#------------------------------------------------------------------------------- # 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 2297 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (29.25318 24.458 120.4) 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 (29.25318 24.458 120.4) 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 = 0.0204 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25875832 grid = 25 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028059658 estimated relative force accuracy = 8.4500828e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1800 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 4 18 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 1.00352 0.118618 6891 2 97.5134 11.7656 2297 Per MPI rank memory allocation (min/avg/max) = 12.46 | 12.83 | 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 0 1e-06 1747.8276 86143.103 1.2514495 422.44549 22.907487 94.906301 0 0 23337.604 4740.2731 -191.3806 -200333.82 -172138.13 6942.1337 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970021 6.20354e-05 6891 2 103.7 0.00711155 2297 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970029 8.4829e-05 6891 2 103.7 0.00970685 2297 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969991 2.77285e-05 6891 2 103.7 0.00308468 2297 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970012 3.5692e-05 6891 2 103.7 0.00408603 2297 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969994 2.01623e-05 6891 2 103.7 0.00227683 2297 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969935 0.000194871 6891 2 103.7 0.0222408 2297 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970021 6.43005e-05 6891 2 103.7 0.00734051 2297 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969998 7.11743e-06 6891 2 103.7 0.000763816 2297 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970007 2.05266e-05 6891 2 103.7 0.00232535 2297 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970021 6.33586e-05 6891 2 103.7 0.00722327 2297 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970024 7.23207e-05 6891 2 103.7 0.0082522 2297 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970012 3.55724e-05 6891 2 103.7 0.00410042 2297 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970007 2.07633e-05 6891 2 103.7 0.00233555 2297 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969951 0.000148456 6891 2 103.7 0.0169571 2297 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969948 0.000157464 6891 2 103.7 0.0179701 2297 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969935 0.000192648 6891 2 103.7 0.0219674 2297 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969952 0.000142312 6891 2 103.7 0.0161997 2297 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970016 4.73702e-05 6891 2 103.7 0.00544614 2297 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970025 7.5318e-05 6891 2 103.7 0.0085818 2297 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.96998 5.99227e-05 6891 2 103.7 0.00681345 2297 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969978 6.5147e-05 6891 2 103.7 0.00738239 2297 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969975 7.56105e-05 6891 2 103.7 0.00860244 2297 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970059 0.000175339 6891 2 103.7 0.0200717 2297 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970034 0.000100322 6891 2 103.7 0.0114932 2297 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969976 7.31634e-05 6891 2 103.7 0.00830116 2297 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97003 8.79678e-05 6891 2 103.7 0.0100577 2297 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97001 2.99972e-05 6891 2 103.7 0.00340664 2297 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970001 3.53914e-06 6891 2 103.7 0.000375337 2297 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970034 0.000102067 6891 2 103.7 0.0117201 2297 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969984 4.75727e-05 6891 2 103.7 0.00541678 2297 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969975 7.62568e-05 6891 2 103.7 0.00873497 2297 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970056 0.000164204 6891 2 103.7 0.0188291 2297 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970021 6.35177e-05 6891 2 103.7 0.00732401 2297 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969984 4.82599e-05 6891 2 103.7 0.00545727 2297 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969975 7.43332e-05 6891 2 103.7 0.00851506 2297 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969943 0.000171151 6891 2 103.7 0.0195383 2297 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969944 0.000165317 6891 2 103.7 0.0189302 2297 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970038 0.000112438 6891 2 103.7 0.0128963 2297 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969991 2.8493e-05 6891 2 103.7 0.00322092 2297 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969995 1.67927e-05 6891 2 103.7 0.00185098 2297 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.969995 1.69875e-05 6891 2 103.7 0.00189827 2297 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970014 4.12719e-05 6891 2 103.7 0.00473373 2297 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.970027 8.11444e-05 6891 2 103.7 0.0092836 2297 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.970007 2.25503e-05 6891 2 103.7 0.00258701 2297 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.970052 0.000154492 6891 2 103.7 0.017693 2297 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969998 6.33526e-06 6891 2 103.7 0.000669778 2297 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.970006 1.77731e-05 6891 2 103.7 0.00203801 2297 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.969969 9.24749e-05 6891 2 103.7 0.0105053 2297 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.969943 0.000171882 6891 2 103.7 0.0196748 2297 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.969916 0.000249709 6891 2 103.7 0.0284889 2297 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.970041 0.000122874 6891 2 103.7 0.0141367 2297 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.970037 0.000111281 6891 2 103.7 0.012747 2297 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970015 4.53215e-05 6891 2 103.7 0.00517893 2297 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.96992 0.000243384 6891 2 103.7 0.0278654 2297 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.969953 0.000141584 6891 2 103.7 0.0161695 2297 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.969984 