#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 100000 100000 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 100 1 100 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 20350 8100 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00088 0.0720092 8304 2 97.6643 9.85495 2768 Per MPI rank memory allocation (min/avg/max) = 14.07 | 16.31 | 17.76 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 -3032.7399 143908.11 1.3942094 410.14353 6.5923076 28.767474 0 0 32423.427 -37472.161 -320.88394 -277806.71 -282820.09 8993.151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.3742e-06 8304 2 103.7 0.00011376 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.09264e-06 8304 2 103.7 0.000107816 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.27999e-06 8304 2 103.7 9.60782e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16683e-06 8304 2 103.7 8.75341e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.177e-06 8304 2 103.7 9.72365e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.97878e-06 8304 2 103.7 0.00011642 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.31419e-06 8304 2 103.7 0.000101183 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.14296e-06 8304 2 103.7 9.48326e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.26519e-06 8304 2 103.7 0.000104098 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.39652e-06 8304 2 103.7 9.92421e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.35017e-06 8304 2 103.7 0.000115431 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.65092e-06 8304 2 103.7 0.000110593 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.27925e-06 8304 2 103.7 8.97053e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.12233e-06 8304 2 103.7 9.45269e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.09312e-06 8304 2 103.7 8.87455e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.57515e-06 8304 2 103.7 0.000108522 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21284e-06 8304 2 103.7 0.000114773 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.41113e-06 8304 2 103.7 0.000103212 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.53603e-06 8304 2 103.7 9.47822e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.36363e-06 8304 2 103.7 9.77633e-05 2768 1000000 1000000 -984.39296 143908.11 1.3942094 295.65385 45.945174 85.966549 0 0 29150.09 -19656.285 -320.88394 -277671.63 -268045.91 6482.7542 Loop time of 25423.3 on 8 procs for 1000000 steps with 10381 atoms Performance: 3.398 ns/day, 7.062 hours/ns, 39.334 timesteps/s 98.6% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2736.9 | 13542 | 19954 |5476.4 | 53.27 Bond | 1.0957 | 5.2504 | 8.9383 | 116.0 | 0.02 Kspace | 3688.3 | 10112 | 20930 |6344.7 | 39.77 Neigh | 997.92 | 999.23 | 1000.7 | 3.1 | 3.93 Comm | 229.93 | 272.77 | 297.07 | 145.2 | 1.07 Output | 0.025736 | 0.028781 | 0.031627 | 1.1 | 0.00 Modify | 446.1 | 462.33 | 491.7 | 80.7 | 1.82 Other | | 30.05 | | | 0.12 Nlocal: 1297.62 ave 1610 max 560 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10453.8 ave 13033 max 8292 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593814 ave 845417 max 110790 min Histogram: 2 0 0 0 0 0 0 1 3 2 Total # of neighbors = 4750509 Ave neighs/atom = 457.61574 Ave special neighs/atom = 1.6595704 Neighbor list builds = 49677 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 20350 8100 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.36363e-06 8304 2 103.7 9.77633e-05 2768 Per MPI rank memory allocation (min/avg/max) = 14.06 | 16.42 | 17.76 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 1000000 1000000 -983.87019 143908.11 1.3942094 295.65385 45.945174 85.966549 0 0 29150.09 -19656.285 -320.88394 -277671.63 -268045.91 6482.7542 Loop time of 3.30275e-06 on 8 procs for 0 steps with 10381 atoms 121.1% 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 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 | | 3.303e-06 | | |100.00 Nlocal: 1297.62 ave 1610 max 560 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10453.8 ave 13033 max 8292 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593814 ave 845417 max 110790 min Histogram: 2 0 0 0 0 0 0 1 3 2 Total # of neighbors = 4750509 Ave neighs/atom = 457.61574 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out