#------------------------------------------------------------------------------- # Stage 2.3: NVE integration for Deposition for 100 ps with a timestep of 0.2 fs #------------------------------------------------------------------------------- group deposition_atoms_TMOS id 577 578 579 580 581 582 583 584 8 atoms in group deposition_atoms_TMOS group deposition_atoms_TMOS id 585 586 587 588 589 590 591 592 16 atoms in group deposition_atoms_TMOS group deposition_atoms_TMOS id 593 17 atoms in group deposition_atoms_TMOS delete_atoms group deposition_atoms_TMOS WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140) Deleted 17 atoms, new total = 576 molecule depositing_species_TMOS deposition_TMOS.dat Read molecule template depositing_species_TMOS: 1 molecules 0 fragments 17 atoms with max type 4 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_TMOS block EDGE EDGE EDGE EDGE 50 60 units box region evaporation_region block EDGE EDGE EDGE EDGE 90 EDGE units box group evaporation_group dynamic all region evaporation_region every 1000 dynamic group evaporation_group defined 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 (src/output.cpp:903) thermo ${Nthermo} thermo 0 fix 1 movable nve fix 2 evaporation_group reax/c/species 1 1 1000 removed_fragments.out element C H O Si terse yes fix 3 all evaporate 1000 1000 evaporation_region 382 molecule yes fix dlan subset_thermoset langevin 300 300 20.0 1 tally yes fix 4 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 5 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 6 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c fix deposition_TMOS_1 deposition_atoms_TMOS deposit 25 0 20000 382 region deposition_region_TMOS mol depositing_species_TMOS vz -0.0075482320826285908 -0.0092256169898793892 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box fix deposition_TMOS_2 deposition_atoms_TMOS nve dump trj all custom 50000 2.3.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 50000 1 50000 v_etotal v_pe v_ke file 2.3.energies.txt dump trj_TMOS deposition_atoms_TMOS custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs timestep 0.2 run 500000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - pair reaxff command: @Article{Aktulga12, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } - fix qeq/reaxff command: @Article{Aktulga12, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 4 4 17 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 525.6 | 525.6 | 525.6 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 -26202.214 39548.481 0.48416308 298.11815 0 0 0 0 -70840.707 -11679.505 0 0 -82520.212 510.96431 500000 100000 -499.92646 39548.481 0.59931621 321.33774 0 0 0 0 -102931.94 -16786.08 0 0 -119718.02 550.76189 Loop time of 17754.3 on 1 procs for 500000 steps with 916 atoms Performance: 0.487 ns/day, 49.317 hours/ns, 28.162 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12964 | 12964 | 12964 | 0.0 | 73.02 Bond | 0.11897 | 0.11897 | 0.11897 | 0.0 | 0.00 Neigh | 84.144 | 84.144 | 84.144 | 0.0 | 0.47 Comm | 5.833 | 5.833 | 5.833 | 0.0 | 0.03 Output | 0.0047807 | 0.0047807 | 0.0047807 | 0.0 | 0.00 Modify | 4699.3 | 4699.3 | 4699.3 | 0.0 | 26.47 Other | | 1.344 | | | 0.01 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4802 ave 4802 max 4802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 303863 ave 303863 max 303863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303863 Ave neighs/atom = 331.72817 Ave special neighs/atom = 0 Neighbor list builds = 6385 Dangerous builds = 0 write_dump all xyz final_2.3.xyz modify element C H O Si undump trj unfix trjE undump trj_TMOS write_dump deposition_atoms_TMOS 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) = 545.6 | 545.6 | 545.6 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 -499.69527 39548.481 0.59931621 321.33774 0 0 0 0 -102931.94 -16786.079 0 0 -119718.02 550.76189 Loop time of 9e-07 on 1 procs for 0 steps with 916 atoms 222.2% CPU use with 1 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 | | 9e-07 | | |100.00 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4802 ave 4802 max 4802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 303863 ave 303863 max 303863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303863 Ave neighs/atom = 331.72817 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix 5 unfix 6 unfix deposition_TMOS_1 unfix deposition_TMOS_2 unfix dlan Total wall time: 4:55:54