#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (30 30 66.477992) 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 (30 30 66.477992) 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 ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25669611 grid = 24 24 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0023816765 estimated relative force accuracy = 7.1723479e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 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 = 5 5 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 1 0.97 8.84848e-13 6000 1 103.7 8.6942e-11 2000 Per MPI rank memory allocation (min/avg/max) = 9.615 | 10.01 | 10.06 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-06 289.75468 59830.193 1.0000033 298.93643 0 0 0 0 5240.7095 78787.558 -104.25214 -105658.42 -21630.153 3563.3997 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970032 9.49269e-05 6000 1 103.7 0.0108424 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969995 1.72655e-05 6000 1 103.7 0.00192781 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970005 1.505e-05 6000 1 103.7 0.00169167 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970016 4.75024e-05 6000 1 103.7 0.00545163 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969968 9.75459e-05 6000 1 103.7 0.0110776 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970029 8.70094e-05 6000 1 103.7 0.0099297 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970013 3.89238e-05 6000 1 103.7 0.00441444 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969945 0.000167962 6000 1 103.7 0.0191564 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970003 9.89701e-06 6000 1 103.7 0.00114436 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970065 0.000194396 6000 1 103.7 0.0222982 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.96999 3.29761e-05 6000 1 103.7 0.00372488 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970064 0.000192779 6000 1 103.7 0.0220681 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.970083 0.000249926 6000 1 103.7 0.0285461 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.96997 9.03459e-05 6000 1 103.7 0.0102895 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970031 9.44516e-05 6000 1 103.7 0.0107364 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969991 2.86202e-05 6000 1 103.7 0.00323397 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970045 0.000133528 6000 1 103.7 0.0153268 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970111 0.000332169 6000 1 103.7 0.0379809 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970016 4.91411e-05 6000 1 103.7 0.00562453 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969952 0.000143961 6000 1 103.7 0.0164059 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970085 0.000252295 6000 1 103.7 0.0288664 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970002 6.04866e-06 6000 1 103.7 0.000682538 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.969999 5.44196e-06 6000 1 103.7 0.000574625 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969986 4.47832e-05 6000 1 103.7 0.00504187 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969975 7.56219e-05 6000 1 103.7 0.00854207 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969869 0.000395918 6000 1 103.7 0.0455957 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97001 3.18336e-05 6000 1 103.7 0.00359601 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970006 1.83486e-05 6000 1 103.7 0.00205365 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969982 5.63168e-05 6000 1 103.7 0.00637216 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970028 8.23451e-05 6000 1 103.7 0.00938203 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.969995 1.74348e-05 6000 1 103.7 0.00194917 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970007 2.19231e-05 6000 1 103.7 0.00252108 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97004 0.000120419 6000 1 103.7 0.0138147 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969996 1.28573e-05 6000 1 103.7 0.00140564 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970061 0.000179859 6000 1 103.7 0.020615 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969976 7.49148e-05 6000 1 103.7 0.00856682 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970017 4.97828e-05 6000 1 103.7 0.00574406 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969992 2.64953e-05 6000 1 103.7 0.00299926 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970023 6.9782e-05 6000 1 103.7 0.007955 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970041 0.000122911 6000 1 103.7 0.0140383 2000 2000000 2000000 -1.3545933 59931.66 0.99831027 300.25962 0 0 0 0 5153.7872 78852.465 -104.07563 -105653.76 -21647.507 3579.1726 Loop time of 11339.6 on 32 procs for 2000000 steps with 6000 atoms Performance: 15.239 ns/day, 1.575 hours/ns, 176.372 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 | 6223.3 | 6284.1 | 6369.4 | 38.0 | 55.42 Bond | 2.0892 | 2.4456 | 3.4343 | 17.1 | 0.02 Kspace | 2265.5 | 2348.8 | 2410.9 | 61.5 | 20.71 Neigh | 496.75 | 497.25 | 497.66 | 1.0 | 4.39 Comm | 850.26 | 858.55 | 868.45 | 18.2 | 7.57 Output | 0.0068978 | 0.0086901 | 0.010388 | 1.1 | 0.00 Modify | 1058.2 | 1170.1 | 1296.2 | 286.9 | 10.32 Other | | 178.5 | | | 1.57 Nlocal: 187.5 ave 205 max 171 min Histogram: 2 1 7 2 2 8 4 2 2 2 Nghost: 6538.88 ave 6639 max 6447 min Histogram: 3 3 1 4 8 4 1 3 3 2 Neighs: 107794 ave 119028 max 97566 min Histogram: 2 2 4 5 3 7 2 2 3 2 Total # of neighbors = 3449396 Ave neighs/atom = 574.89933 Ave special neighs/atom = 2 Neighbor list builds = 107063 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) = 0.25666658 grid = 24 24 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0023848591 estimated relative force accuracy = 7.1819324e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970041 0.000122911 6000 1 103.7 0.0140383 2000 Per MPI rank memory allocation (min/avg/max) = 9.99 | 10.02 | 10.06 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 276.50293 59931.66 0.99831027 300.25962 0 0 0 0 5153.7872 78840.329 -104.07563 -105641.62 -21647.508 3579.1726 Loop time of 7.40006e-06 on 32 procs for 0 steps with 6000 atoms 112.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.4e-06 | | |100.00 Nlocal: 187.5 ave 205 max 171 min Histogram: 2 1 7 2 2 8 4 2 2 2 Nghost: 6538.88 ave 6639 max 6447 min Histogram: 3 3 1 4 8 4 1 3 3 2 Neighs: 107794 ave 119028 max 97566 min Histogram: 2 2 4 5 3 7 2 2 3 2 Total # of neighbors = 3449396 Ave neighs/atom = 574.89933 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:01:31