4.80467e-05 6891 2 103.7 0.00541801 2297 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.969962 0.000114606 6891 2 103.7 0.0131054 2297 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.970045 0.0001328 6891 2 103.7 0.0152705 2297 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.970013 3.98439e-05 6891 2 103.7 0.00455674 2297 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969969 9.1937e-05 6891 2 103.7 0.0104597 2297 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.969998 5.9177e-06 6891 2 103.7 0.000613427 2297 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.970041 0.000123693 6891 2 103.7 0.0141009 2297 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.970025 7.37058e-05 6891 2 103.7 0.00840821 2297 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.969981 5.83226e-05 6891 2 103.7 0.006641 2297 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.969957 0.000129273 6891 2 103.7 0.0147459 2297 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.970001 3.10741e-06 6891 2 103.7 0.000334167 2297 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.969962 0.000112718 6891 2 103.7 0.0128442 2297 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.970067 0.000201548 6891 2 103.7 0.0230744 2297 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97004 0.000116921 6891 2 103.7 0.0134023 2297 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.969987 4.09998e-05 6891 2 103.7 0.00461271 2297 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.970035 0.000106132 6891 2 103.7 0.0121448 2297 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97001 3.05452e-05 6891 2 103.7 0.00348768 2297 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.970041 0.000121349 6891 2 103.7 0.0139192 2297 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.970031 9.24715e-05 6891 2 103.7 0.0105941 2297 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.969958 0.000125474 6891 2 103.7 0.014309 2297 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.969977 6.91196e-05 6891 2 103.7 0.00781857 2297 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.969988 3.81754e-05 6891 2 103.7 0.00430855 2297 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.970032 9.52504e-05 6891 2 103.7 0.0109137 2297 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.970006 1.93159e-05 6891 2 103.7 0.00221679 2297 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.970026 7.7309e-05 6891 2 103.7 0.00885373 2297 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.969997 1.01579e-05 6891 2 103.7 0.00112954 2297 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.970057 0.00016557 6891 2 103.7 0.0189236 2297 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.969983 5.22055e-05 6891 2 103.7 0.00595127 2297 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.969947 0.000161549 6891 2 103.7 0.0184179 2297 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.970039 0.000114837 6891 2 103.7 0.0131754 2297 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.969982 5.67255e-05 6891 2 103.7 0.0063856 2297 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.969952 0.000148022 6891 2 103.7 0.016928 2297 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.96997 9.20398e-05 6891 2 103.7 0.0105179 2297 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.969989 3.54617e-05 6891 2 103.7 0.0040209 2297 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.969991 2.82316e-05 6891 2 103.7 0.00313212 2297 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.969905 0.000283442 6891 2 103.7 0.0324739 2297 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.969984 4.97823e-05 6891 2 103.7 0.005681 2297 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.71003e-06 6891 2 103.7 0.000130051 2297 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.970043 0.000128374 6891 2 103.7 0.0147389 2297 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.970047 0.00014049 6891 2 103.7 0.0160869 2297 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.96993 0.000211075 6891 2 103.7 0.0241238 2297 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.970048 0.000141372 6891 2 103.7 0.0161314 2297 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.970035 0.000104097 6891 2 103.7 0.0119223 2297 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.970024 7.24826e-05 6891 2 103.7 0.00822847 2297 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.969987 4.11825e-05 6891 2 103.7 0.0046561 2297 5000000 5000000 -153.94865 80485.548 1.3394174 297.90367 123.30642 145.14562 0 0 19690.498 19984.516 -204.83328 -200257.43 -160313.97 4895.5123 Loop time of 41519.2 on 32 procs for 5000000 steps with 7811 atoms Performance: 10.405 ns/day, 2.307 hours/ns, 120.426 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17966 | 19848 | 26163 |1608.4 | 47.80 Bond | 6.5045 | 20.124 | 62.484 | 351.3 | 0.05 Kspace | 6540.6 | 12907 | 14806 |2013.7 | 31.09 Neigh | 1985 | 1990.8 | 1995.7 | 6.7 | 4.79 Comm | 2229.4 | 2308.8 | 2437.6 | 119.5 | 5.56 Output | 0.012004 | 0.014037 | 0.015962 | 1.0 | 0.00 Modify | 3604 | 3886 | 4286.1 | 371.1 | 9.36 Other | | 558.3 | | | 1.34 Nlocal: 244.094 ave 299 max 220 min Histogram: 5 6 8 4 5 0 2 1 0 1 Nghost: 6745.97 ave 7092 max 6447 min Histogram: 2 7 3 8 0 0 1 2 7 2 Neighs: 136455 ave 186798 max 116217 min Histogram: 6 9 5 7 0 1 0 2 1 1 Total # of neighbors = 4366570 Ave neighs/atom = 559.02829 Ave special neighs/atom = 1.9743951 Neighbor list builds = 269359 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) = 0.25671212 grid = 25 24 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0033834134 estimated relative force accuracy = 1.0189049e-05 using double precision KISS FFT 3d grid and FFT values/proc = 5415 1248 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.969987 4.11825e-05 6891 2 103.7 0.0046561 2297 Per MPI rank memory allocation (min/avg/max) = 12.83 | 12.95 | 13.43 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 -232.98833 80485.548 1.3394174 297.90367 123.30642 145.14562 0 0 19690.498 18413.282 -204.83328 -198685.96 -160313.73 4895.5123 Loop time of 7.78872e-06 on 32 procs for 0 steps with 7811 atoms 119.2% 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 | | 7.789e-06 | | |100.00 Nlocal: 244.094 ave 299 max 220 min Histogram: 5 6 8 4 5 0 2 1 0 1 Nghost: 6745.97 ave 7092 max 6447 min Histogram: 2 7 3 8 0 0 1 2 7 2 Neighs: 136455 ave 186798 max 116217 min Histogram: 6 9 5 7 0 1 0 2 1 1 Total # of neighbors = 4366570 Ave neighs/atom = 559.02829 Ave special neighs/atom = 1.9743951 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out