#------------------------------------------------------------------------------- # 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) = 0.20345675 grid = 20 20 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0025370673 estimated relative force accuracy = 7.6403028e-06 using double precision KISS FFT 3d grid and FFT values/proc = 2601 400 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 = 17 ghost atom cutoff = 17 binsize = 8.5, bins = 4 4 8 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 6.26388e-13 6000 1 103.7 8.05329e-11 2000 Per MPI rank memory allocation (min/avg/max) = 9.899 | 10.05 | 10.31 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 -384.91124 59830.193 1.0000033 304.23151 0 0 0 0 4992.6661 57167.525 -53.651864 -83762.556 -21602.365 3626.5185 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970032 9.58747e-05 6000 1 103.7 0.0109702 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969995 1.51624e-05 6000 1 103.7 0.00168851 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970003 8.63091e-06 6000 1 103.7 0.000965177 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969977 6.9136e-05 6000 1 103.7 0.00783732 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970021 6.22418e-05 6000 1 103.7 0.00713998 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97001 3.10678e-05 6000 1 103.7 0.0035195 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969914 0.000259761 6000 1 103.7 0.0297687 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970056 0.000168026 6000 1 103.7 0.0192759 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969998 8.27077e-06 6000 1 103.7 0.000907244 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969968 9.66609e-05 6000 1 103.7 0.0110631 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.970081 0.000240216 6000 1 103.7 0.0275504 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970054 0.000162109 6000 1 103.7 0.0185478 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969919 0.00024639 6000 1 103.7 0.0280732 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969976 7.3569e-05 6000 1 103.7 0.00836305 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970021 6.26217e-05 6000 1 103.7 0.00718214 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969991 2.78522e-05 6000 1 103.7 0.00309931 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970032 9.73387e-05 6000 1 103.7 0.011147 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970039 0.000117807 6000 1 103.7 0.0135151 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970031 9.27314e-05 6000 1 103.7 0.0106396 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970061 0.000181073 6000 1 103.7 0.0207944 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969942 0.000175877 6000 1 103.7 0.0200603 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970029 8.71777e-05 6000 1 103.7 0.0100331 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.969922 0.000237167 6000 1 103.7 0.0271055 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970008 2.28722e-05 6000 1 103.7 0.00258343 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969983 5.28027e-05 6000 1 103.7 0.0060206 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970051 0.000155105 6000 1 103.7 0.0177731 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.969958 0.000125803 6000 1 103.7 0.0143545 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970031 9.35746e-05 6000 1 103.7 0.0106973 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970018 5.35229e-05 6000 1 103.7 0.00610065 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970022 6.36748e-05 6000 1 103.7 0.00733116 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970098 0.000294857 6000 1 103.7 0.0337113 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969973 8.30413e-05 6000 1 103.7 0.00944542 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969991 2.89491e-05 6000 1 103.7 0.00325327 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970042 0.000127597 6000 1 103.7 0.0146922 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970059 0.000177936 6000 1 103.7 0.0203358 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969994 1.99725e-05 6000 1 103.7 0.00224136 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970079 0.000237173 6000 1 103.7 0.027173 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969924 0.00022737 6000 1 103.7 0.0260407 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969936 0.000195402 6000 1 103.7 0.0223318 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969992 2.43763e-05 6000 1 103.7 0.00273757 2000 2000000 2000000 162.90082 59968.797 0.99769205 301.44522 0 0 0 0 5163.3883 57050.981 -53.52786 -83760.227 -21545.858 3593.3052 Loop time of 17879.9 on 32 procs for 2000000 steps with 6000 atoms Performance: 9.665 ns/day, 2.483 hours/ns, 111.858 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11456 | 11602 | 11811 | 64.1 | 64.89 Bond | 2.2832 | 2.6715 | 3.8612 | 17.6 | 0.01 Kspace | 2233.2 | 2450.8 | 2607 | 148.2 | 13.71 Neigh | 857.31 | 857.6 | 857.92 | 0.6 | 4.80 Comm | 1356.1 | 1374.1 | 1395.6 | 31.4 | 7.69 Output | 0.007521 | 0.0093454 | 0.011053 | 1.1 | 0.00 Modify | 1495.7 | 1508.4 | 1531.9 | 20.3 | 8.44 Other | | 83.75 | | | 0.47 Nlocal: 187.5 ave 204 max 173 min Histogram: 2 2 3 7 5 3 5 2 1 2 Nghost: 9966.38 ave 10061 max 9813 min Histogram: 1 0 2 4 1 3 7 8 2 4 Neighs: 192933 ave 214114 max 176311 min Histogram: 1 3 3 7 8 3 4 0 2 1 Total # of neighbors = 6173841 Ave neighs/atom = 1028.9735 Ave special neighs/atom = 2 Neighbor list builds = 107086 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) = 0.20338201 grid = 20 20 32 stencil order = 5 estimated absolute RMS force accuracy = 0.002551532 estimated relative force accuracy = 7.6838628e-06 using double precision KISS FFT 3d grid and FFT values/proc = 2601 400 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969992 2.43763e-05 6000 1 103.7 0.00273757 2000 Per MPI rank memory allocation (min/avg/max) = 10.28 | 10.3 | 10.31 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 108.85839 59968.797 0.99769205 301.44522 0 0 0 0 5163.3883 57020.233 -53.52786 -83729.479 -21545.858 3593.3052 Loop time of 1.29996e-05 on 32 procs for 0 steps with 6000 atoms 103.1% 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 | | 1.3e-05 | | |100.00 Nlocal: 187.5 ave 204 max 173 min Histogram: 2 2 3 7 5 3 5 2 1 2 Nghost: 9966.38 ave 10061 max 9813 min Histogram: 1 0 2 4 1 3 7 8 2 4 Neighs: 192933 ave 214114 max 176311 min Histogram: 1 3 3 7 8 3 4 0 2 1 Total # of neighbors = 6173841 Ave neighs/atom = 1028.9735 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: 9:49:34