#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 5 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 1937 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (32.7352 32.7352 95.3) 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 (32.7352 32.7352 95.3) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 100000 fix 2 movable ave/time 1 499999 500000 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 500 1 500 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 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0144 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25643696 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0033099351 estimated relative force accuracy = 9.9677713e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5600 1568 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 = 5 5 14 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 0.998758 0.643659 5811 2 97.872 15.8915 1937 Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.71 | 13.08 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 -3906.3296 102122.84 1.4409303 399.30509 18.026657 16.959693 0 0 25812.892 -52432.236 -230.70952 -212209.58 -238793.93 6799.9133 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969956 0.000131666 5811 2 103.7 0.0150469 1937 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969975 7.71221e-05 5811 2 103.7 0.00880407 1937 SHAKE stats (type/ave/delta/count) on step 150000 2 0.96993 0.000212795 5811 2 103.7 0.0243936 1937 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970004 1.22978e-05 5811 2 103.7 0.00142823 1937 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970007 2.16305e-05 5811 2 103.7 0.00244679 1937 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969955 0.000138822 5811 2 103.7 0.0158572 1937 SHAKE stats (type/ave/delta/count) on step 350000 2 0.96998 6.13615e-05 5811 2 103.7 0.00697972 1937 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970045 0.000137907 5811 2 103.7 0.0157791 1937 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970027 7.95618e-05 5811 2 103.7 0.00908746 1937 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969989 3.4183e-05 5811 2 103.7 0.00387287 1937 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970002 7.35406e-06 5811 2 103.7 0.000818001 1937 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969991 3.02453e-05 5811 2 103.7 0.00338981 1937 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970022 6.65661e-05 5811 2 103.7 0.00762861 1937 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969993 2.26368e-05 5811 2 103.7 0.00255634 1937 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969997 1.10742e-05 5811 2 103.7 0.00120369 1937 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970018 5.35577e-05 5811 2 103.7 0.0061267 1937 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970008 2.27047e-05 5811 2 103.7 0.00262204 1937 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969992 2.61746e-05 5811 2 103.7 0.00292179 1937 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970002 6.2135e-06 5811 2 103.7 0.000665767 1937 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970051 0.000150857 5811 2 103.7 0.0172917 1937 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969989 3.40209e-05 5811 2 103.7 0.00386021 1937 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970049 0.000148678 5811 2 103.7 0.0170384 1937 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970027 8.25266e-05 5811 2 103.7 0.00946915 1937 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970049 0.000147736 5811 2 103.7 0.0169872 1937 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969985 4.62025e-05 5811 2 103.7 0.00522145 1937 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970021 6.44396e-05 5811 2 103.7 0.00734255 1937 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970037 0.000111819 5811 2 103.7 0.0128315 1937 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970064 0.000194756 5811 2 103.7 0.0222948 1937 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970015 4.61362e-05 5811 2 103.7 0.00518199 1937 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969945 0.00016805 5811 2 103.7 0.0191454 1937 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970003 8.95466e-06 5811 2 103.7 0.00100191 1937 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970014 4.14086e-05 5811 2 103.7 0.00476931 1937 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969949 0.000157143 5811 2 103.7 0.0179778 1937 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969998 8.12248e-06 5811 2 103.7 0.000877717 1937 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969912 0.000267129 5811 2 103.7 0.0305797 1937 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969964 0.000107637 5811 2 103.7 0.0122898 1937 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969913 0.000258649 5811 2 103.7 0.0295721 1937 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970069 0.000205893 5811 2 103.7 0.0236583 1937 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969978 6.71771e-05 5811 2 103.7 0.00765564 1937 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970033 9.63313e-05 5811 2 103.7 0.0110475 1937 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.970022 6.60289e-05 5811 2 103.7 0.0075094 1937 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970021 6.44544e-05 5811 2 103.7 0.00728558 1937 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.969975 7.67341e-05 5811 2 103.7 0.00870247 1937 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.970004 1.26816e-05 5811 2 103.7 0.00147283 1937 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.970044 0.000132655 5811 2 103.7 0.0152033 1937 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.970032 9.6105e-05 5811 2 103.7 0.0109874 1937 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.969993 2.18984e-05 5811 2 103.7 0.0024616 1937 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.96998 6.02167e-05 5811 2 103.7 0.00683511 1937 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97001 2.98231e-05 5811 2 103.7 0.00342545 1937 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.969931 0.00020884 5811 2 103.7 0.0239175 1937 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.970061 0.000180209 5811 2 103.7 0.0205492 1937 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.970017 5.20441e-05 5811 2 103.7 0.00596284 1937 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970016 4.86806e-05 5811 2 103.7 0.00555839 1937 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.969963 0.000113304 5811 2 103.7 0.0129459 1937 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.970003 9.9772e-06 5811 2 103.7 0.00114049 1937 