#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 20 ps with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 2812 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (36.8271 36.8271 69.281874) with tilt (0 0 0) kspace_style pppm 0.00001 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 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (36.8271 36.8271 69.281874) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 0.9869233 0.9869233 100 drag 0 mtk yes nreset 400 fix 2 movable ave/time 1 1999 2000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 2 1 2 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 20000 2.4.restart dump sci all custom 2000 2.4.xyz id mol type q xs ys zs timestep 1 run 20000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0151 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25615969 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031432339 estimated relative force accuracy = 9.4657554e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5544 1800 generated 0 of 36 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 10 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/tri stencil: half/bin/3d/tri bin: standard SHAKE stats (type/ave/delta/count) on step 0 2 0.996059 0.664658 8436 2 97.2022 34.6427 2812 Per MPI rank memory allocation (min/avg/max) = 12.87 | 13 | 13.16 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 7362.5594 93962.523 1.2789064 429.73544 61.834271 215.71841 0 0 21137.571 51382.007 -220.49494 -206540.97 -133743.84 8166.1181 20000 20000 19.835008 98060.452 1.2254611 299.90831 40.573271 103.51482 0 0 18753.988 47858.453 -211.28049 -207238.13 -140481.61 5699.0569 Loop time of 166.436 on 32 procs for 20000 steps with 9188 atoms Performance: 10.382 ns/day, 2.312 hours/ns, 120.166 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 83.033 | 89.712 | 96.857 | 36.8 | 53.90 Bond | 0.027371 | 0.062225 | 0.10635 | 10.5 | 0.04 Kspace | 31.2 | 38.323 | 44.968 | 56.5 | 23.03 Neigh | 7.1354 | 7.1547 | 7.1751 | 0.5 | 4.30 Comm | 10.178 | 10.328 | 10.493 | 2.7 | 6.21 Output | 0.011427 | 0.013583 | 0.01565 | 1.1 | 0.01 Modify | 16.314 | 17.819 | 20.055 | 35.6 | 10.71 Other | | 3.023 | | | 1.82 Nlocal: 287.125 ave 304 max 257 min Histogram: 1 0 1 2 4 6 4 6 3 5 Nghost: 7167.91 ave 7249 max 7082 min Histogram: 1 5 3 2 4 6 3 2 3 3 Neighs: 154533 ave 167827 max 134841 min Histogram: 1 0 3 0 6 6 5 5 4 2 Total # of neighbors = 4945048 Ave neighs/atom = 538.20723 Ave special neighs/atom = 1.9037875 Neighbor list builds = 1075 Dangerous builds = 0 undump sci restart 0 dump sci all custom 20000 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) = 0.25692855 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0029052084 estimated relative force accuracy = 8.7489488e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5852 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 20000 2 0.970021 6.50982e-05 8436 2 103.7 0.00740203 2812 Per MPI rank memory allocation (min/avg/max) = 12.91 | 13.03 | 13.17 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 20000 20000 146.13084 98060.452 1.2254611 299.90831 40.573271 103.51482 0 0 18753.988 48475.633 -211.28049 -207855.28 -140481.57 5699.0569 Loop time of 1.31087e-05 on 32 procs for 0 steps with 9188 atoms 111.1% 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 | | 1.311e-05 | | |100.00 Nlocal: 287.125 ave 304 max 257 min Histogram: 1 0 1 2 4 6 4 6 3 5 Nghost: 7167.91 ave 7249 max 7082 min Histogram: 1 5 3 2 4 6 3 2 3 3 Neighs: 154533 ave 167827 max 134841 min Histogram: 1 0 3 0 6 6 5 5 4 2 Total # of neighbors = 4945048 Ave neighs/atom = 538.20723 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_Custom.out