#------------------------------------------------------------------------------- # 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 2009 = # 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) = 0.2565108 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0032176618 estimated relative force accuracy = 9.6898931e-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 4.1167e-09 6027 2 103.7 4.56681e-07 2009 Per MPI rank memory allocation (min/avg/max) = 12.31 | 12.83 | 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 1017.2469 101772.3 1.4532829 295.40983 30.725731 33.305597 0 0 24188.697 -30969.501 -235.73777 -209717.36 -216434.13 5136.3098 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.25062e-06 6027 2 103.7 9.2109e-05 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.19826e-06 6027 2 103.7 8.85077e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.2149e-06 6027 2 103.7 9.8409e-05 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25643e-06 6027 2 103.7 0.000111234 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.29595e-06 6027 2 103.7 0.00010498 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.20603e-06 6027 2 103.7 9.74149e-05 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.22251e-06 6027 2 103.7 9.08972e-05 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.36493e-06 6027 2 103.7 0.000110461 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.14361e-06 6027 2 103.7 9.52443e-05 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.14533e-06 6027 2 103.7 9.77771e-05 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.32087e-06 6027 2 103.7 9.6655e-05 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.32393e-06 6027 2 103.7 0.000106544 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.46743e-06 6027 2 103.7 0.000118443 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.52794e-06 6027 2 103.7 0.000112683 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.20173e-06 6027 2 103.7 9.50964e-05 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.42537e-06 6027 2 103.7 9.22941e-05 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.32558e-06 6027 2 103.7 9.20076e-05 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.28705e-06 6027 2 103.7 9.87045e-05 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.30631e-06 6027 2 103.7 9.13703e-05 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.25226e-06 6027 2 103.7 8.83977e-05 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.50083e-06 6027 2 103.7 0.000107653 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.19064e-06 6027 2 103.7 0.000117714 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.09433e-06 6027 2 103.7 0.000108053 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.31354e-06 6027 2 103.7 0.000127364 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.06828e-06 6027 2 103.7 9.02675e-05 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.89851e-06 6027 2 103.7 0.000125199 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.52624e-06 6027 2 103.7 0.000117811 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.22527e-06 6027 2 103.7 0.000100919 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.19052e-06 6027 2 103.7 9.62444e-05 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.72088e-06 6027 2 103.7 0.000139734 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.6045e-06 6027 2 103.7 0.00011803 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.50548e-06 6027 2 103.7 0.000136144 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.23319e-06 6027 2 103.7 9.19693e-05 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.37977e-06 6027 2 103.7 0.000101131 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.15107e-06 6027 2 103.7 9.81965e-05 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.17664e-06 6027 2 103.7 0.000101495 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.07239e-06 6027 2 103.7 0.000107384 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.45926e-06 6027 2 103.7 9.40543e-05 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.19809e-06 6027 2 103.7 0.000101823 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.37267e-06 6027 2 103.7 9.30271e-05 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.21333e-06 6027 2 103.7 9.70136e-05 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.46406e-06 6027 2 103.7 0.0001227 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.85611e-06 6027 2 103.7 0.000126434 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.63772e-06 6027 2 103.7 0.00011006 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.4125e-06 6027 2 103.7 9.84685e-05 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.04109e-06 6027 2 103.7 9.37248e-05 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.62788e-06 6027 2 103.7 0.000120959 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.10924e-06 6027 2 103.7 0.000107199 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.27169e-06 6027 2 103.7 0.00012687 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.56931e-06 6027 2 103.7 0.000143332 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.21025e-06 6027 2 103.7 9.20354e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.6545e-06 6027 2 103.7 0.00012466 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.22292e-06 6027 2 103.7 0.000109027 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.21487e-06 6027 2 103.7 9.28152e-05 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.05597e-06 6027 2 103.7 9.22363e-05 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.29483e-06 6027 2 103.7 0.000101586 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.80344e-06 6027 2 103.7 0.00015074 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.12272e-06 6027 2 103.7 9.48037e-05 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.28595e-06 6027 2 103.7 0.00010529 