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 -41.652847 0) to (20.826424 41.652847 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8313986 5.8313986 4.1652847 Created 199 atoms using lattice units in orthogonal box = (0 -41.652847 0) to (20.826424 41.652847 4.1652847) create_atoms CPU = 0.000 seconds 199 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8313986 5.8313986 4.1652847 Created 201 atoms using lattice units in orthogonal box = (0 -41.652847 0) to (20.826424 41.652847 4.1652847) create_atoms CPU = 0.000 seconds 201 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-XXXXXXw9wpGG/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 = 4 14 1 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 0 atoms, new total = 400 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 = 4 14 1 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) = 249.1 | 249.1 | 249.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -31776.284 0 -31776.284 48224.054 54 0 -34341.391 0 -34341.391 11151.849 Loop time of 5.17824 on 1 procs for 54 steps with 400 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 = -31776.2839993744 -34341.3582080823 -34341.3911465085 Force two-norm initial, final = 3607.1262 3.153471 Force max component initial, final = 679.7912 0.58621694 Final line search alpha, max atom move = 0.15138642 0.088745283 Iterations, force evaluations = 54 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2224 | 4.2224 | 4.2224 | 0.0 | 81.54 Neigh | 0.069095 | 0.069095 | 0.069095 | 0.0 | 1.33 Comm | 0.003628 | 0.003628 | 0.003628 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.88126 | 0.88126 | 0.88126 | 0.0 | 17.02 Other | | 0.001891 | | | 0.04 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6757 ave 6757 max 6757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 138574 ave 138574 max 138574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138574 Ave neighs/atom = 346.435 Neighbor list builds = 2 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 249.1 | 249.1 | 249.1 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -34341.391 0 -34341.391 11151.849 7226.6011 63 0 -34350.771 0 -34350.771 -126.31008 7285.2677 Loop time of 0.553769 on 1 procs for 9 steps with 400 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 = -34341.3911464398 -34350.759041655 -34350.7713794977 Force two-norm initial, final = 2493.5939 24.861001 Force max component initial, final = 2270.1166 15.625159 Final line search alpha, max atom move = 2.687771e-05 0.0004199685 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49474 | 0.49474 | 0.49474 | 0.0 | 89.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031631 | 0.00031631 | 0.00031631 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.057693 | 0.057693 | 0.057693 | 0.0 | 10.42 Other | | 0.001021 | | | 0.18 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6750 ave 6750 max 6750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 138486 ave 138486 max 138486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138486 Ave neighs/atom = 346.215 Neighbor list builds = 0 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 = 4 14 1 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) = 248.5 | 248.5 | 248.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -34350.771 0 -34350.771 -126.31009 Loop time of 9.22e-07 on 1 procs for 0 steps with 400 atoms 325.4% 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 | | 9.22e-07 | | |100.00 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6750 ave 6750 max 6750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137999 ave 137999 max 137999 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 = 137999 Ave neighs/atom = 344.9975 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) = 248.5 | 248.5 | 248.5 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 -1489.5904 -34350.771 20.805093 83.982871 4.1695112 -126.31008 -127.98369 -107.62707 -127.16135 -149.16266 2.6764445 211.0673 Loop time of 9.72e-07 on 1 procs for 0 steps with 400 atoms 308.6% 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 | | 9.72e-07 | | |100.00 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6750 ave 6750 max 6750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137999 ave 137999 max 137999 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 152160 ave 152160 max 152160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152160 Ave neighs/atom = 380.4 Neighbor list builds = 0 Dangerous builds = 0 400 -1489.59041916746 eV 2.67644452626516 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06