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 -72.698274 0) to (41.972368 72.698274 6.5817925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1926445 5.5616166 6.5817925 Created 1463 atoms using lattice units in orthogonal box = (0 -72.698274 0) to (41.972368 72.698274 6.5817925) create_atoms CPU = 0.001 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1926445 5.5616166 6.5817925 Created 1465 atoms using lattice units in orthogonal box = (0 -72.698274 0) to (41.972368 72.698274 6.5817925) create_atoms CPU = 0.001 seconds 1465 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 = 9 32 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 3 atoms, new total = 2925 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 = 9 32 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) = 15.62 | 15.62 | 15.62 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15496.19 0 -15496.19 102853.21 114 0 -16761.186 0 -16761.186 11596.314 Loop time of 4.50532 on 1 procs for 114 steps with 2925 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 = -15496.1896107975 -16761.1702609885 -16761.1864946279 Force two-norm initial, final = 1188.9278 0.67321211 Force max component initial, final = 265.46249 0.13964066 Final line search alpha, max atom move = 0.8881514 0.12402205 Iterations, force evaluations = 114 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4497 | 4.4497 | 4.4497 | 0.0 | 98.76 Neigh | 0.034464 | 0.034464 | 0.034464 | 0.0 | 0.76 Comm | 0.012241 | 0.012241 | 0.012241 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008956 | | | 0.20 Nlocal: 2925 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15744 ave 15744 max 15744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 360274 ave 360274 max 360274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360274 Ave neighs/atom = 123.1706 Neighbor list builds = 4 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 : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -16761.186 0 -16761.186 11596.314 40166.293 120 0 -16762.492 0 -16762.492 -14.656399 40340.903 Loop time of 0.199089 on 1 procs for 6 steps with 2925 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 = -16761.1864946279 -16762.4909731292 -16762.4917076638 Force two-norm initial, final = 610.51941 2.4427595 Force max component initial, final = 572.41429 1.6731537 Final line search alpha, max atom move = 7.472847e-05 0.00012503222 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19668 | 0.19668 | 0.19668 | 0.0 | 98.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048327 | 0.00048327 | 0.00048327 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001925 | | | 0.97 Nlocal: 2925 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15394 ave 15394 max 15394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 360332 ave 360332 max 360332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360332 Ave neighs/atom = 123.19043 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 = 9 32 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) = 14.5 | 14.5 | 14.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16762.492 0 -16762.492 -14.656399 Loop time of 6.71e-07 on 1 procs for 0 steps with 2925 atoms 149.0% 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 | | 6.71e-07 | | |100.00 Nlocal: 2925 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15387 ave 15387 max 15387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 359828 ave 359828 max 359828 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 = 359828 Ave neighs/atom = 123.01812 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) = 14.5 | 14.5 | 14.5 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 -16762.492 -16762.492 41.962886 146.07937 6.5809921 -14.656399 -14.656399 -66.435843 -27.504801 49.971448 2.4266894 1424.8688 Loop time of 8.92e-07 on 1 procs for 0 steps with 2925 atoms 448.4% 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 | | 8.92e-07 | | |100.00 Nlocal: 2925 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15387 ave 15387 max 15387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 359828 ave 359828 max 359828 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 719656 ave 719656 max 719656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 719656 Ave neighs/atom = 246.03624 Neighbor list builds = 0 Dangerous builds = 0 2925 -16762.4917076638 eV 2.42668935859682 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04