#------------------------------------------------------------------------------- # 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 8303 = # of frozen angles find clusters CPU = 0.002 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) = 0.32489129 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0034280733 estimated relative force accuracy = 1.0323541e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.992518 1.12928 24909 2 96.605 63.2761 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.54 | 15.01 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 26935.622 278556.86 1.3074059 428.54084 571.12129 1095.4738 0 0 83132.65 318013.41 -1345.0391 -800663.24 -397850.59 24265.468 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.17246e-06 24909 2 103.7 0.000100881 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.34519e-06 24909 2 103.7 0.000125977 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.31022e-06 24909 2 103.7 9.7244e-05 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.30214e-06 24909 2 103.7 0.000104154 8303 200000 200000 2762.8481 278556.86 1.3074059 299.53628 120.77847 270.05382 0 0 66907.421 263259.31 -1345.0391 -815039.38 -484481.82 16960.783 Loop time of 3051 on 32 procs for 200000 steps with 27300 atoms Performance: 5.664 ns/day, 4.238 hours/ns, 65.552 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1247.2 | 1351.8 | 1464.6 | 142.2 | 44.31 Bond | 0.66327 | 1.1391 | 2.0828 | 31.5 | 0.04 Kspace | 1180.2 | 1291.2 | 1392.5 | 143.7 | 42.32 Neigh | 90.574 | 90.735 | 90.905 | 1.0 | 2.97 Comm | 136.92 | 142.18 | 146.64 | 27.1 | 4.66 Output | 0.02382 | 0.028748 | 0.033579 | 1.7 | 0.00 Modify | 160.25 | 162.46 | 166.59 | 15.5 | 5.32 Other | | 11.46 | | | 0.38 Nlocal: 853.125 ave 882 max 795 min Histogram: 1 0 0 1 3 4 8 7 5 3 Nghost: 7287.06 ave 7377 max 7181 min Histogram: 3 1 2 4 3 2 8 5 1 3 Neighs: 265914 ave 285535 max 243249 min Histogram: 2 1 4 0 6 6 3 7 1 2 Total # of neighbors = 8509259 Ave neighs/atom = 311.69447 Ave special neighs/atom = 1.892967 Neighbor list builds = 10747 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) = 0.32489129 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0034280733 estimated relative force accuracy = 1.0323541e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.30214e-06 24909 2 103.7 0.000104154 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.65 | 15.19 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 2763.7685 278556.86 1.3074059 299.53628 120.77847 270.05382 0 0 66907.421 263259.31 -1345.0391 -815039.38 -484481.82 16960.783 Loop time of 7.50759e-06 on 32 procs for 0 steps with 27300 atoms 127.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.508e-06 | | |100.00 Nlocal: 853.125 ave 882 max 795 min Histogram: 1 0 0 1 3 4 8 7 5 3 Nghost: 7287.06 ave 7377 max 7181 min Histogram: 3 1 2 4 3 2 8 5 1 3 Neighs: 265914 ave 285535 max 243249 min Histogram: 2 1 4 0 6 6 3 7 1 2 Total # of neighbors = 8509259 Ave neighs/atom = 311.69447 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out