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 = 3.7999997 3.7999997 3.7999997 Created orthogonal box = (0 -42.485288 0) to (20.813455 42.485288 9.3080602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5502547 5.0982345 6.2053735 Created 600 atoms using lattice units in orthogonal box = (0 -42.485288 0) to (20.813455 42.485288 9.3080602) create_atoms CPU = 0.000 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5502547 5.0982345 6.2053735 Created 612 atoms using lattice units in orthogonal box = (0 -42.485288 0) to (20.813455 42.485288 9.3080602) create_atoms CPU = 0.000 seconds 612 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 = 5 19 2 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 12 atoms, new total = 1200 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 = 5 19 2 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) = 7.911 | 7.911 | 7.911 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6258.8899 0 -6258.8899 147337.84 17 0 -6862.045 0 -6862.045 23044.82 Loop time of 0.275123 on 1 procs for 17 steps with 1200 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 = -6258.88985991692 -6862.04101690531 -6862.04501475858 Force two-norm initial, final = 747.62961 0.37390543 Force max component initial, final = 107.90944 0.043611944 Final line search alpha, max atom move = 1 0.043611944 Iterations, force evaluations = 17 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27368 | 0.27368 | 0.27368 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082578 | 0.00082578 | 0.00082578 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006152 | | | 0.22 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7365 ave 7365 max 7365 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148800 ave 148800 max 148800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148800 Ave neighs/atom = 124 Neighbor list builds = 0 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.911 | 7.911 | 7.911 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -6862.045 0 -6862.045 23044.82 16461.596 29 0 -6864.4381 0 -6864.4381 0.97074111 16603.395 Loop time of 0.135897 on 1 procs for 12 steps with 1200 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 = -6862.04501475858 -6864.4378941318 -6864.43807211756 Force two-norm initial, final = 507.76059 2.6111943 Force max component initial, final = 479.44641 1.4768758 Final line search alpha, max atom move = 0.00084862122 0.0012533082 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13398 | 0.13398 | 0.13398 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036947 | 0.00036947 | 0.00036947 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00155 | | | 1.14 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7233 ave 7233 max 7233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147168 ave 147168 max 147168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147168 Ave neighs/atom = 122.64 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 = 5 19 2 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) = 7.542 | 7.542 | 7.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6864.4381 0 -6864.4381 0.97074111 Loop time of 5.41e-07 on 1 procs for 0 steps with 1200 atoms 184.8% 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 | | 5.41e-07 | | |100.00 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7269 ave 7269 max 7269 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146880 ave 146880 max 146880 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 = 146880 Ave neighs/atom = 122.4 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) = 7.542 | 7.542 | 7.542 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 -6864.4381 -6864.4381 20.795353 85.867999 9.2982079 0.97074111 0.97074111 121.03456 24.240796 -142.36313 2.4639015 841.39554 Loop time of 6.92e-07 on 1 procs for 0 steps with 1200 atoms 144.5% 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 | | 6.92e-07 | | |100.00 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7269 ave 7269 max 7269 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146880 ave 146880 max 146880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293760 ave 293760 max 293760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293760 Ave neighs/atom = 244.8 Neighbor list builds = 0 Dangerous builds = 0 1200 -6864.43807211756 eV 2.46390148497708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00