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_ADP_WangXuQian_2021_AuRh__SM_066295357485_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.0800001 4.0800001 4.0800001 Created orthogonal box = (0 -49.298829 0) to (60.378488 49.298829 9.9939184) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.789718 6.0779378 6.6626122 Created 1752 atoms using lattice units in orthogonal box = (0 -49.298829 0) to (60.378488 49.298829 9.9939184) create_atoms CPU = 0.001 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.789718 6.0779378 6.6626122 Created 1758 atoms using lattice units in orthogonal box = (0 -49.298829 0) to (60.378488 49.298829 9.9939184) create_atoms CPU = 0.001 seconds 1758 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 13 22 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 18 atoms, new total = 3492 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_066295357485_000#item-citation 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: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 13 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 9.247 | 9.247 | 9.247 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9639.4601 0 -9639.4601 126351.53 75 0 -13270.904 0 -13270.904 -174.79238 Loop time of 2.555 on 1 procs for 75 steps with 3492 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9639.46013524939 -13270.8920696532 -13270.9041637691 Force two-norm initial, final = 2266.2277 0.32761952 Force max component initial, final = 279.32032 0.030610783 Final line search alpha, max atom move = 1 0.030610783 Iterations, force evaluations = 75 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5339 | 2.5339 | 2.5339 | 0.0 | 99.18 Neigh | 0.008572 | 0.008572 | 0.008572 | 0.0 | 0.34 Comm | 0.0058577 | 0.0058577 | 0.0058577 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006629 | | | 0.26 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11891 ave 11891 max 11891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 346998 ave 346998 max 346998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346998 Ave neighs/atom = 99.369416 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 : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.25 | 9.25 | 9.25 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -13270.904 0 -13270.904 -174.79238 59495.569 76 0 -13270.913 0 -13270.913 507.43324 59472.973 Loop time of 0.0551057 on 1 procs for 1 steps with 3492 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13270.9041637691 -13270.9041637691 -13270.9127261896 Force two-norm initial, final = 29.58474 35.349919 Force max component initial, final = 28.210619 25.314849 Final line search alpha, max atom move = 3.5447644e-05 0.00089735175 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054489 | 0.054489 | 0.054489 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012681 | 0.00012681 | 0.00012681 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004899 | | | 0.89 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12285 ave 12285 max 12285 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 347616 ave 347616 max 347616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 347616 Ave neighs/atom = 99.546392 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: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 13 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.881 | 8.881 | 8.881 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13270.913 0 -13270.913 507.43324 Loop time of 5.11e-07 on 1 procs for 0 steps with 3492 atoms 391.4% 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 | | 5.11e-07 | | |100.00 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12282 ave 12282 max 12282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 347616 ave 347616 max 347616 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 = 347616 Ave neighs/atom = 99.546392 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 : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.881 | 8.881 | 8.881 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 -13270.913 -13270.913 60.345274 98.597338 9.9956536 507.43324 507.43324 209.50335 630.70675 682.08963 2.6902259 1898.2682 Loop time of 6.31e-07 on 1 procs for 0 steps with 3492 atoms 317.0% 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 | | 6.31e-07 | | |100.00 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12282 ave 12282 max 12282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 347616 ave 347616 max 347616 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 695232 ave 695232 max 695232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 695232 Ave neighs/atom = 199.09278 Neighbor list builds = 0 Dangerous builds = 0 3492 -13270.9127261896 eV 2.69022592376309 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02