#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 ns 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 (40.919 40.919 56.118318) 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 (40.919 40.919 56.118318) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 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 2.5_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_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 2.5_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 ... 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) = 0.25688897 grid = 32 32 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0029772252 estimated relative force accuracy = 8.9658253e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5865 2048 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 9 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 0.97 8.05467e-13 8436 2 103.7 7.72928e-11 2812 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.12 | 13.24 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 1924.4789 93962.523 1.2789064 289.94673 42.448003 74.567025 0 0 19546.342 47015.134 -220.49494 -207862.2 -141183.71 5509.7603 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970024 7.03933e-05 8436 2 103.7 0.00806526 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.96999 3.05294e-05 8436 2 103.7 0.00343646 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969978 6.57932e-05 8436 2 103.7 0.00744272 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970061 0.000182136 8436 2 103.7 0.0208899 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.96999 3.26732e-05 8436 2 103.7 0.00368725 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969997 1.0692e-05 8436 2 103.7 0.00116734 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969996 1.42181e-05 8436 2 103.7 0.00154101 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970048 0.000146085 8436 2 103.7 0.0166827 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97006 0.000183202 8436 2 103.7 0.0209791 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969963 0.000113188 8436 2 103.7 0.0129049 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969983 5.24664e-05 8436 2 103.7 0.00595916 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970026 7.81512e-05 8436 2 103.7 0.00895365 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970003 9.41488e-06 8436 2 103.7 0.00107645 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97005 0.000151019 8436 2 103.7 0.0173058 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970006 1.68423e-05 8436 2 103.7 0.00191464 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969993 2.22115e-05 8436 2 103.7 0.00249081 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 2.0986e-06 8436 2 103.7 0.000176842 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970004 1.11544e-05 8436 2 103.7 0.00126252 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969961 0.000118403 8436 2 103.7 0.0135328 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969997 1.10154e-05 8436 2 103.7 0.00119796 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969916 0.000253245 8436 2 103.7 0.0289794 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970009 2.76209e-05 8436 2 103.7 0.00315161 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969996 1.27413e-05 8436 2 103.7 0.00141287 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 2.35789e-06 8436 2 103.7 0.000219536 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969973 8.2238e-05 8436 2 103.7 0.00938526 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969985 4.81143e-05 8436 2 103.7 0.00541727 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.96997 9.04495e-05 8436 2 103.7 0.0103692 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970029 8.81948e-05 8436 2 103.7 0.0101118 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969963 0.000113492 8436 2 103.7 0.012909 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.96999 3.08134e-05 8436 2 103.7 0.00348847 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97003 9.08687e-05 8436 2 103.7 0.0103958 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970035 0.000105 8436 2 103.7 0.0120036 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969961 0.00011646 8436 2 103.7 0.0132591 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969999 3.41006e-06 8436 2 103.7 0.000334831 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970047 0.000141266 8436 2 103.7 0.0161852 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969964 0.000109095 8436 2 103.7 0.0124633 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969949 0.000155684 8436 2 103.7 0.0177849 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970029 8.67172e-05 8436 2 103.7 0.00992221 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969961 0.000118173 8436 2 103.7 0.0135041 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.96999 3.24263e-05 8436 2 103.7 0.00361716 2812 2000000 2000000 -49.903042 98084.363 1.2251624 301.08122 42.475172 57.662407 0 0 18766.723 48204.56 -211.22899 -207832.96 -140761.54 5721.3452 Loop time of 16097.2 on 32 procs for 2000000 steps with 9188 atoms Performance: 10.735 ns/day, 2.236 hours/ns, 124.245 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8743.4 | 9058.5 | 9428.2 | 157.8 | 56.27 Bond | 2.4484 | 5.5817 | 8.9675 | 77.8 | 0.03 Kspace | 2953.5 | 3326.9 | 3644 | 263.3 | 20.67 Neigh | 762.95 | 763.69 | 764.39 | 1.5 | 4.74 Comm | 986.43 | 1001.7 | 1014.8 | 25.5 | 6.22 Output | 0.0088976 | 0.011111 | 0.013225 | 1.2 | 0.00 Modify | 1464.1 | 1598.9 | 1865.3 | 376.9 | 9.93 Other | | 341.9 | | | 2.12 Nlocal: 287.125 ave 310 max 270 min Histogram: 1 0 8 8 5 4 3 0 1 2 Nghost: 7134.44 ave 7200 max 7074 min Histogram: 3 3 3 4 5 4 3 3 0 4 Neighs: 154443 ave 170953 max 144249 min Histogram: 1 3 9 7 3 4 3 0 1 1 Total # of neighbors = 4942181 Ave neighs/atom = 537.89519 Ave special neighs/atom = 1.9037875 Neighbor list builds = 104902 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) = 0.25583308 grid = 32 32 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0031514971 estimated relative force accuracy = 9.4906398e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5865 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.96999 3.24263e-05 8436 2 103.7 0.00361716 2812 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.14 | 13.24 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 -110.19518 98084.363 1.2251624 301.08122 42.475172 57.662407 0 0 18766.723 47356.657 -211.22899 -206985.06 -140761.54 5721.3452 Loop time of 1.15505e-05 on 32 procs for 0 steps with 9188 atoms 108.5% 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 | | 1.155e-05 | | |100.00 Nlocal: 287.125 ave 310 max 270 min Histogram: 1 0 8 8 5 4 3 0 1 2 Nghost: 7134.44 ave 7200 max 7074 min Histogram: 3 3 3 4 5 4 3 3 0 4 Neighs: 154443 ave 170953 max 144249 min Histogram: 1 3 9 7 3 4 3 0 1 1 Total # of neighbors = 4942181 Ave neighs/atom = 537.89519 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 8:32:51