#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 10 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 3728 = # 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 1000 1000 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 1 1 1 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 10000 2.4.restart dump sci all custom 1000 2.4.xyz id mol type q xs ys zs timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26033976 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027780168 estimated relative force accuracy = 8.3659151e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.0015 0.65392 11184 2 97.1394 32.4373 3728 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.16 | 15.85 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 359767.79 138675.73 1.4225848 417.38844 167.39207 553.27732 0 0 277410.73 -49456.078 -397.61848 -378544.84 -149869.52 11461.162 10000 10000 349798.04 138675.73 1.4225848 297.19378 264.5575 390.11988 0 0 272100.85 -51641.943 -397.61848 -380109.93 -158996.35 8160.7101 Loop time of 225.65 on 16 procs for 10000 steps with 13901 atoms Performance: 3.829 ns/day, 6.268 hours/ns, 44.316 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 116.02 | 137.53 | 174.21 | 175.6 | 60.95 Bond | 0.053975 | 0.14818 | 0.30792 | 24.4 | 0.07 Kspace | 28.879 | 65.74 | 87.385 | 255.2 | 29.13 Neigh | 10.298 | 10.306 | 10.316 | 0.2 | 4.57 Comm | 4.309 | 4.5003 | 4.6881 | 5.3 | 1.99 Output | 0.020635 | 0.023105 | 0.025361 | 1.0 | 0.01 Modify | 6.5646 | 6.696 | 6.9539 | 3.7 | 2.97 Other | | 0.7098 | | | 0.31 Nlocal: 868.812 ave 1012 max 771 min Histogram: 3 2 4 1 2 0 0 0 0 4 Nghost: 10646.6 ave 11156 max 9868 min Histogram: 4 0 0 0 0 0 4 4 0 4 Neighs: 504016 ave 648964 max 409275 min Histogram: 3 3 3 3 0 0 0 0 0 4 Total # of neighbors = 8064255 Ave neighs/atom = 580.12049 Ave special neighs/atom = 1.8838932 Neighbor list builds = 559 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 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) = 0.26033976 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027780168 estimated relative force accuracy = 8.3659151e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.97 1.25881e-06 11184 2 103.7 9.24479e-05 3728 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.33 | 15.86 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 10000 10000 349799.05 138675.73 1.4225848 297.19378 264.5575 390.11988 0 0 272100.85 -51641.943 -397.61848 -380109.93 -158996.35 8160.7101 Loop time of 6.73306e-06 on 16 procs for 0 steps with 13901 atoms 108.6% CPU use with 16 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 | | 6.733e-06 | | |100.00 Nlocal: 868.812 ave 1012 max 771 min Histogram: 3 2 4 1 2 0 0 0 0 4 Nghost: 10646.6 ave 11156 max 9868 min Histogram: 4 0 0 0 0 0 4 4 0 4 Neighs: 504016 ave 648964 max 409275 min Histogram: 3 3 3 3 0 0 0 0 0 4 Total # of neighbors = 8064255 Ave neighs/atom = 580.12049 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out