#------------------------------------------------------------------------------- # 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 2009 = # 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 96.6) 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 96.6) 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 = 0.0108 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25612274 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0032834538 estimated relative force accuracy = 9.8880237e-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 0.999993 0.0882309 6027 2 97.8107 9.76229 2009 Per MPI rank memory allocation (min/avg/max) = 12.27 | 12.72 | 13.09 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 -5300.4729 103515.91 1.4288039 400.90595 4.6837102 11.281487 0 0 25299.393 -43125.644 -231.76702 -209489.44 -227299.73 6970.5778 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970006 1.81441e-05 6027 2 103.7 0.00200771 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969966 0.000100964 6027 2 103.7 0.0114796 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969953 0.000142216 6027 2 103.7 0.0162515 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970028 8.36083e-05 6027 2 103.7 0.00958607 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970036 0.000108437 6027 2 103.7 0.0124232 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969999 4.3895e-06 6027 2 103.7 0.000460525 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970065 0.000194423 6027 2 103.7 0.022262 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970007 2.22022e-05 6027 2 103.7 0.00257419 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970018 5.31374e-05 6027 2 103.7 0.00609839 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969949 0.000152964 6027 2 103.7 0.0174661 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969959 0.000124809 6027 2 103.7 0.0142553 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970014 4.29538e-05 6027 2 103.7 0.00492934 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970045 0.00013387 6027 2 103.7 0.0153561 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970007 2.06846e-05 6027 2 103.7 0.00233218 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.96994 0.00018047 6027 2 103.7 0.0206473 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.96999 3.18566e-05 6027 2 103.7 0.00360109 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970004 1.26669e-05 6027 2 103.7 0.00138825 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969987 4.16379e-05 6027 2 103.7 0.00473166 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.9168e-06 6027 2 103.7 0.000171147 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970054 0.000165045 6027 2 103.7 0.0189205 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969983 5.29996e-05 6027 2 103.7 0.00600134 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970007 2.22192e-05 6027 2 103.7 0.00250309 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970017 5.20453e-05 6027 2 103.7 0.00594251 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969985 4.47752e-05 6027 2 103.7 0.00509217 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970058 0.000175384 6027 2 103.7 0.0200864 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970003 9.11635e-06 6027 2 103.7 0.00103332 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969948 0.00015699 6027 2 103.7 0.01794 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.96993 0.000209739 6027 2 103.7 0.0240187 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970013 3.90273e-05 6027 2 103.7 0.00444889 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969996 1.4851e-05 6027 2 103.7 0.00167231 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970049 0.000148677 6027 2 103.7 0.0170313 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969955 0.000135375 6027 2 103.7 0.0154235 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969989 3.52761e-05 6027 2 103.7 0.00399529 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969981 5.95989e-05 6027 2 103.7 0.00677044 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97004 0.000120375 6027 2 103.7 0.0138391 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969967 0.000100555 6027 2 103.7 0.011462 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970053 0.000159154 6027 2 103.7 0.018242 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969958 0.00012494 6027 2 103.7 0.0142949 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969997 9.38419e-06 6027 2 103.7 0.00104044 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.96998 6.06975e-05 6027 2 103.7 0.00689798 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.969979 6.3455e-05 6027 2 103.7 0.00721712 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970029 8.81704e-05 6027 2 103.7 0.0100609 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.970066 0.000199274 6027 2 103.7 0.0227815 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.970015 4.52818e-05 6027 2 103.7 0.00509246 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.970008 2.51109e-05 6027 2 103.7 0.00280151 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969919 0.000242535 6027 2 103.7 0.0276704 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.970009 2.68684e-05 6027 2 103.7 0.00309749 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.970033 0.000100508 6027 2 103.7 0.0114405 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.970008 2.50869e-05 6027 2 103.7 0.00282936 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.969929 0.000217671 6027 2 103.7 0.0249255 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.970059 0.000178285 6027 2 103.7 0.0204243 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.969992 2.62112e-05 6027 2 103.7 0.00291851 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970057 0.000171518 6027 2 103.7 0.0196296 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.96999 3.13337e-05 6027 2 103.7 0.00352592 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.970061 0.000179866 6027 2 103.7 0.0205023 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.969994 1.96913e-05 6027 2 103.7 0.00220457 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.969978 6.72096e-05 6027 2 103.7 0.00765812 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.62807e-06 