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.970069 0.000207961 5811 2 103.7 0.0237785 1937 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.970056 0.000168293 5811 2 103.7 0.0192888 1937 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.969952 0.000145776 5811 2 103.7 0.0165512 1937 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.969972 8.41581e-05 5811 2 103.7 0.00959787 1937 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.970069 0.000208738 5811 2 103.7 0.023949 1937 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.970113 0.000339147 5811 2 103.7 0.0388601 1937 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.970004 1.32539e-05 5811 2 103.7 0.00147651 1937 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.970062 0.000190146 5811 2 103.7 0.021794 1937 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.969986 4.2342e-05 5811 2 103.7 0.00479384 1937 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.969979 6.45788e-05 5811 2 103.7 0.00730441 1937 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.970018 5.37863e-05 5811 2 103.7 0.00613526 1937 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.970027 8.05047e-05 5811 2 103.7 0.0092149 1937 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.970017 5.25772e-05 5811 2 103.7 0.00597685 1937 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.96999 3.1129e-05 5811 2 103.7 0.00352248 1937 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.970046 0.000142448 5811 2 103.7 0.0162432 1937 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.970011 3.19355e-05 5811 2 103.7 0.0036391 1937 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.96996 0.000120544 5811 2 103.7 0.0137314 1937 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.969957 0.000129898 5811 2 103.7 0.0148444 1937 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.969994 1.92188e-05 5811 2 103.7 0.00213298 1937 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.969982 5.38737e-05 5811 2 103.7 0.00610949 1937 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.970023 6.97457e-05 5811 2 103.7 0.00797837 1937 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.969941 0.000175827 5811 2 103.7 0.020189 1937 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.96998 6.04986e-05 5811 2 103.7 0.00688811 1937 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.969961 0.00011769 5811 2 103.7 0.013424 1937 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.969967 0.000102029 5811 2 103.7 0.0116541 1937 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.969981 5.71846e-05 5811 2 103.7 0.00650714 1937 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.969997 1.00307e-05 5811 2 103.7 0.00111277 1937 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.969995 1.69753e-05 5811 2 103.7 0.00187997 1937 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.969993 2.20072e-05 5811 2 103.7 0.00247073 1937 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.970047 0.000141034 5811 2 103.7 0.0160606 1937 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.969985 4.66442e-05 5811 2 103.7 0.00527392 1937 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.969988 3.84664e-05 5811 2 103.7 0.00438964 1937 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.970003 8.82908e-06 5811 2 103.7 0.000940017 1937 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.970035 0.000105338 5811 2 103.7 0.0120199 1937 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.970034 0.000102493 5811 2 103.7 0.0117534 1937 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.970037 0.00011216 5811 2 103.7 0.0128901 1937 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.969995 1.75867e-05 5811 2 103.7 0.00197589 1937 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.970014 4.39255e-05 5811 2 103.7 0.00494402 1937 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.969995 1.56563e-05 5811 2 103.7 0.00176399 1937 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.969972 8.35703e-05 5811 2 103.7 0.00952059 1937 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.969995 1.779e-05 5811 2 103.7 0.00199777 1937 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.970047 0.000139774 5811 2 103.7 0.0160701 1937 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.970035 0.000103955 5811 2 103.7 0.011929 1937 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.970019 5.5796e-05 5811 2 103.7 0.00639473 1937 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.969981 5.64418e-05 5811 2 103.7 0.00638168 1937 5000000 5000000 979.72742 100321.18 1.466808 294.98512 31.776601 41.259748 0 0 25798.635 -42908.424 -234.85282 -212165.26 -229202.02 5023.4102 Loop time of 38764.9 on 32 procs for 5000000 steps with 7651 atoms Performance: 11.144 ns/day, 2.154 hours/ns, 128.983 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 | 4719.1 | 16726 | 23582 |5674.2 | 43.15 Bond | 4.8515 | 10.812 | 20.587 | 145.6 | 0.03 Kspace | 7151.4 | 14050 | 26105 |6222.7 | 36.24 Neigh | 1931.5 | 1938 | 1950 | 12.6 | 5.00 Comm | 1564.4 | 1956.4 | 2160.8 | 479.6 | 5.05 Output | 0.012099 | 0.014077 | 0.016026 | 1.0 | 0.00 Modify | 3263.7 | 3701.8 | 4039.1 | 344.6 | 9.55 Other | | 381.7 | | | 0.98 Nlocal: 239.094 ave 306 max 119 min Histogram: 8 0 0 0 0 2 2 2 6 12 Nghost: 5591.47 ave 7036 max 3830 min Histogram: 8 0 0 4 4 0 0 4 4 8 Neighs: 112682 ave 164179 max 27507 min Histogram: 8 0 0 0 2 2 4 0 3 13 Total # of neighbors = 3605828 Ave neighs/atom = 471.28846 Ave special neighs/atom = 1.5765259 Neighbor list builds = 266019 Dangerous builds = 1 undump sci restart 0 dump sci all custom 5000000 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) = 0.25681581 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0032470589 estimated relative force accuracy = 9.7784213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5600 1568 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.969981 5.64418e-05 5811 2 103.7 0.00638168 1937 Per MPI rank memory allocation (min/avg/max) = 12.31 | 12.84 | 13.1 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 5000000 5000000 906.06887 100321.18 1.466808 294.98512 31.776601 41.259748 0 0 25798.635 -42596.996 -234.85282 -212476.72 -229202.04 5023.4102 Loop time of 7.82753e-06 on 32 procs for 0 steps with 7651 atoms 113.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.828e-06 | | |100.00 Nlocal: 239.094 ave 306 max 119 min Histogram: 8 0 0 0 0 2 2 2 6 12 Nghost: 5591.47 ave 7036 max 3830 min Histogram: 8 0 0 4 4 0 0 4 4 8 Neighs: 112682 ave 164179 max 27507 min Histogram: 8 0 0 0 2 2 4 0 3 13 Total # of neighbors = 3605828 Ave neighs/atom = 471.28846 Ave special neighs/atom = 1.5765259 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out