#------------------------------------------------------------------------------- # 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1928 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (40.281352 40.281352 40.281352) 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 (40.281352 40.281352 40.281352) 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 ... WARNING: System is not charge neutral, net charge = 0.0171 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25969541 grid = 32 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0026097487 estimated relative force accuracy = 7.8591807e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5175 1024 generated 0 of 28 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 = 6 6 6 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 0.97 6.45484e-13 5784 2 103.7 7.52465e-11 1928 Per MPI rank memory allocation (min/avg/max) = 12.73 | 12.91 | 12.94 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 3605.1468 65360.011 1.3291045 298.96649 31.496455 34.335384 0 0 17482.918 14473.426 -161.84744 -158047.41 -126025.23 3972.8016 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969959 0.0001255 5784 2 103.7 0.0143256 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969979 6.24256e-05 5784 2 103.7 0.00714529 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970049 0.000147151 5784 2 103.7 0.0168415 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969957 0.000129484 5784 2 103.7 0.0147909 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.96996 0.000120816 5784 2 103.7 0.0137874 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970033 9.91966e-05 5784 2 103.7 0.0113416 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969968 9.50938e-05 5784 2 103.7 0.010804 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970035 0.000105527 5784 2 103.7 0.0120203 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970001 4.19146e-06 5784 2 103.7 0.000440118 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969995 1.62596e-05 5784 2 103.7 0.00183212 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969971 8.93811e-05 5784 2 103.7 0.0101595 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970009 2.69997e-05 5784 2 103.7 0.00303269 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969993 2.08079e-05 5784 2 103.7 0.00230371 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970024 7.27636e-05 5784 2 103.7 0.00831041 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970112 0.000337831 5784 2 103.7 0.0387137 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969989 3.37988e-05 5784 2 103.7 0.00383838 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969988 3.76404e-05 5784 2 103.7 0.00427194 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970012 3.62244e-05 5784 2 103.7 0.00411921 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969993 2.32855e-05 5784 2 103.7 0.00262919 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970062 0.000183402 5784 2 103.7 0.0210605 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970039 0.000116329 5784 2 103.7 0.0133663 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969955 0.00013387 5784 2 103.7 0.0153222 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.96997 8.97125e-05 5784 2 103.7 0.0102231 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970057 0.000172321 5784 2 103.7 0.019674 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970083 0.000250976 5784 2 103.7 0.0287716 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970032 9.65748e-05 5784 2 103.7 0.0109802 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969971 8.95566e-05 5784 2 103.7 0.0102043 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969961 0.000118355 5784 2 103.7 0.013527 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969937 0.000189123 5784 2 103.7 0.0216238 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970028 8.20097e-05 5784 2 103.7 0.00933453 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970013 3.83788e-05 5784 2 103.7 0.00436887 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970021 6.43825e-05 5784 2 103.7 0.00729355 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.96994 0.000183421 5784 2 103.7 0.0209186 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969945 0.000166559 5784 2 103.7 0.0190167 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.96991 0.000271565 5784 2 103.7 0.0311616 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969926 0.000224916 5784 2 103.7 0.0256944 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969986 4.27873e-05 5784 2 103.7 0.00486043 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969975 7.71048e-05 5784 2 103.7 0.00876037 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97002 5.97018e-05 5784 2 103.7 0.00685813 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970068 0.000199964 5784 2 103.7 0.0229566 1928 2000000 2000000 196.69108 69179.134 1.2557296 291.55537 27.053235 29.690453 0 0 16533.534 15819.505 -152.91245 -158035.7 -125625.92 3874.3193 Loop time of 11549.2 on 32 procs for 2000000 steps with 6387 atoms Performance: 14.962 ns/day, 1.604 hours/ns, 173.172 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 | 5960 | 6236.8 | 6618.5 | 183.0 | 54.00 Bond | 2.1274 | 4.3286 | 7.9436 | 72.8 | 0.04 Kspace | 2173.6 | 2553.3 | 2832.9 | 289.0 | 22.11 Neigh | 481.19 | 481.69 | 482.09 | 1.2 | 4.17 Comm | 834.78 | 852.24 | 870.58 | 32.8 | 7.38 Output | 0.0074362 | 0.0092611 | 0.011007 | 1.1 | 0.00 Modify | 1263.6 | 1294.9 | 1307.4 | 22.2 | 11.21 Other | | 125.9 | | | 1.09 Nlocal: 199.594 ave 209 max 182 min Histogram: 1 1 1 1 2 5 7 6 5 3 Nghost: 6361.5 ave 6430 max 6303 min Histogram: 2 3 6 3 3 4 4 5 0 2 Neighs: 105829 ave 111752 max 96853 min Histogram: 1 2 0 3 1 6 9 3 5 2 Total # of neighbors = 3386531 Ave neighs/atom = 530.22248 Ave special neighs/atom = 1.8738062 Neighbor list builds = 100348 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) = 0.25842145 grid = 32 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0027925299 estimated relative force accuracy = 8.409621e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5175 1024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970068 0.000199964 5784 2 103.7 0.0229566 1928 Per MPI rank memory allocation (min/avg/max) = 12.73 | 12.91 | 12.94 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 583.36169 69179.134 1.2557296 291.55537 27.053235 29.690453 0 0 16533.534 15051.244 -152.91245 -157267.44 -125625.92 3874.3193 Loop time of 1.35464e-05 on 32 procs for 0 steps with 6387 atoms 109.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.355e-05 | | |100.00 Nlocal: 199.594 ave 209 max 182 min Histogram: 1 1 1 1 2 5 7 6 5 3 Nghost: 6361.5 ave 6430 max 6303 min Histogram: 2 3 6 3 3 4 4 5 0 2 Neighs: 105829 ave 111752 max 96853 min Histogram: 1 2 0 3 1 6 9 3 5 2 Total # of neighbors = 3386531 Ave neighs/atom = 530.22248 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:12:58