#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 2000 = # 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.21402839 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0025757468 estimated relative force accuracy = 7.7567851e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.72129e-13 6000 1 103.7 7.83302e-11 2000 Per MPI rank memory allocation (min/avg/max) = 8.256 | 10.05 | 11.55 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 -137.02653 121004.85 0.49444624 302.59032 0 0 0 0 5037.5587 61851.893 -32.587809 -88102.471 -21213.019 3606.9552 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.26425e-06 6000 1 103.7 9.40459e-05 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.3624e-06 6000 1 103.7 8.82122e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 2.03664e-06 6000 1 103.7 0.000141134 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.19057e-06 6000 1 103.7 0.000107177 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.07727e-06 6000 1 103.7 8.96993e-05 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.26919e-06 6000 1 103.7 0.000111375 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.27558e-06 6000 1 103.7 0.000111528 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.33058e-06 6000 1 103.7 0.000115936 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.36119e-06 6000 1 103.7 9.94369e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.18731e-06 6000 1 103.7 0.000106483 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.32526e-06 6000 1 103.7 9.81494e-05 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.4232e-06 6000 1 103.7 9.71861e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.54386e-06 6000 1 103.7 0.000120395 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.19625e-06 6000 1 103.7 8.56853e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.8691e-06 6000 1 103.7 0.000135026 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.24042e-06 6000 1 103.7 9.80491e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.2066e-06 6000 1 103.7 0.000100519 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.32174e-06 6000 1 103.7 0.00010621 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.20436e-06 6000 1 103.7 8.70109e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.33551e-06 6000 1 103.7 0.000101706 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.7841e-06 6000 1 103.7 0.000135247 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.16187e-06 6000 1 103.7 0.000100587 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.10637e-06 6000 1 103.7 9.64836e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.76596e-06 6000 1 103.7 0.000133957 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.36338e-06 6000 1 103.7 0.00010305 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.13152e-06 6000 1 103.7 9.79187e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.19169e-06 6000 1 103.7 0.000128275 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.19428e-06 6000 1 103.7 9.22113e-05 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.07632e-06 6000 1 103.7 0.000111659 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.34378e-06 6000 1 103.7 0.000107329 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.36883e-06 6000 1 103.7 0.000128531 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.27368e-06 6000 1 103.7 0.000112848 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.32244e-06 6000 1 103.7 8.73593e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.44064e-06 6000 1 103.7 0.000114844 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.82495e-06 6000 1 103.7 0.000133687 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.07445e-06 6000 1 103.7 9.92341e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.51591e-06 6000 1 103.7 9.98816e-05 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.60679e-06 6000 1 103.7 0.000104954 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.25368e-06 6000 1 103.7 0.00012544 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.3178e-06 6000 1 103.7 0.000106411 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.38845e-06 6000 1 103.7 9.37121e-05 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.63451e-06 6000 1 103.7 0.000112042 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.02946e-06 6000 1 103.7 8.6582e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.15845e-06 6000 1 103.7 9.52846e-05 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.27184e-06 6000 1 103.7 0.00010852 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.31681e-06 6000 1 103.7 0.000126946 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.72555e-06 6000 1 103.7 0.000129483 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.28247e-06 6000 1 103.7 0.000119742 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.18631e-06 6000 1 103.7 9.70096e-05 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.82711e-06 6000 1 103.7 0.000118094 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.49088e-06 6000 1 103.7 0.000100421 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.35132e-06 6000 1 103.7 0.000109559 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.29151e-06 6000 1 103.7 0.000108703 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.54496e-06 6000 1 103.7 0.000100036 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.17585e-06 6000 1 103.7 0.000107689 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.37974e-06 6000 1 103.7 0.000107829 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.10988e-06 6000 1 103.7 9.79883e-05 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.1796e-06 6000 1 103.7 0.000117451 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.12896e-06 6000 1 103.7 0.00010204 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.32385e-06 6000 1 103.7 0.000111263 2000 3000000 3000000 -57.760759 121004.85 0.49444624 303.82809 0 0 0 0 5094.1417 61688.808 -32.587809 -88097.357 -21314.407 3621.7097 Loop time of 35307.4 on 32 procs for 3000000 steps with 6000 atoms Performance: 7.341 ns/day, 3.269 hours/ns, 84.968 timesteps/s 98.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8829 | 12573 | 28410 |11260.9 | 35.61 Bond | 2.0588 | 3.3632 | 5.1145 | 33.7 | 0.01 Kspace | 3555.6 | 19499 | 32330 |9113.1 | 55.23 Neigh | 1464.9 | 1478.3 | 1507.5 | 36.3 | 4.19 Comm | 94.629 | 577.91 | 849.9 |1174.6 | 1.64 Output | 0.0096057 | 0.011189 | 0.012529 | 0.8 | 0.00 Modify | 948.08 | 1111 | 1321.1 | 439.7 | 3.15 Other | | 64.77 | | | 0.18 Nlocal: 187.5 ave 384 max 0 min Histogram: 16 0 0 0 0 0 0 0 3 13 Nghost: 5172.34 ave 10455 max 16 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 146347 ave 343178 max 0 min Histogram: 16 0 0 0 0 0 4 0 4 8 Total # of neighbors = 4683105 Ave neighs/atom = 780.5175 Ave special neighs/atom = 2 Neighbor list builds = 148445 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 2.5.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) = 0.21402839 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0025757468 estimated relative force accuracy = 7.7567851e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.32385e-06 6000 1 103.7 0.000111263 2000 Per MPI rank memory allocation (min/avg/max) = 8.256 | 10.05 | 11.55 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 3000000 3000000 -57.386413 121004.85 0.49444624 303.82809 0 0 0 0 5094.1417 61688.808 -32.587809 -88097.357 -21314.407 3621.7097 Loop time of 7.73541e-06 on 32 procs for 0 steps with 6000 atoms 112.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.735e-06 | | |100.00 Nlocal: 187.5 ave 384 max 0 min Histogram: 16 0 0 0 0 0 0 0 3 13 Nghost: 5172.34 ave 10455 max 16 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 146347 ave 343178 max 0 min Histogram: 16 0 0 0 0 0 4 0 4 8 Total # of neighbors = 4683105 Ave neighs/atom = 780.5175 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: 26:12:07