#------------------------------------------------------------------------------- # Stage 2.4: 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 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 npt temp 298.2 298.2 100 iso 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 2.4_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 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.996396 0.671164 8304 2 97.063 29.2392 2768 Per MPI rank memory allocation (min/avg/max) = 11.62 | 11.73 | 12.2 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 14728.258 92859.489 1.3074058 428.55654 61.920788 322.8213 0 0 24859.725 -169619.75 -448.40969 0 -144375.28 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970001 1.83347e-06 8304 2 103.7 0.000107358 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969984 1.24363e-06 8304 2 103.7 9.6345e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969969 1.52692e-06 8304 2 103.7 0.000106925 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.3635e-06 8304 2 103.7 9.80002e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969952 1.1678e-06 8304 2 103.7 9.52764e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969986 1.60337e-06 8304 2 103.7 0.000117049 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970001 1.21354e-06 8304 2 103.7 9.84807e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969945 1.34862e-06 8304 2 103.7 0.000124435 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969978 1.41681e-06 8304 2 103.7 0.000123851 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969967 1.41704e-06 8304 2 103.7 0.00011563 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969997 1.39024e-06 8304 2 103.7 0.000100622 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970053 1.72728e-06 8304 2 103.7 0.000120056 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969989 1.08875e-06 8304 2 103.7 9.69758e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969973 1.37107e-06 8304 2 103.7 0.000125696 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969988 2.76549e-06 8304 2 103.7 0.000181801 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970036 1.78803e-06 8304 2 103.7 0.000122023 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970084 1.80351e-06 8304 2 103.7 0.000114927 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970065 1.31089e-06 8304 2 103.7 0.000131508 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969917 1.36262e-06 8304 2 103.7 0.000122653 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969874 1.66625e-06 8304 2 103.7 0.000111616 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969992 1.58613e-06 8304 2 103.7 0.000110172 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970021 1.36826e-06 8304 2 103.7 9.42123e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970024 1.8156e-06 8304 2 103.7 0.000111545 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970031 1.58733e-06 8304 2 103.7 9.31042e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969902 1.5116e-06 8304 2 103.7 0.000174029 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970055 1.42627e-06 8304 2 103.7 0.000130577 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969914 1.40194e-06 8304 2 103.7 9.19272e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970019 2.49927e-06 8304 2 103.7 0.000149955 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970058 1.59878e-06 8304 2 103.7 0.00010801 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970021 1.30971e-06 8304 2 103.7 0.000101468 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970037 1.80566e-06 8304 2 103.7 0.000131198 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969989 1.54265e-06 8304 2 103.7 0.000130559 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969982 2.03454e-06 8304 2 103.7 0.000119286 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969993 1.48318e-06 8304 2 103.7 0.000131919 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970057 1.65529e-06 8304 2 103.7 0.000148807 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969982 1.22652e-06 8304 2 103.7 9.70198e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97007 1.72389e-06 8304 2 103.7 0.000114995 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970014 1.50625e-06 8304 2 103.7 9.74898e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970036 1.26998e-06 8304 2 103.7 9.91048e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970037 1.2345e-06 8304 2 103.7 0.000101183 2768 2000000 2000000 283.21458 96460.259 1.2586016 300.36792 55.534849 116.70854 0 0 20535.743 -166862.67 -431.67098 0 -146154.68 5669.291 Loop time of 6434.5 on 32 procs for 2000000 steps with 9101 atoms Performance: 26.855 ns/day, 0.894 hours/ns, 310.824 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3698.8 | 4282 | 4799.7 | 380.3 | 66.55 Bond | 1.7259 | 4.058 | 11.935 | 102.3 | 0.06 Neigh | 333.43 | 333.96 | 334.57 | 2.6 | 5.19 Comm | 567.48 | 1047.3 | 1609.1 | 729.9 | 16.28 Output | 0.010885 | 0.013103 | 0.015219 | 1.2 | 0.00 Modify | 705.42 | 741.48 | 790.69 | 83.7 | 11.52 Other | | 25.74 | | | 0.40 Nlocal: 284.406 ave 304 max 266 min Histogram: 2 3 4 4 4 4 3 2 5 1 Nghost: 4865.75 ave 4922 max 4833 min Histogram: 4 4 4 8 5 2 2 1 1 1 Neighs: 85034.2 ave 95350 max 75036 min Histogram: 3 1 2 6 6 3 5 2 1 3 Total # of neighbors = 2721094 Ave neighs/atom = 298.98846 Ave special neighs/atom = 1.8929788 Neighbor list builds = 97128 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970037 1.2345e-06 8304 2 103.7 0.000101183 2768 Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.8 | 12.22 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 501.89756 96460.259 1.2586016 300.36792 55.534849 116.70854 0 0 20535.743 -166862.67 -431.67098 0 -146154.68 5669.291 Loop time of 1.02732e-05 on 32 procs for 0 steps with 9101 atoms 108.9% 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 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 | | 1.027e-05 | | |100.00 Nlocal: 284.406 ave 304 max 266 min Histogram: 2 3 4 4 4 4 3 2 5 1 Nghost: 4865.75 ave 4922 max 4833 min Histogram: 4 4 4 8 5 2 2 1 1 1 Neighs: 85034.2 ave 95350 max 75036 min Histogram: 3 1 2 6 6 3 5 2 1 3 Total # of neighbors = 2721094 Ave neighs/atom = 298.98846 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_NVT.out