#------------------------------------------------------------------------------- # 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 2768 = # 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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.993895 0.733015 8304 2 97.2293 38.3724 2768 Per MPI rank memory allocation (min/avg/max) = 12.63 | 12.8 | 13.25 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 15214.743 92859.489 1.3074058 428.55654 35.917863 279.70316 0 0 24405.317 99494.573 -448.40969 -272092.34 -147876.83 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.20737e-06 8304 2 103.7 9.70321e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.96693e-06 8304 2 103.7 0.000114983 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.08409e-06 8304 2 103.7 9.09452e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.142e-06 8304 2 103.7 9.1345e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.4666e-06 8304 2 103.7 0.00010125 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.45673e-06 8304 2 103.7 0.000113439 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.58434e-06 8304 2 103.7 0.000109031 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.41771e-06 8304 2 103.7 0.000101815 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.38278e-06 8304 2 103.7 0.00012674 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.76593e-06 8304 2 103.7 0.000119294 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.31107e-06 8304 2 103.7 9.8998e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.20019e-06 8304 2 103.7 9.14457e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.18296e-06 8304 2 103.7 0.000105801 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.27388e-06 8304 2 103.7 8.8892e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.5826e-06 8304 2 103.7 0.000128039 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.60245e-06 8304 2 103.7 0.000122645 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.71857e-06 8304 2 103.7 0.000124601 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.43711e-06 8304 2 103.7 0.000112859 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.05363e-06 8304 2 103.7 9.00512e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.35509e-06 8304 2 103.7 9.57708e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.72707e-06 8304 2 103.7 0.0001415 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.16023e-06 8304 2 103.7 9.70142e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.26503e-06 8304 2 103.7 0.000108323 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.10772e-06 8304 2 103.7 9.65581e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.1663e-06 8304 2 103.7 0.00010557 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.78192e-06 8304 2 103.7 0.000126724 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.10282e-06 8304 2 103.7 8.58273e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.31128e-06 8304 2 103.7 0.000111586 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.28878e-06 8304 2 103.7 9.15153e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26151e-06 8304 2 103.7 9.88025e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.14238e-06 8304 2 103.7 8.7532e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.35532e-06 8304 2 103.7 0.00010485 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.43207e-06 8304 2 103.7 0.000111613 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.22329e-06 8304 2 103.7 9.12148e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.18935e-06 8304 2 103.7 0.000103814 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.17511e-06 8304 2 103.7 0.00010162 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.22831e-06 8304 2 103.7 9.29601e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.31089e-06 8304 2 103.7 9.58061e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.42788e-06 8304 2 103.7 9.7163e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.18161e-06 8304 2 103.7 9.29511e-05 2768 2000000 2000000 2797.5588 92859.489 1.3074058 297.16539 38.366501 73.386745 0 0 22353.541 89612.027 -448.40969 -273869.34 -161792.02 5608.845 Loop time of 11363.1 on 32 procs for 2000000 steps with 9101 atoms Performance: 15.207 ns/day, 1.578 hours/ns, 176.008 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 | 4488.4 | 4818.4 | 5182.9 | 238.3 | 42.40 Bond | 2.0982 | 5.3005 | 11.222 | 96.4 | 0.05 Kspace | 4274.6 | 4641.1 | 4970.8 | 242.2 | 40.84 Neigh | 322.29 | 322.95 | 323.64 | 2.2 | 2.84 Comm | 722.25 | 727.85 | 735.54 | 11.8 | 6.41 Output | 0.011906 | 0.014232 | 0.016378 | 1.1 | 0.00 Modify | 804.52 | 809.95 | 813.77 | 8.8 | 7.13 Other | | 37.55 | | | 0.33 Nlocal: 284.406 ave 305 max 266 min Histogram: 2 3 4 4 6 3 2 3 4 1 Nghost: 4993.22 ave 5061 max 4911 min Histogram: 1 1 0 6 5 7 4 5 0 3 Neighs: 88673 ave 100301 max 78808 min Histogram: 1 0 5 7 8 4 3 1 2 1 Total # of neighbors = 2837535 Ave neighs/atom = 311.78277 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98342 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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.18161e-06 8304 2 103.7 9.29511e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.66 | 13.14 | 13.34 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 2798.5451 92859.489 1.3074058 297.16539 38.366501 73.386745 0 0 22353.541 89612.027 -448.40969 -273869.34 -161792.02 5608.845 Loop time of 7.26147e-06 on 32 procs for 0 steps with 9101 atoms 117.5% 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 | | 7.261e-06 | | |100.00 Nlocal: 284.406 ave 305 max 266 min Histogram: 2 3 4 4 6 3 2 3 4 1 Nghost: 4993.22 ave 5061 max 4911 min Histogram: 1 1 0 6 5 7 4 5 0 3 Neighs: 88673 ave 100301 max 78808 min Histogram: 1 0 5 7 8 4 3 1 2 1 Total # of neighbors = 2837535 Ave neighs/atom = 311.78277 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out