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.24476e-06 6027 2 103.7 0.000146925 2009 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.248e-06 6027 2 103.7 9.92498e-05 2009 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.29702e-06 6027 2 103.7 9.48289e-05 2009 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.20132e-06 6027 2 103.7 9.69229e-05 2009 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.26954e-06 6027 2 103.7 8.95941e-05 2009 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.12671e-06 6027 2 103.7 9.40669e-05 2009 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.21926e-06 6027 2 103.7 9.28511e-05 2009 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.36105e-06 6027 2 103.7 0.000115059 2009 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.39454e-06 6027 2 103.7 0.000108321 2009 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.06155e-06 6027 2 103.7 9.02027e-05 2009 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.20451e-06 6027 2 103.7 0.000120752 2009 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.37476e-06 6027 2 103.7 9.26236e-05 2009 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.1777e-06 6027 2 103.7 9.96838e-05 2009 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.35706e-06 6027 2 103.7 0.000105826 2009 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.29941e-06 6027 2 103.7 9.78972e-05 2009 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.29921e-06 6027 2 103.7 9.75143e-05 2009 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.52184e-06 6027 2 103.7 0.000117621 2009 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.06431e-06 6027 2 103.7 9.65416e-05 2009 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.67633e-06 6027 2 103.7 0.000102901 2009 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.2667e-06 6027 2 103.7 9.23654e-05 2009 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.5968e-06 6027 2 103.7 0.000130911 2009 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.20848e-06 6027 2 103.7 0.000114185 2009 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.18782e-06 6027 2 103.7 0.000101476 2009 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.21217e-06 6027 2 103.7 9.8923e-05 2009 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.2101e-06 6027 2 103.7 0.000107406 2009 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.13801e-06 6027 2 103.7 9.36703e-05 2009 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.28636e-06 6027 2 103.7 8.85214e-05 2009 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.10225e-06 6027 2 103.7 0.000102909 2009 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.21189e-06 6027 2 103.7 0.000105953 2009 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.04224e-06 6027 2 103.7 9.55375e-05 2009 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.35999e-06 6027 2 103.7 8.81649e-05 2009 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.17823e-06 6027 2 103.7 0.000105141 2009 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.05598e-06 6027 2 103.7 9.03344e-05 2009 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.30149e-06 6027 2 103.7 0.000103383 2009 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.36914e-06 6027 2 103.7 0.000100266 2009 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.30051e-06 6027 2 103.7 0.000103271 2009 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.44187e-06 6027 2 103.7 9.73433e-05 2009 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.39655e-06 6027 2 103.7 0.000102143 2009 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.22017e-06 6027 2 103.7 0.000108619 2009 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.34973e-06 6027 2 103.7 9.07994e-05 2009 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.71602e-06 6027 2 103.7 0.000150406 2009 5000000 5000000 1179.5102 101772.3 1.4532829 293.0914 31.159321 42.338106 0 0 24314.758 -31183.065 -235.73777 -209718.57 -216513.38 5095.9992 Loop time of 52029.6 on 32 procs for 5000000 steps with 7843 atoms Performance: 8.303 ns/day, 2.891 hours/ns, 96.099 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 | 5061.3 | 17300 | 24175 |5594.7 | 33.25 Bond | 5.1188 | 12.142 | 23.451 | 164.7 | 0.02 Kspace | 7417.9 | 14352 | 26609 |6182.1 | 27.58 Neigh | 1807.7 | 1814 | 1825.3 | 11.9 | 3.49 Comm | 1706.5 | 2183.8 | 2420.1 | 507.3 | 4.20 Output | 0.0088462 | 0.010904 | 0.012829 | 1.1 | 0.00 Modify | 16081 | 16264 | 16615 | 144.1 | 31.26 Other | | 103.3 | | | 0.20 Nlocal: 245.094 ave 314 max 121 min Histogram: 8 0 0 0 0 3 2 0 10 9 Nghost: 5737.25 ave 7103 max 4022 min Histogram: 8 0 0 4 4 0 0 4 4 8 Neighs: 116712 ave 169699 max 29180 min Histogram: 8 0 0 0 1 3 3 1 3 13 Total # of neighbors = 3734768 Ave neighs/atom = 476.19125 Ave special neighs/atom = 1.5930129 Neighbor list builds = 241424 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) = 0.2565108 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0032176618 estimated relative force accuracy = 9.6898931e-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 1.71602e-06 6027 2 103.7 0.000150406 2009 Per MPI rank memory allocation (min/avg/max) = 12.7 | 13.52 | 13.87 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 1179.8787 101772.3 1.4532829 293.0914 31.159321 42.338106 0 0 24314.758 -31183.065 -235.73777 -209718.57 -216513.38 5095.9992 Loop time of 1.71281e-05 on 32 procs for 0 steps with 7843 atoms 104.4% 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 | | 1.713e-05 | | |100.00 Nlocal: 245.094 ave 314 max 121 min Histogram: 8 0 0 0 0 3 2 0 10 9 Nghost: 5737.25 ave 7103 max 4022 min Histogram: 8 0 0 4 4 0 0 4 4 8 Neighs: 116712 ave 169699 max 29180 min Histogram: 8 0 0 0 1 3 3 1 3 13 Total # of neighbors = 3734768 Ave neighs/atom = 476.19125 Ave special neighs/atom = 1.5930129 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: 25:27:55