#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 200 ps 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 20000 20000 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 20 1 20 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 200000 2.4.restart dump sci all custom 20000 2.4.xyz id mol type q xs ys zs timestep 1 run 200000 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 0.994387 0.703974 8304 2 97.4104 23.2752 2768 Per MPI rank memory allocation (min/avg/max) = 12.63 | 12.84 | 13.22 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 8828.9298 92859.489 1.3074058 428.55654 109.80162 220.88661 0 0 23523.134 93391.742 -448.40969 -272779.85 -155534.29 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23455e-06 8304 2 103.7 0.000114895 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.37313e-06 8304 2 103.7 9.38675e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.21884e-06 8304 2 103.7 0.000103874 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.3532e-06 8304 2 103.7 9.05463e-05 2768 200000 200000 2450.5952 92859.489 1.3074058 297.68012 40.563187 82.868926 0 0 22236.996 89776.168 -448.40969 -273796.57 -161659.98 5618.5602 Loop time of 1158.06 on 32 procs for 200000 steps with 9101 atoms Performance: 14.921 ns/day, 1.608 hours/ns, 172.702 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 | 448.64 | 488.35 | 535.83 | 97.5 | 42.17 Bond | 0.2185 | 0.55804 | 1.2184 | 34.2 | 0.05 Kspace | 426.36 | 474.33 | 512.95 | 98.5 | 40.96 Neigh | 32.165 | 32.21 | 32.239 | 0.4 | 2.78 Comm | 72.898 | 73.805 | 74.651 | 5.6 | 6.37 Output | 0.010478 | 0.012691 | 0.014789 | 1.2 | 0.00 Modify | 84.296 | 84.67 | 85.218 | 2.5 | 7.31 Other | | 4.131 | | | 0.36 Nlocal: 284.406 ave 303 max 265 min Histogram: 1 3 3 2 4 8 5 1 3 2 Nghost: 4976.59 ave 5012 max 4926 min Histogram: 2 2 1 2 3 5 6 2 4 5 Neighs: 88641.8 ave 100039 max 79164 min Histogram: 3 1 5 4 5 5 5 2 1 1 Total # of neighbors = 2836537 Ave neighs/atom = 311.67311 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9824 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 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 200000 2 0.97 1.3532e-06 8304 2 103.7 9.05463e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.64 | 12.98 | 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 200000 200000 2451.5685 92859.489 1.3074058 297.68012 40.563187 82.868926 0 0 22236.996 89776.168 -448.40969 -273796.57 -161659.98 5618.5602 Loop time of 1.04735e-05 on 32 procs for 0 steps with 9101 atoms 94.3% 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 | | 1.047e-05 | | |100.00 Nlocal: 284.406 ave 303 max 265 min Histogram: 1 3 3 2 4 8 5 1 3 2 Nghost: 4976.59 ave 5012 max 4926 min Histogram: 2 2 1 2 3 5 6 2 4 5 Neighs: 88641.8 ave 100039 max 79164 min Histogram: 3 1 5 4 5 5 5 2 1 1 Total # of neighbors = 2836537 Ave neighs/atom = 311.67311 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