#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # 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 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 nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal 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_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) = 0.25531659 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0033458596 estimated relative force accuracy = 1.0075957e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4312 960 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.991964 1.02705 6027 2 97.8314 32.9599 2009 Per MPI rank memory allocation (min/avg/max) = 12.29 | 12.7 | 12.88 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 13593.984 67083.794 1.2789064 429.78001 60.470145 151.24366 0 0 15799.992 38827.382 -157.46178 -146934.28 -92095.196 5832.8145 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.28158e-06 6027 2 103.7 9.9968e-05 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.02211e-06 6027 2 103.7 9.19553e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.20381e-06 6027 2 103.7 9.38299e-05 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.51281e-06 6027 2 103.7 0.000101451 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.10571e-06 6027 2 103.7 9.77351e-05 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.4862e-06 6027 2 103.7 0.000127821 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.27409e-06 6027 2 103.7 0.000104078 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.14614e-06 6027 2 103.7 0.000100102 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.24678e-06 6027 2 103.7 0.000100861 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.30381e-06 6027 2 103.7 0.000109493 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.12836e-06 6027 2 103.7 9.28148e-05 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.85374e-06 6027 2 103.7 0.000137696 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.20427e-06 6027 2 103.7 9.27123e-05 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.2167e-06 6027 2 103.7 9.62255e-05 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.63411e-06 6027 2 103.7 0.000133349 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.22021e-06 6027 2 103.7 8.87806e-05 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.29499e-06 6027 2 103.7 9.67113e-05 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.47092e-06 6027 2 103.7 0.000116758 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.42423e-06 6027 2 103.7 0.000101798 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.19742e-06 6027 2 103.7 9.25969e-05 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.19889e-06 6027 2 103.7 0.000104335 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.15021e-06 6027 2 103.7 9.20558e-05 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.29061e-06 6027 2 103.7 9.61681e-05 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.71704e-06 6027 2 103.7 0.000147495 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.09969e-06 6027 2 103.7 9.17395e-05 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.12669e-06 6027 2 103.7 9.21422e-05 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.12895e-06 6027 2 103.7 9.80427e-05 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.09654e-06 6027 2 103.7 9.61908e-05 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.33169e-06 6027 2 103.7 9.5901e-05 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.33742e-06 6027 2 103.7 0.000101164 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.12361e-06 6027 2 103.7 9.42559e-05 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.028e-06 6027 2 103.7 9.52958e-05 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.12785e-06 6027 2 103.7 0.00010312 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.83264e-06 6027 2 103.7 0.000137392 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.05478e-06 6027 2 103.7 9.59096e-05 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.17269e-06 6027 2 103.7 9.4357e-05 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.35285e-06 6027 2 103.7 9.93155e-05 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.61423e-06 6027 2 103.7 0.000122288 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.20819e-06 6027 2 103.7 0.000112544 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.45839e-06 6027 2 103.7 9.41879e-05 2009 2000000 2000000 2351.9465 67083.794 1.2789064 302.94426 31.952035 46.68592 0 0 13960.292 32831.486 -157.46178 -147549.77 -100679.36 4111.4469 Loop time of 11067.7 on 32 procs for 2000000 steps with 6563 atoms Performance: 15.613 ns/day, 1.537 hours/ns, 180.706 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 | 6023.1 | 6575.2 | 7008.4 | 309.5 | 59.41 Bond | 2.2395 | 4.2702 | 8.5424 | 82.5 | 0.04 Kspace | 2032.7 | 2465.6 | 3019.9 | 506.2 | 22.28 Neigh | 370.4 | 370.87 | 371.19 | 1.0 | 3.35 Comm | 862.48 | 870.99 | 881.94 | 15.9 | 7.87 Output | 0.011052 | 0.012957 | 0.01479 | 1.0 | 0.00 Modify | 737.94 | 746.11 | 752.9 | 15.2 | 6.74 Other | | 34.59 | | | 0.31 Nlocal: 205.094 ave 220 max 183 min Histogram: 1 0 2 2 3 8 6 7 1 2 Nghost: 6678.69 ave 6710 max 6644 min Histogram: 1 1 6 3 4 5 4 2 2 4 Neighs: 115220 ave 126100 max 104426 min Histogram: 1 5 5 1 5 2 3 4 4 2 Total # of neighbors = 3687028 Ave neighs/atom = 561.79004 Ave special neighs/atom = 1.9037026 Neighbor list builds = 96053 Dangerous builds = 1 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) = 0.25531659 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0033458596 estimated relative force accuracy = 1.0075957e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4312 960 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.45839e-06 6027 2 103.7 9.41879e-05 2009 Per MPI rank memory allocation (min/avg/max) = 12.67 | 12.8 | 12.88 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 2352.8547 67083.794 1.2789064 302.94426 31.952035 46.68592 0 0 13960.292 32831.486 -157.46178 -147549.77 -100679.36 4111.4469 Loop time of 7.37937e-06 on 32 procs for 0 steps with 6563 atoms 114.8% 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 | | 7.379e-06 | | |100.00 Nlocal: 205.094 ave 220 max 183 min Histogram: 1 0 2 2 3 8 6 7 1 2 Nghost: 6678.69 ave 6710 max 6644 min Histogram: 1 1 6 3 4 5 4 2 2 4 Neighs: 115220 ave 126100 max 104426 min Histogram: 1 5 5 1 5 2 3 4 4 2 Total # of neighbors = 3687028 Ave neighs/atom = 561.79004 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out