#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 10 ps with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 104.1) 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 104.1) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 200 fix 2 movable ave/time 1 999 1000 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 1 1 1 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 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 ... 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 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 15 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 0.999903 0.0672861 8436 2 97.8403 10.9928 2812 Per MPI rank memory allocation (min/avg/max) = 12.5 | 13.2 | 13.69 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 -2947.1632 141184.09 1.4079299 413.07421 6.4926157 32.267397 0 0 34073.032 -52641.573 -312.04795 -284219.18 -302748.96 9046.3299 10000 10000 330.73509 140324.36 1.4165559 321.23332 47.64824 73.550849 0 0 32191.411 -35510.346 -313.95979 -284050.97 -287248.7 7035.0133 Loop time of 103.746 on 32 procs for 10000 steps with 10808 atoms Performance: 8.328 ns/day, 2.882 hours/ns, 96.389 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.721 | 46.087 | 63.996 | 287.8 | 44.42 Bond | 0.011244 | 0.029408 | 0.065649 | 9.0 | 0.03 Kspace | 18.036 | 36.037 | 68.578 | 326.7 | 34.74 Neigh | 4.8719 | 4.8883 | 4.9141 | 0.5 | 4.71 Comm | 3.8426 | 5.0034 | 5.455 | 23.6 | 4.82 Output | 0.012755 | 0.015133 | 0.017395 | 1.1 | 0.01 Modify | 10.49 | 10.879 | 11.779 | 12.2 | 10.49 Other | | 0.8076 | | | 0.78 Nlocal: 337.75 ave 415 max 160 min Histogram: 4 4 0 0 0 0 0 2 6 16 Nghost: 6500.91 ave 7762 max 4768 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 159408 ave 221146 max 43856 min Histogram: 8 0 0 0 0 4 0 1 4 15 Total # of neighbors = 5101068 Ave neighs/atom = 471.9715 Ave special neighs/atom = 1.6184308 Neighbor list builds = 561 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) = 0.25552995 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034154209 estimated relative force accuracy = 1.0285439e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.969992 2.46357e-05 8436 2 103.7 0.00277421 2812 Per MPI rank memory allocation (min/avg/max) = 12.5 | 13.27 | 13.69 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 298.77653 140324.36 1.4165559 321.23332 47.64824 73.550849 0 0 32191.411 -35342.464 -313.95979 -284218.84 -287248.7 7035.0133 Loop time of 2.04617e-05 on 32 procs for 0 steps with 10808 atoms 104.9% 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 | | 2.046e-05 | | |100.00 Nlocal: 337.75 ave 415 max 160 min Histogram: 4 4 0 0 0 0 0 2 6 16 Nghost: 6500.91 ave 7762 max 4768 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 159408 ave 221146 max 43856 min Histogram: 8 0 0 0 0 4 0 1 4 15 Total # of neighbors = 5101068 Ave neighs/atom = 471.9715 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out