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 -60.647461 0) to (30.323731 60.647461 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1493127 5.1493127 4.1652847 Created 424 atoms using lattice units in orthogonal box = (0 -60.647461 0) to (30.323731 60.647461 4.1652847) create_atoms CPU = 0.000 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1493127 5.1493127 4.1652847 Created 426 atoms using lattice units in orthogonal box = (0 -60.647461 0) to (30.323731 60.647461 4.1652847) create_atoms CPU = 0.000 seconds 426 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-XXXXXXA4pwkg/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 = 6 21 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 2 atoms, new total = 848 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 = 6 21 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) = 408.9 | 408.9 | 408.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -69793.783 0 -69793.783 27059.357 77 0 -72858.83 0 -72858.83 13201.156 Loop time of 15.4541 on 1 procs for 77 steps with 848 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -69793.7825314386 -72858.7699009334 -72858.83044886 Force two-norm initial, final = 4971.4468 4.2934703 Force max component initial, final = 1635.7581 0.50086981 Final line search alpha, max atom move = 0.13635644 0.068296823 Iterations, force evaluations = 77 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.532 | 12.532 | 12.532 | 0.0 | 81.09 Neigh | 0.057455 | 0.057455 | 0.057455 | 0.0 | 0.37 Comm | 0.0093601 | 0.0093601 | 0.0093601 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.8509 | 2.8509 | 2.8509 | 0.0 | 18.45 Other | | 0.004482 | | | 0.03 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11878 ave 11878 max 11878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288113 ave 288113 max 288113 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288113 Ave neighs/atom = 339.7559 Neighbor list builds = 1 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 : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 408.8 | 408.8 | 408.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -72858.83 0 -72858.83 13201.156 15320.394 87 0 -72879.239 0 -72879.239 114.23031 15464.877 Loop time of 1.14386 on 1 procs for 10 steps with 848 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 = -72858.8304488267 -72879.23350581 -72879.2388678686 Force two-norm initial, final = 5427.7974 48.846089 Force max component initial, final = 4446.2502 32.552046 Final line search alpha, max atom move = 1.8142922e-05 0.00059058923 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96108 | 0.96108 | 0.96108 | 0.0 | 84.02 Neigh | 0.056724 | 0.056724 | 0.056724 | 0.0 | 4.96 Comm | 0.00064392 | 0.00064392 | 0.00064392 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.12361 | 0.12361 | 0.12361 | 0.0 | 10.81 Other | | 0.001809 | | | 0.16 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11829 ave 11829 max 11829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287584 ave 287584 max 287584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287584 Ave neighs/atom = 339.13208 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 = 6 21 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) = 408.2 | 408.2 | 408.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -72879.239 0 -72879.239 114.23031 Loop time of 1.202e-06 on 1 procs for 0 steps with 848 atoms 249.6% 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 | | 1.202e-06 | | |100.00 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11829 ave 11829 max 11829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287608 ave 287608 max 287608 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 = 287608 Ave neighs/atom = 339.16038 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) = 408.2 | 408.2 | 408.2 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 -3160.3429 -72879.239 30.349942 122.38877 4.1633894 114.23031 115.74386 142.63778 147.56097 57.032823 2.7361498 531.66185 Loop time of 1.102e-06 on 1 procs for 0 steps with 848 atoms 363.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.102e-06 | | |100.00 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11829 ave 11829 max 11829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287608 ave 287608 max 287608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 321300 ave 321300 max 321300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321300 Ave neighs/atom = 378.89151 Neighbor list builds = 0 Dangerous builds = 0 848 -3160.34288646241 eV 2.73614978579183 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17