#------------------------------------------------------------------------------- # 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 4018 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (40.9194 40.9194 115) 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 (40.9194 40.9194 115) 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 = 0.0216 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32534663 grid = 45 45 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0032776969 estimated relative force accuracy = 9.870687e-06 using double precision KISS FFT 3d grid and FFT values/proc = 16200 6348 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 8 8 20 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 1.00006 0.0729435 12054 2 97.8181 9.87316 4018 Per MPI rank memory allocation (min/avg/max) = 13.27 | 13.73 | 14.04 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 -2610.7159 192555.69 1.3951015 406.075 9.3240439 226.82985 0 0 46205.238 47272.584 -847.6545 -497063.98 -403350.01 13444.273 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970017 5.21786e-05 12054 2 103.7 0.00598273 4018 SHAKE stats (type/ave/delta/count) on step 100000 2 0.96998 6.30771e-05 12054 2 103.7 0.00714727 4018 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97001 3.14627e-05 12054 2 103.7 0.00358241 4018 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969979 6.52301e-05 12054 2 103.7 0.00744646 4018 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970006 1.8582e-05 12054 2 103.7 0.00207873 4018 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970006 1.76488e-05 12054 2 103.7 0.00200666 4018 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969985 4.64889e-05 12054 2 103.7 0.00528357 4018 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969995 1.7449e-05 12054 2 103.7 0.00196165 4018 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969988 3.62519e-05 12054 2 103.7 0.00409389 4018 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969996 1.45356e-05 12054 2 103.7 0.00160626 4018 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970003 8.43842e-06 12054 2 103.7 0.00093904 4018 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969984 4.92379e-05 12054 2 103.7 0.00559902 4018 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970039 0.00011902 12054 2 103.7 0.0136203 4018 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970088 0.000263645 12054 2 103.7 0.0301464 4018 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970002 4.99037e-06 12054 2 103.7 0.000546002 4018 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969983 5.24665e-05 12054 2 103.7 0.00597199 4018 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969984 5.07283e-05 12054 2 103.7 0.00573864 4018 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.9508e-06 12054 2 103.7 0.000164973 4018 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970005 1.45705e-05 12054 2 103.7 0.00165338 4018 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970012 3.52191e-05 12054 2 103.7 0.00397777 4018 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970001 4.26492e-06 12054 2 103.7 0.000468319 4018 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969994 1.95385e-05 12054 2 103.7 0.00219135 4018 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970005 1.66745e-05 12054 2 103.7 0.00187675 4018 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969949 0.000154855 12054 2 103.7 0.0177372 4018 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970005 1.67155e-05 12054 2 103.7 0.00184791 4018 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970019 5.63778e-05 12054 2 103.7 0.00643923 4018 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969999 4.67804e-06 12054 2 103.7 0.000501157 4018 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969971 8.73177e-05 12054 2 103.7 0.00998296 4018 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970008 2.52601e-05 12054 2 103.7 0.00287955 4018 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969983 5.06426e-05 12054 2 103.7 0.00576595 4018 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970054 0.000160198 12054 2 103.7 0.0183483 4018 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969991 2.73704e-05 12054 2 103.7 0.00309398 4018 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970014 4.31015e-05 12054 2 103.7 0.00493904 4018 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969979 6.35445e-05 12054 2 103.7 0.00723895 4018 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97002 6.09489e-05 12054 2 103.7 0.00695939 4018 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970034 0.000102543 12054 2 103.7 0.0117819 4018 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970036 0.000108067 12054 2 103.7 0.0123948 4018 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 2.41758e-06 12054 2 103.7 0.00023999 4018 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970016 4.88662e-05 12054 2 103.7 0.00552948 4018 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970012 3.59568e-05 12054 2 103.7 0.00410012 4018 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.970029 8.85355e-05 12054 2 103.7 0.0101436 4018 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970012 3.66479e-05 12054 2 103.7 0.00417478 4018 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.970034 0.000100629 12054 2 103.7 0.0115256 4018 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.970003 9.85106e-06 12054 2 103.7 0.00108546 4018 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.970051 0.000153972 12054 2 103.7 0.0175732 4018 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.970006 1.94081e-05 12054 2 103.7 0.00222894 4018 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.970016 4.92631e-05 12054 2 103.7 0.00563095 4018 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.969978 6.82584e-05 12054 2 103.7 0.0077935 4018 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.970024 7.35655e-05 12054 2 103.7 0.00836534 4018 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.969988 3.6108e-05 12054 2 103.7 0.00408471 4018 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.970022 6.84542e-05 12054 2 103.7 0.00777798 4018 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.970016 4.87928e-05 12054 2 103.7 0.00558344 4018 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970066 0.000199962 12054 2 103.7 0.0229342 4018 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.970039 0.000118329 12054 2 103.7 0.0135111 4018 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.969984 4.98449e-05 12054 2 103.7 0.00564633 4018 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.970021 6.28255e-05 