#------------------------------------------------------------------------------- # 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 2699 = # of frozen angles find clusters CPU = 0.002 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) = 0.25726526 grid = 24 50 48 stencil order = 5 estimated absolute RMS force accuracy = 0.003196358 estimated relative force accuracy = 9.6257371e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7220 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.993949 0.730229 8097 2 96.4702 41.8577 2699 Per MPI rank memory allocation (min/avg/max) = 13.02 | 13.21 | 13.74 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 43459.842 87908.451 1.3825941 427.22241 64.939915 296.99891 0 0 34735.501 36210.415 -235.50695 -216808.56 -145500.71 7943.8987 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.25443e-06 8097 2 103.7 9.82687e-05 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.40093e-06 8097 2 103.7 9.14448e-05 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.22324e-06 8097 2 103.7 9.67235e-05 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.0829e-06 8097 2 103.7 0.000104576 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.11089e-06 8097 2 103.7 9.74567e-05 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.38811e-06 8097 2 103.7 0.000104 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.12007e-06 8097 2 103.7 9.67549e-05 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.35444e-06 8097 2 103.7 0.000109187 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.17473e-06 8097 2 103.7 9.52882e-05 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.12358e-06 8097 2 103.7 0.000102417 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.23603e-06 8097 2 103.7 9.6842e-05 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.16812e-06 8097 2 103.7 0.000102169 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.13695e-06 8097 2 103.7 9.24911e-05 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.23583e-06 8097 2 103.7 9.13599e-05 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.10139e-06 8097 2 103.7 9.17758e-05 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.13704e-06 8097 2 103.7 0.000102482 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.16453e-06 8097 2 103.7 0.000106404 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.33388e-06 8097 2 103.7 0.000101849 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.37134e-06 8097 2 103.7 9.74798e-05 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.10653e-06 8097 2 103.7 9.27674e-05 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.12101e-06 8097 2 103.7 9.17729e-05 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.13841e-06 8097 2 103.7 9.50102e-05 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.35463e-06 8097 2 103.7 9.00169e-05 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.41243e-06 8097 2 103.7 0.000105382 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.26917e-06 8097 2 103.7 9.41699e-05 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.32875e-06 8097 2 103.7 0.000118789 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.27917e-06 8097 2 103.7 0.000102487 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.31381e-06 8097 2 103.7 0.000105238 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.21928e-06 8097 2 103.7 0.000117372 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.47951e-06 8097 2 103.7 0.000120276 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.26292e-06 8097 2 103.7 0.000116963 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.21384e-06 8097 2 103.7 9.71929e-05 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.31617e-06 8097 2 103.7 9.48246e-05 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.06646e-06 8097 2 103.7 9.33385e-05 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.19703e-06 8097 2 103.7 9.68668e-05 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.37845e-06 8097 2 103.7 9.74589e-05 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.22121e-06 8097 2 103.7 9.09797e-05 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.82083e-06 8097 2 103.7 0.000146834 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.34388e-06 8097 2 103.7 0.000113426 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.2726e-06 8097 2 103.7 0.000111584 2699 2000000 2000000 6164.2219 87908.451 1.3825941 297.68356 36.042263 62.943163 0 0 25155.176 17426.253 -235.50695 -219124.39 -176443.97 5535.2153 Loop time of 17413 on 32 procs for 2000000 steps with 8938 atoms Performance: 9.924 ns/day, 2.418 hours/ns, 114.857 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 | 8888.9 | 9583.7 | 10690 | 370.8 | 55.04 Bond | 2.3383 | 5.3968 | 10.174 | 105.9 | 0.03 Kspace | 3608.2 | 4710.2 | 5417 | 529.0 | 27.05 Neigh | 748.83 | 749.38 | 750.05 | 1.2 | 4.30 Comm | 1161.1 | 1190.5 | 1217.7 | 45.0 | 6.84 Output | 0.013306 | 0.015599 | 0.017755 | 1.1 | 0.00 Modify | 1108.3 | 1125.5 | 1147.1 | 32.9 | 6.46 Other | | 48.3 | | | 0.28 Nlocal: 279.312 ave 301 max 247 min Histogram: 1 0 0 3 4 7 8 5 2 2 Nghost: 7727.12 ave 7805 max 7582 min Histogram: 1 0 5 1 1 1 8 4 5 6 Neighs: 163107 ave 178544 max 140960 min Histogram: 1 0 0 3 6 7 5 6 2 2 Total # of neighbors = 5219435 Ave neighs/atom = 583.96006 Ave special neighs/atom = 1.8722309 Neighbor list builds = 97496 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) = 0.25726526 grid = 24 50 48 stencil order = 5 estimated absolute RMS force accuracy = 0.003196358 estimated relative force accuracy = 9.6257371e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7220 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.2726e-06 8097 2 103.7 0.000111584 2699 Per MPI rank memory allocation (min/avg/max) = 13.05 | 13.29 | 13.73 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 6165.4217 87908.451 1.3825941 297.68356 36.042263 62.943163 0 0 25155.176 17426.253 -235.50695 -219124.39 -176443.97 5535.2153 Loop time of 1.25905e-05 on 32 procs for 0 steps with 8938 atoms 109.5% 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 | | 1.259e-05 | | |100.00 Nlocal: 279.312 ave 301 max 247 min Histogram: 1 0 0 3 4 7 8 5 2 2 Nghost: 7727.12 ave 7805 max 7582 min Histogram: 1 0 5 1 1 1 8 4 5 6 Neighs: 163107 ave 178544 max 140960 min Histogram: 1 0 0 3 6 7 5 6 2 2 Total # of neighbors = 5219435 Ave neighs/atom = 583.96006 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out