#------------------------------------------------------------------------------- # 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 0.999261 0.542488 8304 2 97.216 21.8043 2768 Per MPI rank memory allocation (min/avg/max) = 11.58 | 11.66 | 11.98 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 6403.5255 92859.489 1.3074058 428.55654 28.451217 195.03501 0 0 24294.516 -182180.46 -448.40969 0 -157662.45 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970009 1.75615e-06 8304 2 103.7 0.000115538 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970011 1.42332e-06 8304 2 103.7 0.0001084 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969918 1.68705e-06 8304 2 103.7 0.000135374 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970053 1.98182e-06 8304 2 103.7 0.000105431 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969911 1.73736e-06 8304 2 103.7 0.000142402 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969949 1.16166e-06 8304 2 103.7 0.000101101 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970035 1.47116e-06 8304 2 103.7 9.9028e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.96999 1.29798e-06 8304 2 103.7 0.000100575 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97007 1.67796e-06 8304 2 103.7 0.000117252 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970119 2.12363e-06 8304 2 103.7 0.000145841 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969991 1.33049e-06 8304 2 103.7 9.7779e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97006 1.74969e-06 8304 2 103.7 0.000129367 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970064 1.82363e-06 8304 2 103.7 0.000112973 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970029 1.66646e-06 8304 2 103.7 0.000106261 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969992 1.26387e-06 8304 2 103.7 9.1342e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970058 1.45753e-06 8304 2 103.7 0.000105212 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970023 1.24345e-06 8304 2 103.7 9.4615e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970022 1.41518e-06 8304 2 103.7 9.73306e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.31138e-06 8304 2 103.7 9.99406e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970012 1.53711e-06 8304 2 103.7 0.000106337 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.96999 1.42299e-06 8304 2 103.7 9.82136e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970104 1.87223e-06 8304 2 103.7 0.000124846 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.96996 1.58193e-06 8304 2 103.7 0.000118179 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970057 1.49106e-06 8304 2 103.7 0.000125332 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970054 1.465e-06 8304 2 103.7 0.000104407 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970001 1.24928e-06 8304 2 103.7 0.00010687 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969995 1.26451e-06 8304 2 103.7 9.95474e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970044 1.94631e-06 8304 2 103.7 0.000127238 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970031 1.26187e-06 8304 2 103.7 9.13499e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969998 1.67458e-06 8304 2 103.7 0.000106602 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969968 1.55749e-06 8304 2 103.7 0.000107206 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969959 1.64344e-06 8304 2 103.7 0.000130497 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969911 1.4274e-06 8304 2 103.7 0.000110421 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970013 1.54646e-06 8304 2 103.7 0.000114833 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969962 1.47174e-06 8304 2 103.7 0.000106477 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970033 1.42539e-06 8304 2 103.7 0.000104958 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969992 1.60954e-06 8304 2 103.7 0.000116661 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969936 1.73507e-06 8304 2 103.7 0.000108807 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969977 1.79258e-06 8304 2 103.7 0.000119989 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970119 2.69107e-06 8304 2 103.7 0.000175439 2768 2000000 2000000 -412.57832 94659.812 1.2825404 297.98425 41.66013 98.733098 0 0 20885.545 -173113.53 -439.88145 0 -152087.6 5624.3006 Loop time of 5875.86 on 32 procs for 2000000 steps with 9101 atoms Performance: 29.408 ns/day, 0.816 hours/ns, 340.376 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3941.3 | 4312 | 4676.4 | 305.7 | 73.39 Bond | 1.5153 | 4.0793 | 6.3973 | 72.0 | 0.07 Neigh | 294.66 | 295.87 | 296.75 | 3.9 | 5.04 Comm | 249.2 | 602.03 | 1015.2 | 821.6 | 10.25 Output | 0.010902 | 0.01311 | 0.015208 | 1.2 | 0.00 Modify | 573.51 | 635.06 | 794.52 | 213.1 | 10.81 Other | | 26.8 | | | 0.46 Nlocal: 284.406 ave 310 max 259 min Histogram: 1 2 1 4 6 9 4 3 1 1 Nghost: 4858.53 ave 4964 max 4746 min Histogram: 2 3 0 5 4 5 6 4 2 1 Neighs: 86639.6 ave 94881 max 76689 min Histogram: 2 1 0 5 7 2 7 2 4 2 Total # of neighbors = 2772468 Ave neighs/atom = 304.63334 Ave special neighs/atom = 1.8929788 Neighbor list builds = 97280 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 0.970119 2.69107e-06 8304 2 103.7 0.000175439 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.71 | 11.98 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 306.56034 94659.812 1.2825404 297.98425 41.66013 98.733098 0 0 20885.545 -173113.53 -439.88145 0 -152087.6 5624.3006 Loop time of 7.63547e-06 on 32 procs for 0 steps with 9101 atoms 107.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.635e-06 | | |100.00 Nlocal: 284.406 ave 310 max 259 min Histogram: 1 2 1 4 6 9 4 3 1 1 Nghost: 4858.53 ave 4964 max 4746 min Histogram: 2 3 0 5 4 5 6 4 2 1 Neighs: 86639.6 ave 94881 max 76689 min Histogram: 2 1 0 5 7 2 7 2 4 2 Total # of neighbors = 2772468 Ave neighs/atom = 304.63334 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