12054 2 103.7 0.00720738 4018 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.969989 3.43663e-05 12054 2 103.7 0.00388627 4018 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.969979 6.56144e-05 12054 2 103.7 0.00744817 4018 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.969976 7.39036e-05 12054 2 103.7 0.00840913 4018 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.970031 9.34918e-05 12054 2 103.7 0.0106807 4018 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.969997 9.07846e-06 12054 2 103.7 0.000992463 4018 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.970029 8.90538e-05 12054 2 103.7 0.0101881 4018 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.970013 3.93837e-05 12054 2 103.7 0.00446873 4018 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.969967 0.000100819 12054 2 103.7 0.0114812 4018 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.970055 0.000164299 12054 2 103.7 0.0188413 4018 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.970005 1.48118e-05 12054 2 103.7 0.00166561 4018 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.969989 3.35796e-05 12054 2 103.7 0.00382542 4018 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.969968 9.86056e-05 12054 2 103.7 0.0112934 4018 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.970001 3.23552e-06 12054 2 103.7 0.00032544 4018 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.969989 3.45851e-05 12054 2 103.7 0.00390485 4018 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.970024 7.28731e-05 12054 2 103.7 0.00837661 4018 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.970024 7.28016e-05 12054 2 103.7 0.00836272 4018 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.96996 0.000119886 12054 2 103.7 0.0136907 4018 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.970038 0.000112295 12054 2 103.7 0.0128381 4018 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.970027 7.99483e-05 12054 2 103.7 0.00916555 4018 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.969939 0.000186733 12054 2 103.7 0.0213485 4018 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.970021 6.12317e-05 12054 2 103.7 0.00700975 4018 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97003 9.09128e-05 12054 2 103.7 0.0104279 4018 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.970017 5.22089e-05 12054 2 103.7 0.00598317 4018 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.969995 1.67711e-05 12054 2 103.7 0.00187396 4018 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.969957 0.000128838 12054 2 103.7 0.0147174 4018 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.969992 2.55494e-05 12054 2 103.7 0.00286564 4018 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.970006 1.69028e-05 12054 2 103.7 0.00194252 4018 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.970002 7.17922e-06 12054 2 103.7 0.000791393 4018 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.970019 5.88742e-05 12054 2 103.7 0.00672567 4018 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.969951 0.000149438 12054 2 103.7 0.0170954 4018 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.969956 0.000133157 12054 2 103.7 0.0152066 4018 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.970002 5.21048e-06 12054 2 103.7 0.000557783 4018 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.969997 9.40894e-06 12054 2 103.7 0.00103228 4018 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.96997 9.18872e-05 12054 2 103.7 0.0104323 4018 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.970027 8.23757e-05 12054 2 103.7 0.00942414 4018 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.970005 1.70015e-05 12054 2 103.7 0.00189644 4018 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.969996 1.24484e-05 12054 2 103.7 0.00137194 4018 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.969999 4.06555e-06 12054 2 103.7 0.000402654 4018 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.970004 1.34046e-05 12054 2 103.7 0.00153791 4018 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.970015 4.66538e-05 12054 2 103.7 0.00530603 4018 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.969959 0.000125032 12054 2 103.7 0.0142589 4018 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.970001 3.39935e-06 12054 2 103.7 0.000332607 4018 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.969986 4.30628e-05 12054 2 103.7 0.00488084 4018 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.970037 0.000112302 12054 2 103.7 0.0129068 4018 5000000 5000000 883.65003 189229.23 1.419626 297.91409 54.825879 279.92927 0 0 43785.463 69998.909 -862.55543 -496555.99 -382436.86 9863.2971 Loop time of 58591.2 on 32 procs for 5000000 steps with 15126 atoms Performance: 7.373 ns/day, 3.255 hours/ns, 85.337 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4458.2 | 17936 | 23631 |5451.8 | 30.61 Bond | 5.714 | 17.379 | 29.405 | 172.6 | 0.03 Kspace | 21125 | 26779 | 40367 |4498.9 | 45.70 Neigh | 2011.7 | 2020.8 | 2046.8 | 21.7 | 3.45 Comm | 1847.5 | 2519.1 | 2757.7 | 598.6 | 4.30 Output | 0.015903 | 0.019053 | 0.022103 | 1.4 | 0.00 Modify | 6913.6 | 8329.4 | 9133 | 734.5 | 14.22 Other | | 989.2 | | | 1.69 Nlocal: 472.688 ave 588 max 200 min Histogram: 4 4 0 0 0 0 0 0 10 14 Nghost: 5135.28 ave 6138 max 3448 min Histogram: 4 4 0 0 4 4 0 0 0 16 Neighs: 128634 ave 177282 max 25299 min Histogram: 4 4 0 0 0 0 4 0 5 15 Total # of neighbors = 4116276 Ave neighs/atom = 272.13249 Ave special neighs/atom = 1.65199 Neighbor list builds = 275636 Dangerous builds = 0 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) = 0.32606129 grid = 45 45 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0031698471 estimated relative force accuracy = 9.5459005e-06 using double precision KISS FFT 3d grid and FFT values/proc = 16200 6348 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.970037 0.000112302 12054 2 103.7 0.0129068 4018 Per MPI rank memory allocation (min/avg/max) = 13.27 | 13.82 | 14.07 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 1046.5973 189229.23 1.419626 297.91409 54.825879 279.92927 0 0 43785.463 71069.545 -862.55543 -497626.76 -382437 9863.2971 Loop time of 7.51091e-06 on 32 procs for 0 steps with 15126 atoms 119.4% 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 | | 7.511e-06 | | |100.00 Nlocal: 472.688 ave 588 max 200 min Histogram: 4 4 0 0 0 0 0 0 10 14 Nghost: 5135.28 ave 6138 max 3448 min Histogram: 4 4 0 0 4 4 0 0 0 16 Neighs: 128634 ave 177282 max 25299 min Histogram: 4 4 0 0 0 0 4 0 5 15 Total # of neighbors = 4116276 Ave neighs/atom = 272.13249 Ave special neighs/atom = 1.65199 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out