6027 2 103.7 0.000135496 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.969997 1.15218e-05 6027 2 103.7 0.00126263 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.970015 4.63191e-05 6027 2 103.7 0.00526509 2009 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.970043 0.000128773 6027 2 103.7 0.0147637 2009 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.970044 0.000133811 6027 2 103.7 0.0152974 2009 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.969956 0.000132913 6027 2 103.7 0.0151705 2009 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.969981 5.83805e-05 6027 2 103.7 0.00667741 2009 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.970079 0.00023872 6027 2 103.7 0.0273388 2009 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.970008 2.53161e-05 6027 2 103.7 0.00287779 2009 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.969957 0.000129694 6027 2 103.7 0.014806 2009 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.970024 7.3344e-05 6027 2 103.7 0.00829782 2009 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.970046 0.000139402 6027 2 103.7 0.0159816 2009 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.970031 9.29159e-05 6027 2 103.7 0.0106001 2009 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.969966 0.000104824 6027 2 103.7 0.0119144 2009 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.969931 0.00020691 6027 2 103.7 0.0236406 2009 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.969972 8.56032e-05 6027 2 103.7 0.00971037 2009 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.970002 7.00185e-06 6027 2 103.7 0.000783075 2009 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.970009 2.85546e-05 6027 2 103.7 0.0032362 2009 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.970003 8.56622e-06 6027 2 103.7 0.000956598 2009 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.969946 0.000164486 6027 2 103.7 0.0188119 2009 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.969973 8.05829e-05 6027 2 103.7 0.00918415 2009 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.970031 9.38887e-05 6027 2 103.7 0.0107545 2009 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97001 2.92525e-05 6027 2 103.7 0.00331847 2009 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97001 3.15206e-05 6027 2 103.7 0.00356414 2009 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.970037 0.000109135 6027 2 103.7 0.0124417 2009 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.970015 4.67574e-05 6027 2 103.7 0.00534187 2009 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.969951 0.000148124 6027 2 103.7 0.0168897 2009 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.969923 0.000229833 6027 2 103.7 0.0262725 2009 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.969976 7.28552e-05 6027 2 103.7 0.00824996 2009 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.970015 4.51654e-05 6027 2 103.7 0.00518793 2009 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.96998 6.2168e-05 6027 2 103.7 0.00704621 2009 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.970046 0.000135296 6027 2 103.7 0.0155227 2009 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.969992 2.60552e-05 6027 2 103.7 0.00291573 2009 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.970016 4.9005e-05 6027 2 103.7 0.00561516 2009 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.970037 0.000112745 6027 2 103.7 0.0129095 2009 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.970059 0.000176472 6027 2 103.7 0.0202541 2009 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.970021 6.30769e-05 6027 2 103.7 0.00726408 2009 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.970013 3.89967e-05 6027 2 103.7 0.00447056 2009 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.969981 5.76342e-05 6027 2 103.7 0.00657536 2009 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.969955 0.000138471 6027 2 103.7 0.0158261 2009 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.969979 6.39091e-05 6027 2 103.7 0.00727866 2009 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97005 0.000150538 6027 2 103.7 0.0172264 2009 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.969971 8.8838e-05 6027 2 103.7 0.0101053 2009 5000000 5000000 1136.741 101772.3 1.4532829 295.40983 30.725731 33.305597 0 0 24188.662 -31282.506 -235.73777 -209401.82 -216431.63 5136.3098 Loop time of 39633.6 on 32 procs for 5000000 steps with 7843 atoms Performance: 10.900 ns/day, 2.202 hours/ns, 126.155 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 | 4934.1 | 17319 | 24359 |5622.6 | 43.70 Bond | 4.7955 | 10.626 | 32.659 | 166.8 | 0.03 Kspace | 7051.5 | 14158 | 26594 |6250.8 | 35.72 Neigh | 1993.4 | 1999.4 | 2010 | 11.5 | 5.04 Comm | 1592.4 | 2014.3 | 2219.3 | 465.4 | 5.08 Output | 0.0097592 | 0.011749 | 0.013709 | 1.1 | 0.00 Modify | 3232.4 | 3741.7 | 4090.6 | 391.5 | 9.44 Other | | 390.2 | | | 0.98 Nlocal: 245.094 ave 311 max 127 min Histogram: 8 0 0 0 0 4 0 1 6 13 Nghost: 5762.78 ave 7090 max 4102 min Histogram: 8 0 0 4 4 0 0 4 4 8 Neighs: 116691 ave 168867 max 28730 min Histogram: 8 0 0 0 1 3 4 0 3 13 Total # of neighbors = 3734109 Ave neighs/atom = 476.10723 Ave special neighs/atom = 1.5930129 Neighbor list builds = 264401 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) = 0.2565108 grid = 27 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0032176618 estimated relative force accuracy = 9.6898931e-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 0.969971 8.8838e-05 6027 2 103.7 0.0101053 2009 Per MPI rank memory allocation (min/avg/max) = 12.31 | 12.85 | 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 1018.26 101772.3 1.4532829 295.40983 30.725731 33.305597 0 0 24188.662 -30967.027 -235.73777 -209717.33 -216431.66 5136.3098 Loop time of 7.94072e-06 on 32 procs for 0 steps with 7843 atoms 80.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.941e-06 | | |100.00 Nlocal: 245.094 ave 311 max 127 min Histogram: 8 0 0 0 0 4 0 1 6 13 Nghost: 5762.78 ave 7090 max 4102 min Histogram: 8 0 0 4 4 0 0 4 4 8 Neighs: 116691 ave 168867 max 28730 min Histogram: 8 0 0 0 1 3 4 0 3 13 Total # of neighbors = 3734109 Ave neighs/atom = 476.10723 Ave special neighs/atom = 1.5930129 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out