#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- 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 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) = 0.2765886 grid = 6 6 6 stencil order = 5 estimated absolute RMS force accuracy = 0.00094138881 estimated relative force accuracy = 2.8349644e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1170 36 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:965) Per MPI rank memory allocation (min/avg/max) = 6.67 | 7.337 | 7.671 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 30109.308 179.45959 2.1630931 298.2 0 0 0 0 90.620582 -408.50411 -0.59158899 -414.53576 -732.41929 6.2221429 1000000 1000000 33968.101 179.45959 2.1630931 221.16328 0 0 0 0 93.790309 -405.26499 -0.59158899 -414.42512 -725.8998 4.6147201 Loop time of 187.215 on 6 procs for 1000000 steps with 8 atoms Performance: 461.501 ns/day, 0.052 hours/ns, 5341.452 timesteps/s 98.5% CPU use with 6 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3042 | 13.425 | 20.328 | 181.9 | 7.17 Bond | 0.43666 | 0.46579 | 0.51733 | 4.0 | 0.25 Kspace | 66.274 | 73.779 | 83.31 | 79.7 | 39.41 Neigh | 8.6769e-05 | 9.213e-05 | 9.4491e-05 | 0.0 | 0.00 Comm | 39.559 | 47.73 | 51.831 | 73.4 | 25.49 Output | 0.00090409 | 0.00093616 | 0.0009877 | 0.0 | 0.00 Modify | 43.609 | 47.365 | 55.076 | 73.2 | 25.30 Other | | 4.449 | | | 2.38 Nlocal: 1.33333 ave 3 max 0 min Histogram: 1 0 0 3 0 0 1 0 0 1 Nghost: 1223 ave 1305 max 1173 min Histogram: 2 0 2 0 0 0 0 1 0 1 Neighs: 326.833 ave 661 max 0 min Histogram: 1 0 1 1 1 0 0 0 1 1 Total # of neighbors = 1961 Ave neighs/atom = 245.125 Ave special neighs/atom = 0 Neighbor list builds = 1 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) = 0.2765886 grid = 6 6 6 stencil order = 5 estimated absolute RMS force accuracy = 0.00094138881 estimated relative force accuracy = 2.8349644e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1170 36 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:965) Per MPI rank memory allocation (min/avg/max) = 6.671 | 7.505 | 7.672 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 33968.101 179.45959 2.1630931 221.16328 0 0 0 0 93.790309 -405.26499 -0.59158899 -414.42512 -725.8998 4.6147201 Loop time of 3.81717e-06 on 6 procs for 0 steps with 8 atoms 122.3% CPU use with 6 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 | | 3.817e-06 | | |100.00 Nlocal: 1.33333 ave 3 max 0 min Histogram: 1 0 0 3 0 0 1 0 0 1 Nghost: 1223 ave 1305 max 1173 min Histogram: 2 0 2 0 0 0 0 1 0 1 Neighs: 326.833 ave 661 max 0 min Histogram: 1 0 1 1 1 0 0 0 1 1 Total # of neighbors = 1961 Ave neighs/atom = 245.125 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 log 2.5_NPT.out