LAMMPS (23 Jun 2022) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_001 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.1652847 4.1652847 4.1652847 Created orthogonal box = (0 -79.686589 0) to (46.007074 79.686589 7.2144848) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7879289 6.0962418 7.2144848 Created 1464 atoms using lattice units in orthogonal box = (0 -79.686589 0) to (46.007074 79.686589 7.2144848) create_atoms CPU = 0.001 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7879289 6.0962418 7.2144848 Created 1466 atoms using lattice units in orthogonal box = (0 -79.686589 0) to (46.007074 79.686589 7.2144848) create_atoms CPU = 0.001 seconds 1466 atoms in group lower Displacing atoms ... WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:98) Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXbLNCTK/ffield.reax.AuO with DATE: 2011-02-18 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (3) fix qeq/reax, perpetual, copy from (2) attributes: half, newton off pair build: copy stencil: none bin: none Deleted 4 atoms, new total = 2926 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_974345878378_001#item-citation - pair reaxff command: - fix qeq/reaxff command: The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 27 2 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 Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 729.5 | 729.5 | 729.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -241961.71 0 -241961.71 23858.45 121 0 -251715.23 0 -251715.23 9776.1915 Loop time of 48.7797 on 1 procs for 121 steps with 2926 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -241961.710888713 -251714.979001731 -251715.228716125 Force two-norm initial, final = 8721.865 9.375788 Force max component initial, final = 2121.7816 1.8447596 Final line search alpha, max atom move = 0.08589848 0.15846204 Iterations, force evaluations = 121 205 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.806 | 35.806 | 35.806 | 0.0 | 73.40 Neigh | 0.77218 | 0.77218 | 0.77218 | 0.0 | 1.58 Comm | 0.02154 | 0.02154 | 0.02154 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 12.165 | 12.165 | 12.165 | 0.0 | 24.94 Other | | 0.01503 | | | 0.03 Nlocal: 2926 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19214 ave 19214 max 19214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 903337 ave 903337 max 903337 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 903337 Ave neighs/atom = 308.72761 Neighbor list builds = 6 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : real Current step : 121 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 729.4 | 729.4 | 729.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 121 0 -251715.23 0 -251715.23 9776.1915 52898.72 129 0 -251760.35 0 -251760.35 -17.723305 53272.157 Loop time of 2.78242 on 1 procs for 8 steps with 2926 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -251715.228715787 -251760.338512966 -251760.348991682 Force two-norm initial, final = 15051.074 45.388442 Force max component initial, final = 13617.877 36.11605 Final line search alpha, max atom move = 5.2334735e-06 0.00018901239 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2701 | 2.2701 | 2.2701 | 0.0 | 81.59 Neigh | 0.12609 | 0.12609 | 0.12609 | 0.0 | 4.53 Comm | 0.0010217 | 0.0010217 | 0.0010217 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.38185 | 0.38185 | 0.38185 | 0.0 | 13.72 Other | | 0.00337 | | | 0.12 Nlocal: 2926 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19218 ave 19218 max 19218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 901800 ave 901800 max 901800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 901800 Ave neighs/atom = 308.20232 Neighbor list builds = 1 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 27 2 4 neighbor lists, perpetual/occasional/extra = 2 2 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) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard (4) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 728.9 | 728.9 | 728.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -251760.35 0 -251760.35 -17.723305 Loop time of 1.052e-06 on 1 procs for 0 steps with 2926 atoms 285.2% 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 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 | | 1.052e-06 | | |100.00 Nlocal: 2926 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19209 ave 19209 max 19209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 901823 ave 901823 max 901823 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 901823 Ave neighs/atom = 308.21018 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 728.9 | 728.9 | 728.9 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -10917.362 -251760.35 46.018826 160.42194 7.2160742 -17.723305 -17.958139 -47.114178 -21.313953 14.553714 2.6581099 1718.7923 Loop time of 9.31e-07 on 1 procs for 0 steps with 2926 atoms 537.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 9.31e-07 | | |100.00 Nlocal: 2926 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19209 ave 19209 max 19209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 901823 ave 901823 max 901823 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.10912e+06 ave 1.10912e+06 max 1.10912e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1109124 Ave neighs/atom = 379.0581 Neighbor list builds = 0 Dangerous builds = 0 2926 -10917.3619317208 eV 2.65810992164305 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:53