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 -51.521727 0) to (17.173909 51.521727 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0511497 5.0511497 4.1652847 Created 204 atoms using lattice units in orthogonal box = (0 -51.521727 0) to (17.173909 51.521727 4.1652847) create_atoms CPU = 0.000 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0511497 5.0511497 4.1652847 Created 206 atoms using lattice units in orthogonal box = (0 -51.521727 0) to (17.173909 51.521727 4.1652847) create_atoms CPU = 0.000 seconds 206 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-XXXXXX2VbSwl/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 = 3 18 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 = 408 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 = 3 18 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) = 270.4 | 270.4 | 270.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -33222.895 0 -33222.895 32844.135 58 0 -35021.942 0 -35021.942 15006.1 Loop time of 6.61393 on 1 procs for 58 steps with 408 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -33222.8954927552 -35021.9133124697 -35021.94197661 Force two-norm initial, final = 3438.7252 2.842574 Force max component initial, final = 1128.3162 0.43933131 Final line search alpha, max atom move = 0.12558168 0.055171964 Iterations, force evaluations = 58 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5381 | 5.5381 | 5.5381 | 0.0 | 83.73 Neigh | 0.042365 | 0.042365 | 0.042365 | 0.0 | 0.64 Comm | 0.0048066 | 0.0048066 | 0.0048066 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.0265 | 1.0265 | 1.0265 | 0.0 | 15.52 Other | | 0.002146 | | | 0.03 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8041 ave 8041 max 8041 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141392 ave 141392 max 141392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141392 Ave neighs/atom = 346.54902 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 270.4 | 270.4 | 270.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -35021.942 0 -35021.942 15006.1 7371.1332 69 0 -35034.775 0 -35034.775 -60.802539 7450.7577 Loop time of 0.742574 on 1 procs for 11 steps with 408 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 = -35021.9419766412 -35034.7420088601 -35034.7746374508 Force two-norm initial, final = 2973.878 17.951564 Force max component initial, final = 2443.5584 11.662729 Final line search alpha, max atom move = 1.4964896e-05 0.00017453152 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63428 | 0.63428 | 0.63428 | 0.0 | 85.42 Neigh | 0.042111 | 0.042111 | 0.042111 | 0.0 | 5.67 Comm | 0.00047053 | 0.00047053 | 0.00047053 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.064417 | 0.064417 | 0.064417 | 0.0 | 8.67 Other | | 0.001298 | | | 0.17 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8041 ave 8041 max 8041 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140937 ave 140937 max 140937 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140937 Ave neighs/atom = 345.43382 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 = 3 18 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) = 270.5 | 270.5 | 270.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -35034.775 0 -35034.775 -60.802541 Loop time of 9.41e-07 on 1 procs for 0 steps with 408 atoms 212.5% 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 | | 9.41e-07 | | |100.00 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8041 ave 8041 max 8041 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140922 ave 140922 max 140922 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 = 140922 Ave neighs/atom = 345.39706 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) = 270.5 | 270.5 | 270.5 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 -1519.2516 -35034.775 17.181286 104.13712 4.1642731 -60.80254 -61.608174 8.5436032 -84.641731 -108.72639 2.779088 261.69038 Loop time of 1.002e-06 on 1 procs for 0 steps with 408 atoms 299.4% 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 | | 1.002e-06 | | |100.00 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8041 ave 8041 max 8041 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140922 ave 140922 max 140922 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 154520 ave 154520 max 154520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154520 Ave neighs/atom = 378.72549 Neighbor list builds = 0 Dangerous builds = 0 408 -1519.2516075052 eV 2.77908803931334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07