#------------------------------------------------------------------------------- # Stage 2.3: NVE integration for Deposition for 100000 with a timestep of 0.2 #------------------------------------------------------------------------------- group deposition_atoms_O2 id 2049 2050 2 atoms in group deposition_atoms_O2 delete_atoms group deposition_atoms_O2 WARNING: Ignoring 'compress yes' for molecular system (../delete_atoms.cpp:126) Deleted 2 atoms, new total = 2048 molecule depositing_species_O2 deposition_O2.dat Read molecule template depositing_species_O2: 1 molecules 0 fragments 2 atoms with max type 1 0 bonds with max type 0 0 angles with max type 0 0 dihedrals with max type 0 0 impropers with max type 0 region deposition_region_O2 block EDGE EDGE EDGE EDGE 50 60 units box region evaporation_region block EDGE EDGE EDGE EDGE 90 EDGE units box uncompute thermo_temp compute thermo_temp movable temp thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) thermo ${Nthermo} thermo 0 fix 1 movable nve fix 2 all evaporate 1000 1000 evaporation_region 1 molecule yes fix dlan subset_thermostat langevin 300 300 20.0 4088 tally yes fix 3 movable ave/time 1 50000 50000 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 f_dlan file 2.3_averages.txt off 1 fix 4 movable ave/time 50 1 50 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 f_dlan file 2.3_instantaneous.txt fix deposition_O2_1 deposition_atoms_O2 deposit 50 0 10000 1 region deposition_region_O2 mol depositing_species_O2 vz -0.06989574890928181 -0.085428137555788888 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box fix deposition_O2_2 deposition_atoms_O2 nve dump trj all custom 5000 2.3.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 5000 1 5000 v_etotal v_pe v_ke file 2.3.energies.txt dump trj_O2 deposition_atoms_O2 custom 5000 2.3.trajectory_1.xyz id mol type q xs ys zs compute chunk_1 deposition_atoms_O2 chunk/atom bin/1d z lower 1.0 units box fix chunk_1 deposition_atoms_O2 ave/chunk 1 50000 50000 chunk_1 density/number norm sample file 2.3_distribution_O2_1.out timestep 0.2 run 500000 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.8 ghost atom cutoff = 4.8 binsize = 2.4, bins = 13 13 42 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair tersoff, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.036 | 7.608 | 8.18 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 3321.0139 93956.963 1.0165589 299.37531 0 0 0 0 -212361.64 0 0 0 -212361.64 1712.479 500000 100000 1055.9723 93956.963 1.0431382 385.2209 0 0 0 0 -226275.29 0 0 0 -226275.29 2203.5308 Loop time of 347.311 on 16 procs for 500000 steps with 2142 atoms Performance: 24.877 ns/day, 0.965 hours/ns, 1439.630 timesteps/s 97.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037831 | 134.02 | 299.35 |1166.2 | 38.59 Bond | 0.017907 | 0.027735 | 0.041953 | 5.0 | 0.01 Neigh | 0.0025812 | 0.3593 | 0.80332 | 59.6 | 0.10 Comm | 0.29066 | 67.42 | 234.53 | 893.4 | 19.41 Output | 0.056551 | 0.057472 | 0.058604 | 0.3 | 0.02 Modify | 27.509 | 143.33 | 344.53 |1122.0 | 41.27 Other | | 2.089 | | | 0.60 Nlocal: 133.875 ave 305 max 0 min Histogram: 8 0 0 0 0 0 0 3 1 4 Nghost: 344.75 ave 670 max 0 min Histogram: 4 0 4 0 0 0 0 1 3 4 Neighs: 0 ave 0 max 0 min Histogram: 16 0 0 0 0 0 0 0 0 0 FullNghs: 3570.88 ave 8228 max 0 min Histogram: 8 0 0 0 0 0 0 4 0 4 Total # of neighbors = 57134 Ave neighs/atom = 26.673203 Ave special neighs/atom = 0 Neighbor list builds = 2034 Dangerous builds = 0 write_dump all xyz final_2.3.xyz modify element O Si undump trj unfix trjE undump trj_O2 write_dump deposition_atoms_O2 custom 2.3.deposited_1.xyz id mol type q xs ys zs restart 0 dump sci all custom 500000 2.3.xyz id mol type q xs ys zs run 0 Per MPI rank memory allocation (min/avg/max) = 7.044 | 7.739 | 8.061 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 500000 100000 1055.9723 93956.963 1.0431382 385.2209 0 0 0 0 -226275.29 0 0 0 -226275.29 2203.5308 Loop time of 1.51975e-06 on 16 procs for 0 steps with 2142 atoms 135.7% CPU use with 16 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 | | 1.52e-06 | | |100.00 Nlocal: 133.875 ave 305 max 0 min Histogram: 8 0 0 0 0 0 0 3 1 4 Nghost: 344.75 ave 670 max 0 min Histogram: 4 0 4 0 0 0 0 1 3 4 Neighs: 0 ave 0 max 0 min Histogram: 16 0 0 0 0 0 0 0 0 0 FullNghs: 3570.88 ave 8228 max 0 min Histogram: 8 0 0 0 0 0 0 4 0 4 Total # of neighbors = 57134 Ave neighs/atom = 26.673203 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute chunk_1 unfix chunk_1 unfix 1 unfix 2 unfix 3 unfix 4 unfix deposition_O2_1 unfix deposition_O2_2 unfix dlan Total wall time: 0:05:47