#------------------------------------------------------------------------------- # Stage 2.4: 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 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # 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 2.4_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 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.994778 0.846786 8304 2 97.5168 60.4339 2768 Per MPI rank memory allocation (min/avg/max) = 12.63 | 12.8 | 13.33 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 17362.686 92859.489 1.3074058 428.55654 278.59238 280.75036 0 0 24869.279 102167.44 -448.40969 -271266.43 -143670.36 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.2469e-06 8304 2 103.7 0.000104568 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.56036e-06 8304 2 103.7 0.000135375 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.2464e-06 8304 2 103.7 9.92117e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.53585e-06 8304 2 103.7 0.000111609 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.40172e-06 8304 2 103.7 0.000112042 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.36467e-06 8304 2 103.7 0.000114521 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.09421e-06 8304 2 103.7 9.4233e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.16512e-06 8304 2 103.7 9.82611e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.18806e-06 8304 2 103.7 9.52929e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.54259e-06 8304 2 103.7 0.00011042 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.24686e-06 8304 2 103.7 9.2463e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.09512e-06 8304 2 103.7 9.02092e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.31828e-06 8304 2 103.7 0.000107346 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.25005e-06 8304 2 103.7 0.000100689 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.17508e-06 8304 2 103.7 9.86542e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.23489e-06 8304 2 103.7 9.79932e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.22362e-06 8304 2 103.7 0.000113308 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.51054e-06 8304 2 103.7 0.00012034 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.34766e-06 8304 2 103.7 8.7469e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.06936e-06 8304 2 103.7 9.07937e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.16844e-06 8304 2 103.7 9.0474e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.51791e-06 8304 2 103.7 0.000114457 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.14322e-06 8304 2 103.7 9.26207e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.01065e-06 8304 2 103.7 9.31726e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.3167e-06 8304 2 103.7 9.46531e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.41237e-06 8304 2 103.7 9.81274e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.27587e-06 8304 2 103.7 0.000111282 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.3001e-06 8304 2 103.7 0.000106619 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.37197e-06 8304 2 103.7 9.86833e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.38202e-06 8304 2 103.7 9.69828e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.2485e-06 8304 2 103.7 9.77769e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.09657e-06 8304 2 103.7 0.000101599 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.2011e-06 8304 2 103.7 9.38869e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.26302e-06 8304 2 103.7 8.91684e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.47921e-06 8304 2 103.7 9.92879e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.31136e-06 8304 2 103.7 0.000113494 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.36588e-06 8304 2 103.7 0.000107244 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.20788e-06 8304 2 103.7 0.000117071 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.572e-06 8304 2 103.7 9.34899e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.2766e-06 8304 2 103.7 9.38986e-05 2768 2000000 2000000 3189.048 92859.489 1.3074058 304.93285 40.384506 89.498931 0 0 22450.437 89562.679 -448.40969 -273843.16 -161700.16 5755.4518 Loop time of 11392.3 on 32 procs for 2000000 steps with 9101 atoms Performance: 15.168 ns/day, 1.582 hours/ns, 175.558 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4375 | 4816.9 | 5219.8 | 288.2 | 42.28 Bond | 2.0504 | 5.4488 | 9.4185 | 79.2 | 0.05 Kspace | 4259.8 | 4662.5 | 5101.4 | 292.6 | 40.93 Neigh | 320.23 | 321.28 | 321.83 | 2.1 | 2.82 Comm | 722.61 | 730.84 | 736.87 | 12.5 | 6.42 Output | 0.010535 | 0.012822 | 0.01495 | 1.2 | 0.00 Modify | 813.28 | 817.32 | 824.79 | 9.8 | 7.17 Other | | 37.88 | | | 0.33 Nlocal: 284.406 ave 307 max 257 min Histogram: 1 0 2 3 9 4 4 3 4 2 Nghost: 4984.66 ave 5040 max 4926 min Histogram: 1 7 1 3 4 2 4 4 2 4 Neighs: 88706.6 ave 97401 max 80162 min Histogram: 3 2 4 1 8 3 4 3 1 3 Total # of neighbors = 2838612 Ave neighs/atom = 311.90111 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98310 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.4.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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.2766e-06 8304 2 103.7 9.38986e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.68 | 13.15 | 13.34 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 3189.9735 92859.489 1.3074058 304.93285 40.384506 89.498931 0 0 22450.437 89562.679 -448.40969 -273843.16 -161700.16 5755.4518 Loop time of 1.15403e-05 on 32 procs for 0 steps with 9101 atoms 105.3% 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 | | 1.154e-05 | | |100.00 Nlocal: 284.406 ave 307 max 257 min Histogram: 1 0 2 3 9 4 4 3 4 2 Nghost: 4984.66 ave 5040 max 4926 min Histogram: 1 7 1 3 4 2 4 4 2 4 Neighs: 88706.6 ave 97401 max 80162 min Histogram: 3 2 4 1 8 3 4 3 1 3 Total # of neighbors = 2838612 Ave neighs/atom = 311.90111 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out