#------------------------------------------------------------------------------- # Stage 2.3: NVT integration for 1 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2109 = # 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 WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 100000 100000 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 2.3_averages.txt off 1 fix 3 movable ave/time 100 1 100 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 2.3_instantaneous.txt restart 1000000 2.3.restart dump sci all custom 100000 2.3.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0038 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24386748 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0036780491 estimated relative force accuracy = 1.1076336e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard SHAKE stats (type/ave/delta/count) on step 0 1 0.97 9.65786e-05 6327 1 103.7 0.00840641 2109 Per MPI rank memory allocation (min/avg/max) = 9.214 | 11.68 | 14.23 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 1050.8117 199228.71 0.34683261 443.40984 0 0 0 0 7951.1985 64632.375 -39.419859 -115823.09 -43239.516 5724.3715 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.12388e-06 6327 1 103.7 9.87463e-05 2109 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.85812e-06 6327 1 103.7 0.000110439 2109 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.19395e-06 6327 1 103.7 0.000116913 2109 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.26497e-06 6327 1 103.7 9.47234e-05 2109 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.30661e-06 6327 1 103.7 0.000103723 2109 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.14091e-06 6327 1 103.7 9.36581e-05 2109 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.39315e-06 6327 1 103.7 9.52708e-05 2109 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.21715e-06 6327 1 103.7 0.000107541 2109 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.55046e-06 6327 1 103.7 0.000123361 2109 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.34342e-06 6327 1 103.7 0.000101098 2109 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.28876e-06 6327 1 103.7 8.99615e-05 2109 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.25501e-06 6327 1 103.7 9.31886e-05 2109 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.27106e-06 6327 1 103.7 0.000102626 2109 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.66604e-06 6327 1 103.7 0.000119942 2109 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.21942e-06 6327 1 103.7 9.40994e-05 2109 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.33571e-06 6327 1 103.7 0.000110962 2109 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.16454e-06 6327 1 103.7 9.23993e-05 2109 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.38721e-06 6327 1 103.7 0.000109597 2109 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.34007e-06 6327 1 103.7 9.68274e-05 2109 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.19776e-06 6327 1 103.7 0.00010031 2109 1000000 1000000 -92.658855 199228.71 0.34683261 297.95317 0 0 0 0 8014.1018 63790.818 -39.419859 -116167.02 -44362.102 3846.5421 Loop time of 23347.6 on 8 procs for 1000000 steps with 6441 atoms Performance: 3.701 ns/day, 6.485 hours/ns, 42.831 timesteps/s 98.3% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3101 | 8928.5 | 18592 |9454.7 | 38.24 Bond | 0.89404 | 1.2003 | 1.4671 | 21.6 | 0.01 Kspace | 2996.7 | 12685 | 21658 |7953.5 | 54.33 Neigh | 1022.1 | 1027.1 | 1035.3 | 15.6 | 4.40 Comm | 68.27 | 181.9 | 275.32 | 640.0 | 0.78 Output | 0.026358 | 0.028746 | 0.030483 | 0.8 | 0.00 Modify | 435.93 | 496.82 | 553.63 | 244.5 | 2.13 Other | | 26.95 | | | 0.12 Nlocal: 805.125 ave 1811 max 0 min Histogram: 4 0 0 0 0 0 0 0 2 2 Nghost: 5298 ave 9977 max 598 min Histogram: 2 2 0 0 0 0 0 0 2 2 Neighs: 388824 ave 791977 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 4 Total # of neighbors = 3110596 Ave neighs/atom = 482.93681 Ave special neighs/atom = 1.9646018 Neighbor list builds = 49562 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.3.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) = 0.24386748 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0036780491 estimated relative force accuracy = 1.1076336e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.19776e-06 6327 1 103.7 0.00010031 2109 Per MPI rank memory allocation (min/avg/max) = 9.396 | 11.96 | 14.26 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 1000000 1000000 -92.407522 199228.71 0.34683261 297.95317 0 0 0 0 8014.1018 63790.818 -39.419859 -116167.02 -44362.102 3846.5421 Loop time of 3.55125e-06 on 8 procs for 0 steps with 6441 atoms 119.7% CPU use with 8 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 | | 3.551e-06 | | |100.00 Nlocal: 805.125 ave 1811 max 0 min Histogram: 4 0 0 0 0 0 0 0 2 2 Nghost: 5298 ave 9977 max 598 min Histogram: 2 2 0 0 0 0 0 0 2 2 Neighs: 388824 ave 791977 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 4 Total # of neighbors = 3110596 Ave neighs/atom = 482.93681 Ave special neighs/atom = 1.9646018 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.4_NVT.out