#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 2066 = # of frozen angles find clusters CPU = 0.000 seconds 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 fix 1 movable npt temp 298.2 298.2 100 iso 0.9869233 0.9869233 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 2.4_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 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.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) = 0.25646456 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0024704977 estimated relative force accuracy = 7.4398305e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.99946 0.0506703 6198 1 97.8947 9.13012 2066 Per MPI rank memory allocation (min/avg/max) = 11.98 | 12.04 | 12.39 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 -3761.5981 63413.107 1.0257024 444.08709 0 0 0 0 10167.824 61878.423 -113.19011 -113474.19 -41427.948 5590.151 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970028 1.30132e-06 6198 1 103.7 0.000106705 2066 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970012 1.7138e-06 6198 1 103.7 0.000102453 2066 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970098 1.74668e-06 6198 1 103.7 0.000127968 2066 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970025 1.41981e-06 6198 1 103.7 9.71013e-05 2066 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970067 1.31202e-06 6198 1 103.7 0.000109828 2066 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970037 1.62245e-06 6198 1 103.7 0.000116332 2066 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970125 2.26004e-06 6198 1 103.7 0.000178202 2066 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970054 1.64451e-06 6198 1 103.7 0.000112068 2066 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970021 1.41542e-06 6198 1 103.7 0.000124661 2066 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969878 1.53555e-06 6198 1 103.7 0.000112562 2066 SHAKE stats (type/ave/delta/count) on step 550000 1 0.96993 1.35097e-06 6198 1 103.7 0.000121627 2066 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970098 1.27239e-06 6198 1 103.7 9.65388e-05 2066 SHAKE stats (type/ave/delta/count) on step 650000 1 0.970001 1.33533e-06 6198 1 103.7 0.000104699 2066 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969944 1.4589e-06 6198 1 103.7 0.000108927 2066 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969988 1.30777e-06 6198 1 103.7 0.000106626 2066 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969962 1.34913e-06 6198 1 103.7 9.75468e-05 2066 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969913 1.0563e-06 6198 1 103.7 8.94526e-05 2066 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969891 1.28784e-06 6198 1 103.7 9.35953e-05 2066 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969985 1.27256e-06 6198 1 103.7 9.9298e-05 2066 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969959 1.29596e-06 6198 1 103.7 9.86538e-05 2066 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970068 1.47984e-06 6198 1 103.7 0.000108521 2066 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970029 2.21402e-06 6198 1 103.7 0.00016959 2066 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.9701 1.449e-06 6198 1 103.7 0.000112979 2066 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969974 1.51649e-06 6198 1 103.7 0.000119364 2066 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969841 1.42974e-06 6198 1 103.7 0.000103849 2066 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969829 1.56343e-06 6198 1 103.7 0.000134704 2066 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.969933 1.22614e-06 6198 1 103.7 8.79695e-05 2066 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970053 1.66936e-06 6198 1 103.7 0.000113026 2066 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970027 1.25796e-06 6198 1 103.7 0.00011521 2066 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970034 2.1375e-06 6198 1 103.7 0.000151636 2066 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.969962 1.48267e-06 6198 1 103.7 9.37752e-05 2066 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970022 1.10056e-06 6198 1 103.7 9.88375e-05 2066 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970056 1.90665e-06 6198 1 103.7 0.000145111 2066 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969999 1.09141e-06 6198 1 103.7 9.17858e-05 2066 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.969974 1.39628e-06 6198 1 103.7 0.00010214 2066 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97009 1.75259e-06 6198 1 103.7 0.000149369 2066 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970081 1.15599e-06 6198 1 103.7 9.08986e-05 2066 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970068 1.50148e-06 6198 1 103.7 0.000111091 2066 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969964 1.39727e-06 6198 1 103.7 9.88186e-05 2066 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969985 1.34121e-06 6198 1 103.7 0.000116918 2066 2000000 2000000 193.94621 64043.975 1.0155987 296.65875 0 0 0 0 6433.8303 75426.42 -112.07512 -113436.68 -31576.434 3734.3288 Loop time of 33234.4 on 8 procs for 2000000 steps with 6290 atoms Performance: 5.199 ns/day, 4.616 hours/ns, 60.179 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22492 | 23747 | 25181 | 587.4 | 71.45 Bond | 2.8548 | 3.2623 | 3.572 | 10.8 | 0.01 Kspace | 4078 | 5510 | 6766.2 |1217.9 | 16.58 Neigh | 1469.4 | 1469.6 | 1469.9 | 0.5 | 4.42 Comm | 516.44 | 517.36 | 518.11 | 2.1 | 1.56 Output | 0.016253 | 0.017353 | 0.018231 | 0.5 | 0.00 Modify | 1631.8 | 1829.6 | 1916.7 | 251.4 | 5.51 Other | | 157.5 | | | 0.47 Nlocal: 786.25 ave 804 max 760 min Histogram: 1 1 1 0 0 0 1 1 1 2 Nghost: 10037.1 ave 10109 max 9967 min Histogram: 1 1 0 1 0 2 2 0 0 1 Neighs: 443446 ave 466913 max 411901 min Histogram: 1 0 0 1 0 2 1 1 1 1 Total # of neighbors = 3547567 Ave neighs/atom = 564.00111 Ave special neighs/atom = 1.9707472 Neighbor list builds = 103236 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25626402 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0024949687 estimated relative force accuracy = 7.5135241e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969985 1.34121e-06 6198 1 103.7 0.000116918 2066 Per MPI rank memory allocation (min/avg/max) = 11.98 | 12.14 | 12.39 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 91.70948 64043.975 1.0155987 296.65875 0 0 0 0 6433.8303 75337.889 -112.07512 -113348.15 -31576.435 3734.3288 Loop time of 3.05862e-06 on 8 procs for 0 steps with 6290 atoms 126.7% CPU use with 8 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 | | 3.059e-06 | | |100.00 Nlocal: 786.25 ave 804 max 760 min Histogram: 1 1 1 0 0 0 1 1 1 2 Nghost: 10037.1 ave 10109 max 9967 min Histogram: 1 1 0 1 0 2 2 0 0 1 Neighs: 443446 ave 466913 max 411901 min Histogram: 1 0 0 1 0 2 1 1 1 1 Total # of neighbors = 3547567 Ave neighs/atom = 564.00111 Ave special neighs/atom = 1.9707472 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 9:15:15