#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (30 30 66.477992) 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 (30 30 66.477992) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 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 2.5_averages.txt off 1 fix 3 movable ave/time 200 1 200 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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.3072063 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0027406224 estimated relative force accuracy = 8.2533029e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 1 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 = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 5 12 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 1 0.97 7.84039e-13 6000 1 103.7 7.60565e-11 2000 Per MPI rank memory allocation (min/avg/max) = 9.684 | 9.726 | 9.754 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 -247.85234 59830.193 1.0000033 290.72933 0 0 0 0 5070.6195 99682.552 -178.76427 -126402.13 -21648.963 3465.5691 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970004 1.29977e-05 6000 1 103.7 0.00146963 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970036 0.000109674 6000 1 103.7 0.0125644 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969986 4.28836e-05 6000 1 103.7 0.00482778 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969941 0.000178651 6000 1 103.7 0.0203769 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970015 4.66208e-05 6000 1 103.7 0.00531777 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969973 8.23834e-05 6000 1 103.7 0.00935302 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969955 0.000135884 6000 1 103.7 0.0155151 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970063 0.000185765 6000 1 103.7 0.0213124 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969988 3.93516e-05 6000 1 103.7 0.00443961 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969952 0.000146706 6000 1 103.7 0.0167321 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.970002 7.36426e-06 6000 1 103.7 0.000813421 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970037 0.000110949 6000 1 103.7 0.0126881 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969963 0.000109023 6000 1 103.7 0.0124417 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969985 4.62286e-05 6000 1 103.7 0.0052737 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969985 4.49288e-05 6000 1 103.7 0.00510041 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970003 7.72077e-06 6000 1 103.7 0.000853216 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969935 0.000198639 6000 1 103.7 0.0226909 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.44408e-06 6000 1 103.7 0.000141715 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970032 9.39502e-05 6000 1 103.7 0.0107062 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970037 0.000112109 6000 1 103.7 0.0128293 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970018 5.28506e-05 6000 1 103.7 0.00608095 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969955 0.000136711 6000 1 103.7 0.0155649 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 2.26192e-06 6000 1 103.7 0.000213461 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969942 0.000173893 6000 1 103.7 0.0198414 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970047 0.000141822 6000 1 103.7 0.0161919 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969993 2.10979e-05 6000 1 103.7 0.00237739 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.969943 0.000170687 6000 1 103.7 0.0194831 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970042 0.000127546 6000 1 103.7 0.0145999 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970031 9.40121e-05 6000 1 103.7 0.0107673 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970083 0.000249852 6000 1 103.7 0.0285276 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.96996 0.000121214 6000 1 103.7 0.0138208 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969919 0.000244448 6000 1 103.7 0.0279705 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970011 3.35214e-05 6000 1 103.7 0.00381723 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969936 0.000190073 6000 1 103.7 0.021657 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.969942 0.000175836 6000 1 103.7 0.0200681 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969948 0.000158448 6000 1 103.7 0.0181083 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970009 2.81895e-05 6000 1 103.7 0.00320692 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970122 0.000371202 6000 1 103.7 0.0425537 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97003 8.98013e-05 6000 1 103.7 0.0102556 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969979 6.50391e-05 6000 1 103.7 0.00741938 2000 2000000 2000000 -1.4543253 59678.034 1.002553 287.786 0 0 0 0 5183.8993 99526.615 -179.22006 -126406.51 -21695.994 3430.4838 Loop time of 8984.93 on 32 procs for 2000000 steps with 6000 atoms Performance: 19.232 ns/day, 1.248 hours/ns, 222.595 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3799.8 | 3829.3 | 3881.5 | 28.2 | 42.62 Bond | 1.9372 | 2.2397 | 3.1997 | 16.2 | 0.02 Kspace | 2682.8 | 2729.6 | 2758.5 | 32.8 | 30.38 Neigh | 306.98 | 307.58 | 308.23 | 2.4 | 3.42 Comm | 643.2 | 648.97 | 655.34 | 14.1 | 7.22 Output | 0.0073474 | 0.0091326 | 0.01084 | 1.1 | 0.00 Modify | 1037 | 1256.6 | 1398.6 | 436.4 | 13.99 Other | | 210.6 | | | 2.34 Nlocal: 187.5 ave 204 max 169 min Histogram: 1 1 3 4 3 8 5 3 3 1 Nghost: 4742.59 ave 4833 max 4674 min Histogram: 3 5 1 4 5 9 1 2 1 1 Neighs: 68147.2 ave 77000 max 60480 min Histogram: 1 0 5 6 6 5 8 0 0 1 Total # of neighbors = 2180712 Ave neighs/atom = 363.452 Ave special neighs/atom = 2 Neighbor list builds = 106994 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.30730849 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0027267418 estimated relative force accuracy = 8.2115019e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969979 6.50391e-05 6000 1 103.7 0.00741938 2000 Per MPI rank memory allocation (min/avg/max) = 9.685 | 9.728 | 9.757 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 2000000 2000000 -147.42827 59678.034 1.002553 287.786 0 0 0 0 5183.8993 99568.569 -179.22006 -126448.46 -21695.994 3430.4838 Loop time of 1.16188e-05 on 32 procs for 0 steps with 6000 atoms 108.7% 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 | | 1.162e-05 | | |100.00 Nlocal: 187.5 ave 204 max 169 min Histogram: 1 1 3 4 3 8 5 3 3 1 Nghost: 4742.59 ave 4833 max 4674 min Histogram: 3 5 1 4 5 9 1 2 1 1 Neighs: 68147.2 ave 77000 max 60480 min Histogram: 1 0 5 6 6 5 8 0 0 1 Total # of neighbors = 2180712 Ave neighs/atom = 363.452 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 4:36:20