 2 103.7 9.73777e-05 3488 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.09267e-06 10464 2 103.7 9.02556e-05 3488 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.35723e-06 10464 2 103.7 0.000101773 3488 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.57611e-06 10464 2 103.7 0.000101977 3488 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.40693e-06 10464 2 103.7 9.05566e-05 3488 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.10998e-06 10464 2 103.7 9.91463e-05 3488 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.33926e-06 10464 2 103.7 0.000103144 3488 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.30771e-06 10464 2 103.7 9.67303e-05 3488 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.21582e-06 10464 2 103.7 8.89533e-05 3488 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.27404e-06 10464 2 103.7 9.51518e-05 3488 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.42464e-06 10464 2 103.7 0.000111962 3488 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.43338e-06 10464 2 103.7 0.000106448 3488 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.29581e-06 10464 2 103.7 0.000103344 3488 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.26199e-06 10464 2 103.7 0.000105167 3488 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.7032e-06 10464 2 103.7 0.000150137 3488 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.45195e-06 10464 2 103.7 9.72051e-05 3488 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.28274e-06 10464 2 103.7 9.46351e-05 3488 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.10583e-06 10464 2 103.7 9.48264e-05 3488 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.10595e-06 10464 2 103.7 8.7142e-05 3488 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.10972e-06 10464 2 103.7 9.92995e-05 3488 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.33909e-06 10464 2 103.7 9.38272e-05 3488 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.3847e-06 10464 2 103.7 9.65212e-05 3488 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.17515e-06 10464 2 103.7 8.96544e-05 3488 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.36369e-06 10464 2 103.7 9.10077e-05 3488 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.37066e-06 10464 2 103.7 9.53748e-05 3488 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.31093e-06 10464 2 103.7 0.000101895 3488 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.03628e-06 10464 2 103.7 9.00402e-05 3488 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.36932e-06 10464 2 103.7 0.000103418 3488 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.35323e-06 10464 2 103.7 9.23852e-05 3488 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.29843e-06 10464 2 103.7 0.000105402 3488 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.3469e-06 10464 2 103.7 9.67502e-05 3488 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.47857e-06 10464 2 103.7 0.000110541 3488 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.29977e-06 10464 2 103.7 9.58896e-05 3488 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.24146e-06 10464 2 103.7 0.000104848 3488 2000000 2000000 -292.25089 122022.49 1.3680167 297.02038 207.94926 307.46515 0 0 31207.246 105144.04 -644.18917 -392877.58 -256010.89 7518.4885 Loop time of 25171.7 on 32 procs for 2000000 steps with 11981 atoms Performance: 6.865 ns/day, 3.496 hours/ns, 79.454 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5223.3 | 6018.3 | 7491.3 | 984.2 | 23.91 Bond | 3.2504 | 12.908 | 32.936 | 269.9 | 0.05 Kspace | 5206.6 | 6706.1 | 7509.1 | 946.6 | 26.64 Neigh | 425.32 | 426.56 | 427.7 | 3.6 | 1.69 Comm | 881.02 | 926.73 | 970.69 | 82.3 | 3.68 Output | 0.01307 | 0.015745 | 0.018267 | 1.3 | 0.00 Modify | 10995 | 11023 | 11048 | 16.1 | 43.79 Other | | 58.57 | | | 0.23 Nlocal: 374.406 ave 440 max 335 min Histogram: 3 7 10 3 1 0 0 4 2 2 Nghost: 5506.34 ave 5629 max 5240 min Histogram: 7 1 0 0 0 0 0 2 11 11 Neighs: 117286 ave 150407 max 99061 min Histogram: 5 6 9 3 1 0 0 1 5 2 Total # of neighbors = 3753155 Ave neighs/atom = 313.25891 Ave special neighs/atom = 1.9988315 Neighbor list builds = 99098 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.6.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) = 0.32529392 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0036767963 estimated relative force accuracy = 1.1072563e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 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 2000000 1 0.97 1.24146e-06 10464 2 103.7 0.000104848 3488 Per MPI rank memory allocation (min/avg/max) = 13.99 | 14.06 | 14.12 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 2000000 2000000 -291.07592 122022.49 1.3680167 297.02038 207.94926 307.46515 0 0 31207.246 105144.04 -644.18917 -392877.58 -256010.89 7518.4885 Loop time of 1.20357e-05 on 32 procs for 0 steps with 11981 atoms 109.1% 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 | | 1.204e-05 | | |100.00 Nlocal: 374.406 ave 440 max 335 min Histogram: 3 7 10 3 1 0 0 4 2 2 Nghost: 5506.34 ave 5629 max 5240 min Histogram: 7 1 0 0 0 0 0 2 11 11 Neighs: 117286 ave 150407 max 99061 min Histogram: 5 6 9 3 1 0 0 1 5 2 Total # of neighbors = 3753155 Ave neighs/atom = 313.25891 Ave special neighs/atom = 1.9988315 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: 17:45:49