#------------------------------------------------------------------------------- # Stage 2.5: 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # of frozen angles find clusters CPU = 0.000 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 v_surfacetension file 2.5_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 v_surfacetension file 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 1.02263e-12 6600 1 103.7 8.76668e-11 2200 Per MPI rank memory allocation (min/avg/max) = 10.87 | 11.17 | 11.65 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 -1002.5966 70192.433 0.93761433 299.04826 0 0 0 0 5840.8431 -29735.603 0 0 -23894.76 3921.2952 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.35745e-06 6600 1 103.7 0.000121361 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.20522e-06 6600 1 103.7 9.62631e-05 2200 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.8511e-06 6600 1 103.7 0.000122837 2200 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.157e-06 6600 1 103.7 9.14582e-05 2200 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.26894e-06 6600 1 103.7 9.39534e-05 2200 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.81653e-06 6600 1 103.7 0.000157429 2200 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 2.61401e-06 6600 1 103.7 0.000118975 2200 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.27855e-06 6600 1 103.7 0.000107748 2200 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.29589e-06 6600 1 103.7 9.47673e-05 2200 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.21749e-06 6600 1 103.7 0.000111091 2200 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.28849e-06 6600 1 103.7 0.000109094 2200 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.32592e-06 6600 1 103.7 0.000119469 2200 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.38934e-06 6600 1 103.7 9.98833e-05 2200 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.24772e-06 6600 1 103.7 0.00010362 2200 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.39935e-06 6600 1 103.7 0.00012182 2200 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.59128e-06 6600 1 103.7 9.95757e-05 2200 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.29078e-06 6600 1 103.7 9.77366e-05 2200 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.68991e-06 6600 1 103.7 0.000109363 2200 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.38567e-06 6600 1 103.7 9.51915e-05 2200 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.29761e-06 6600 1 103.7 0.00012302 2200 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.15362e-06 6600 1 103.7 0.000100877 2200 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.16169e-06 6600 1 103.7 8.93787e-05 2200 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.21117e-06 6600 1 103.7 9.72586e-05 2200 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.32458e-06 6600 1 103.7 9.59468e-05 2200 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.34726e-06 6600 1 103.7 0.000100971 2200 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.66037e-06 6600 1 103.7 0.000119521 2200 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.76002e-06 6600 1 103.7 0.000126559 2200 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.18703e-06 6600 1 103.7 9.87855e-05 2200 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.90033e-06 6600 1 103.7 0.000118496 2200 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.38505e-06 6600 1 103.7 9.80928e-05 2200 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.46188e-06 6600 1 103.7 9.51038e-05 2200 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.5484e-06 6600 1 103.7 0.000143399 2200 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.48872e-06 6600 1 103.7 0.000106305 2200 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.58108e-06 6600 1 103.7 0.000107586 2200 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.37573e-06 6600 1 103.7 9.44578e-05 2200 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.19368e-06 6600 1 103.7 9.70134e-05 2200 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.08727e-06 6600 1 103.7 0.000101635 2200 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.55686e-06 6600 1 103.7 0.000102565 2200 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.43121e-06 6600 1 103.7 0.000138665 2200 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.25269e-06 6600 1 103.7 0.000114795 2200 2000000 2000000 490.34634 70232.4 0.93708077 302.33665 0 0 0 0 5968.7557 -26948.158 0 0 -20979.402 3964.4146 Loop time of 26523.6 on 8 procs for 2000000 steps with 6600 atoms Performance: 6.515 ns/day, 3.684 hours/ns, 75.405 timesteps/s 98.9% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15614 | 19717 | 24028 |2193.2 | 74.34 Bond | 1.9131 | 2.1848 | 2.5384 | 11.8 | 0.01 Neigh | 1324.1 | 1326 | 1327.8 | 3.5 | 5.00 Comm | 529.58 | 4843.6 | 8946.7 |4429.9 | 18.26 Output | 0.015172 | 0.016192 | 0.017074 | 0.5 | 0.00 Modify | 586.03 | 593.4 | 597.71 | 15.8 | 2.24 Other | | 41.87 | | | 0.16 Nlocal: 825 ave 876 max 793 min Histogram: 2 1 1 1 0 1 1 0 0 1 Nghost: 7420 ave 7577 max 7321 min Histogram: 4 0 0 0 0 2 0 1 0 1 Neighs: 437992 ave 552148 max 345870 min Histogram: 4 0 0 0 0 0 0 2 1 1 Total # of neighbors = 3503939 Ave neighs/atom = 530.89985 Ave special neighs/atom = 2 Neighbor list builds = 97506 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.xyz id mol type q xs ys zs run 0 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.25269e-06 6600 1 103.7 0.000114795 2200 Per MPI rank memory allocation (min/avg/max) = 10.87 | 11.17 | 11.65 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 491.21363 70232.4 0.93708077 302.33665 0 0 0 0 5968.7557 -26948.158 0 0 -20979.402 3964.4146 Loop time of 3.226e-06 on 8 procs for 0 steps with 6600 atoms 116.2% CPU use with 8 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 | | 3.226e-06 | | |100.00 Nlocal: 825 ave 876 max 793 min Histogram: 2 1 1 1 0 1 1 0 0 1 Nghost: 7420 ave 7577 max 7321 min Histogram: 4 0 0 0 0 2 0 1 0 1 Neighs: 437992 ave 552148 max 345870 min Histogram: 4 0 0 0 0 0 0 2 1 1 Total # of neighbors = 3503939 Ave neighs/atom = 530.89985 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 14:08:30