#------------------------------------------------------------------------------- # Stage 2.5: 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 2699 = # 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.25725581 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030423457 estimated relative force accuracy = 9.1619338e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 3.03395e-09 8097 2 103.7 3.37987e-07 2699 Per MPI rank memory allocation (min/avg/max) = 14.08 | 14.29 | 14.36 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 -139.98457 97112.971 1.2515496 295.96398 43.466844 82.376858 0 0 22827.512 20321.458 -213.18523 -219072.63 -175797.81 5503.2409 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.53919e-06 8097 2 103.7 0.000114352 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.29639e-06 8097 2 103.7 0.000105723 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.63094e-06 8097 2 103.7 0.000118232 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.28531e-06 8097 2 103.7 9.03491e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 9.97105e-07 8097 2 103.7 9.90048e-05 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.13316e-06 8097 2 103.7 9.08722e-05 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.55553e-06 8097 2 103.7 0.000102397 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.4334e-06 8097 2 103.7 0.000113423 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.25805e-06 8097 2 103.7 0.000111179 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.41583e-06 8097 2 103.7 9.85522e-05 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.64024e-06 8097 2 103.7 0.000111029 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.15428e-06 8097 2 103.7 9.389e-05 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.05378e-06 8097 2 103.7 0.000116888 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.19614e-06 8097 2 103.7 0.000105967 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.33367e-06 8097 2 103.7 9.31712e-05 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.12228e-06 8097 2 103.7 9.70591e-05 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.10949e-06 8097 2 103.7 0.00010576 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.40691e-06 8097 2 103.7 0.000106644 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.1798e-06 8097 2 103.7 0.000101026 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.5039e-06 8097 2 103.7 0.00011136 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.16178e-06 8097 2 103.7 9.09204e-05 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.03976e-06 8097 2 103.7 9.28308e-05 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.56795e-06 8097 2 103.7 0.000111633 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.12894e-06 8097 2 103.7 0.000119755 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.31291e-06 8097 2 103.7 0.000136161 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.0624e-06 8097 2 103.7 9.03977e-05 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.85458e-06 8097 2 103.7 0.000131376 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.31223e-06 8097 2 103.7 9.48603e-05 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.49461e-06 8097 2 103.7 0.000102638 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.1075e-06 8097 2 103.7 9.00255e-05 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.21378e-06 8097 2 103.7 0.000104609 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.16826e-06 8097 2 103.7 0.000111329 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.55511e-06 8097 2 103.7 0.000109108 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.16514e-06 8097 2 103.7 0.00010815 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.19864e-06 8097 2 103.7 0.000102426 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.41115e-06 8097 2 103.7 0.000116896 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.07151e-06 8097 2 103.7 8.88298e-05 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.04577e-06 8097 2 103.7 8.97628e-05 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.24971e-06 8097 2 103.7 8.8306e-05 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26244e-06 8097 2 103.7 8.72219e-05 2699 2000000 2000000 66.522699 97112.971 1.2515496 296.50157 48.60481 60.67225 0 0 23171.812 19829.571 -213.18523 -219094.86 -175984.2 5513.237 Loop time of 21141.4 on 16 procs for 2000000 steps with 8938 atoms Performance: 8.174 ns/day, 2.936 hours/ns, 94.601 timesteps/s 98.8% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13485 | 14553 | 15500 | 613.2 | 68.84 Bond | 3.4437 | 6.1518 | 8.8126 | 68.2 | 0.03 Kspace | 3434.2 | 4382 | 5453 |1121.4 | 20.73 Neigh | 1173.1 | 1174.2 | 1175.7 | 2.8 | 5.55 Comm | 410.8 | 418.8 | 427.25 | 26.1 | 1.98 Output | 0.012653 | 0.01428 | 0.01572 | 0.8 | 0.00 Modify | 566.34 | 568.58 | 572.24 | 8.0 | 2.69 Other | | 38.58 | | | 0.18 Nlocal: 558.625 ave 578 max 535 min Histogram: 1 0 1 2 2 2 4 2 1 1 Nghost: 8632.25 ave 8700 max 8541 min Histogram: 1 2 1 2 0 2 1 1 3 3 Neighs: 295216 ave 310210 max 277728 min Histogram: 1 2 0 2 1 1 6 1 1 1 Total # of neighbors = 4723463 Ave neighs/atom = 528.46979 Ave special neighs/atom = 1.8722309 Neighbor list builds = 98602 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25725581 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030423457 estimated relative force accuracy = 9.1619338e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26244e-06 8097 2 103.7 8.72219e-05 2699 Per MPI rank memory allocation (min/avg/max) = 14.08 | 14.29 | 14.36 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 67.424438 97112.971 1.2515496 296.50157 48.60481 60.67225 0 0 23171.812 19829.571 -213.18523 -219094.86 -175984.2 5513.237 Loop time of 4.22788e-06 on 16 procs for 0 steps with 8938 atoms 121.2% 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 | | 4.228e-06 | | |100.00 Nlocal: 558.625 ave 578 max 535 min Histogram: 1 0 1 2 2 2 4 2 1 1 Nghost: 8632.25 ave 8700 max 8541 min Histogram: 1 2 1 2 0 2 1 1 3 3 Neighs: 295216 ave 310210 max 277728 min Histogram: 1 2 0 2 1 1 6 1 1 1 Total # of neighbors = 4723463 Ave neighs/atom = 528.46979 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_Custom.out