#------------------------------------------------------------------------------- # Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs #------------------------------------------------------------------------------- group deposition_atoms_C2H id 116944 116945 116946 3 atoms in group deposition_atoms_C2H delete_atoms group deposition_atoms_C2H WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140) Deleted 3 atoms, new total = 116944 molecule depositing_species_C2H deposition_C2H.dat Read molecule template depositing_species_C2H: 1 molecules 0 fragments 3 atoms with max type 2 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_C2H block EDGE EDGE EDGE EDGE 1300 1400 units box group deposition_atoms_H id 116947 1 atoms in group deposition_atoms_H delete_atoms group deposition_atoms_H WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140) Deleted 1 atoms, new total = 116943 molecule depositing_species_H deposition_H.dat Read molecule template depositing_species_H: 1 molecules 0 fragments 1 atoms with max type 2 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_H block EDGE EDGE EDGE EDGE 1300 1400 units box region evaporation_region block EDGE EDGE EDGE EDGE 1450 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 Si terse yes fix 3 all evaporate 1000 1000 evaporation_region 823965 molecule yes fix dlan subset_thermoset langevin 300 300 20.0 564023 tally yes fix 4 movable ave/time 1 250000 250000 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 250 1 250 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_C2H_1 deposition_atoms_C2H deposit 50000 0 50 823965 region deposition_region_C2H mol depositing_species_C2H vz -0.024991234191304085 -0.030544841789371658 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box fix deposition_C2H_2 deposition_atoms_C2H nve fix deposition_H_1 deposition_atoms_H deposit 500 0 5000 851 region deposition_region_H mol depositing_species_H vz -0.12453753584042228 -0.15221254380496058 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box fix deposition_H_2 deposition_atoms_H 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_C2H deposition_atoms_C2H custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs dump trj_H deposition_atoms_H custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs timestep 0.2 run 2500000 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 = 12, bins = 34 1 125 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c/kk, perpetual attributes: half, newton off, ghost, kokkos_device pair build: half/bin/ghost/kk/device stencil: full/ghost/bin/3d bin: kk/device (2) fix qeq/reax/kk, perpetual attributes: full, newton off, kokkos_device pair build: full/bin/kk/device stencil: full/bin/3d bin: kk/device WARNING: Fixes cannot yet send exchange data in Kokkos communication, switching to classic exchange/border communication (src/KOKKOS/comm_kokkos.cpp:581) Per MPI rank memory allocation (min/avg/max) = 5174 | 5174 | 5174 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 -6748.716 3259132.2 1.0666859 300.00346 0 0 0 0 -14799838 -13789.387 0 0 -14813628 104575.77 2500000 500000 -3314.4069 3259132.2 1.0992717 889.55868 0 0 0 0 -15786050 -14739.101 0 0 -15800790 310084.04 Loop time of 410270 on 1 procs for 2500000 steps with 123283 atoms Performance: 0.105 ns/day, 227.928 hours/ns, 6.094 timesteps/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7527e+05 | 2.7527e+05 | 2.7527e+05 | 0.0 | 67.10 Bond | 0.71416 | 0.71416 | 0.71416 | 0.0 | 0.00 Neigh | 16674 | 16674 | 16674 | 0.0 | 4.06 Comm | 3406.5 | 3406.5 | 3406.5 | 0.0 | 0.83 Output | 3.0022 | 3.0022 | 3.0022 | 0.0 | 0.00 Modify | 1.1403e+05 | 1.1403e+05 | 1.1403e+05 | 0.0 | 27.79 Other | | 887.2 | | | 0.22 Nlocal: 123283 ave 123283 max 123283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 583315 ave 583315 max 583315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.27221e+07 ave 5.27221e+07 max 5.27221e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6.28993e+07 ave 6.28993e+07 max 6.28993e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62899270 Ave neighs/atom = 510.2023 Ave special neighs/atom = 0 Neighbor list builds = 246481 Dangerous builds = 54390 write_dump all xyz final_2.3.xyz modify element C H Si undump trj unfix trjE undump trj_C2H undump trj_H write_dump deposition_atoms_C2H custom 2.3.deposited_1.xyz id mol type q xs ys zs write_dump deposition_atoms_H custom 2.3.deposited_2.xyz id mol type q xs ys zs restart 0 dump sci all custom 2500000 2.3.xyz id mol type q xs ys zs run 0 Per MPI rank memory allocation (min/avg/max) = 8054 | 8054 | 8054 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 2500000 500000 -3314.4069 3259132.2 1.0992717 915.39824 0 0 0 0 -15786050 -14739.101 0 0 -15800790 310084.04 Loop time of 0.00744418 on 1 procs for 0 steps with 123283 atoms 99.9% 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 | | 0.007444 | | |100.00 Nlocal: 123283 ave 123283 max 123283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 583315 ave 583315 max 583315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.27221e+07 ave 5.27221e+07 max 5.27221e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6.28993e+07 ave 6.28993e+07 max 6.28993e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62899270 Ave neighs/atom = 510.2023 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_C2H_1 unfix deposition_C2H_2 unfix deposition_H_1 unfix deposition_H_2 unfix dlan Total wall time: 113:57:59