#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 3 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 = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (40.919 40.919 112) 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 40.919 112) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 60000 fix 2 movable ave/time 1 299999 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 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) = 0.25902775 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0027900314 estimated relative force accuracy = 8.4020968e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 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 16 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 1.00026 0.0739282 8436 2 97.7786 10.5765 2812 Per MPI rank memory allocation (min/avg/max) = 12.71 | 13.52 | 14.42 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 -1807.6572 187528.83 1.5723118 382.264 7.0133349 24.891422 0 0 50364.089 -150718.38 -450.08886 -384346.47 -484668.86 11366.077 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969989 3.48762e-05 8436 2 103.7 0.00397149 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969978 6.63625e-05 8436 2 103.7 0.00758162 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969987 4.18838e-05 8436 2 103.7 0.00476669 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969977 7.05187e-05 8436 2 103.7 0.00800556 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970071 0.000214954 8436 2 103.7 0.024604 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969974 7.96053e-05 8436 2 103.7 0.00906786 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970034 0.000101553 8436 2 103.7 0.0116256 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969993 2.34705e-05 8436 2 103.7 0.00264014 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969997 9.25056e-06 8436 2 103.7 0.00100136 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.96999 3.06131e-05 8436 2 103.7 0.00345041 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.96997 9.08237e-05 8436 2 103.7 0.010376 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97003 8.97506e-05 8436 2 103.7 0.0102983 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969986 4.1399e-05 8436 2 103.7 0.00468964 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969979 6.56065e-05 8436 2 103.7 0.00743329 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970007 2.15361e-05 8436 2 103.7 0.0024518 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970021 6.31556e-05 8436 2 103.7 0.00724404 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969967 9.98003e-05 8436 2 103.7 0.0114139 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970038 0.000114481 8436 2 103.7 0.0130904 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969988 3.76804e-05 8436 2 103.7 0.00427989 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969988 3.66302e-05 8436 2 103.7 0.00418366 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969999 4.45735e-06 8436 2 103.7 0.000438919 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970016 4.94848e-05 8436 2 103.7 0.00565409 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970009 2.78426e-05 8436 2 103.7 0.00318566 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970022 6.5869e-05 8436 2 103.7 0.00750914 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97002 6.14346e-05 8436 2 103.7 0.00703859 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970009 2.70452e-05 8436 2 103.7 0.00303178 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970002 6.22627e-06 8436 2 103.7 0.00069715 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970026 7.90839e-05 8436 2 103.7 0.00901621 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969961 0.000117793 8436 2 103.7 0.0134661 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970059 0.000176513 8436 2 103.7 0.0201976 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969974 7.93545e-05 8436 2 103.7 0.00905539 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970026 7.59186e-05 8436 2 103.7 0.00871785 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969974 7.93557e-05 8436 2 103.7 0.00903282 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969975 7.47833e-05 8436 2 103.7 0.00851186 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969945 0.000167885 8436 2 103.7 0.0191392 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969954 0.000140118 8436 2 103.7 0.016035 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969985 4.68381e-05 8436 2 103.7 0.00530174 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970025 7.62455e-05 8436 2 103.7 0.00872828 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969992 2.5116e-05 8436 2 103.7 0.00284763 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970001 2.75116e-06 8436 2 103.7 0.00027991 2812 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.969992 2.44434e-05 8436 2 103.7 0.00276744 2812 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970031 9.12275e-05 8436 2 103.7 0.0104689 2812 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.96996 0.000122019 8436 2 103.7 0.0139149 2812 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.969998 6.64997e-06 8436 2 103.7 0.000733872 2812 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.970001 3.72366e-06 8436 2 103.7 0.000376391 2812 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969982 5.36157e-05 8436 2 103.7 0.00604528 2812 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97004 0.000120324 8436 2 103.7 0.0137956 2812 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.969974 7.79493e-05 8436 2 103.7 0.00887752 2812 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.969968 9.72565e-05 8436 2 103.7 0.0111103 2812 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.970008 2.51883e-05 8436 2 103.7 0.00283634 2812 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.969967 9.88677e-05 8436 2 103.7 0.0112982 2812 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.969952 0.000144827 8436 2 103.7 0.0165756 2812 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970008 2.42605e-05 8436 2 103.7 0.00273583 2812 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.970061 0.000183338 8436 2 103.7 0.0209517 2812 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.970011 3.1891e-05 8436 2 103.7 0.00362565 2812 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.970011 3.35904e-05 8436 2 103.7 0.00380363 2812 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.969954 0.000139616 8436 2 103.7 0.0159221 2812 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.969978 6.80469e-05 8436 2 103.7 0.00775605 2812 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.969963 0.000112056 8436 2 103.7 0.0128133 2812 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969995 1.73882e-05 8436 2 103.7 0.0019757 2812 3000000 3000000 1779.9166 187465.26 1.5728449 290.6352 54.225535 76.526449 0 0 49681.007 -133233.15 -450.24149 -384152.75 -467574.14 8641.625 Loop time of 41846.4 on 32 procs for 3000000 steps with 12788 atoms Performance: 6.194 ns/day, 3.875 hours/ns, 71.691 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4388.6 | 15499 | 26529 |7350.3 | 37.04 Bond | 3.1016 | 8.1634 | 18.794 | 163.4 | 0.02 Kspace | 7736 | 18795 | 29899 |6693.0 | 44.91 Neigh | 2280.3 | 2285.8 | 2295.2 | 9.8 | 5.46 Comm | 910.24 | 1174.7 | 1325.2 | 433.2 | 2.81 Output | 0.015116 | 0.017854 | 0.020512 | 1.2 | 0.00 Modify | 3211.5 | 3461.9 | 3916.1 | 407.8 | 8.27 Other | | 621.9 | | | 1.49 Nlocal: 399.625 ave 559 max 206 min Histogram: 4 8 0 4 0 0 0 0 3 13 Nghost: 6372.91 ave 8677 max 3828 min Histogram: 4 4 0 4 4 4 0 4 0 8 Neighs: 175244 ave 299783 max 47629 min Histogram: 12 0 0 0 4 2 2 0 0 12 Total # of neighbors = 5607820 Ave neighs/atom = 438.52205 Ave special neighs/atom = 1.3678449 Neighbor list builds = 161062 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25903784 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0027883831 estimated relative force accuracy = 8.397133e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969995 1.73882e-05 8436 2 103.7 0.0019757 2812 Per MPI rank memory allocation (min/avg/max) = 12.71 | 13.63 | 14.42 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 3000000 3000000 1763.1723 187465.26 1.5728449 290.6352 54.225535 76.526449 0 0 49681.007 -133218.26 -450.24149 -384167.64 -467574.14 8641.625 Loop time of 7.77297e-06 on 32 procs for 0 steps with 12788 atoms 113.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.773e-06 | | |100.00 Nlocal: 399.625 ave 559 max 206 min Histogram: 4 8 0 4 0 0 0 0 3 13 Nghost: 6372.91 ave 8677 max 3828 min Histogram: 4 4 0 4 4 4 0 4 0 8 Neighs: 175244 ave 299783 max 47629 min Histogram: 12 0 0 0 4 2 2 0 0 12 Total # of neighbors = 5607820 Ave neighs/atom = 438.52205 Ave special neighs/atom = 1.3678449 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out