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 -41.626911 0) to (8.4970575 41.626911 9.3080602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0982345 5.5502547 6.2053735 Created 240 atoms using lattice units in orthogonal box = (0 -41.626911 0) to (8.4970575 41.626911 9.3080602) create_atoms CPU = 0.000 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0982345 5.5502547 6.2053735 Created 242 atoms using lattice units in orthogonal box = (0 -41.626911 0) to (8.4970575 41.626911 9.3080602) create_atoms CPU = 0.000 seconds 242 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 = 2 18 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 2 atoms, new total = 480 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 = 2 18 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) = 7.293 | 7.293 | 7.293 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2014.685 0 -2014.685 198729.22 72 0 -2745.3325 0 -2745.3325 21116.643 Loop time of 0.517307 on 1 procs for 72 steps with 480 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 = -2014.68497057398 -2745.33006315182 -2745.33245283347 Force two-norm initial, final = 1093.6564 0.21191662 Force max component initial, final = 355.79732 0.039996511 Final line search alpha, max atom move = 1 0.039996511 Iterations, force evaluations = 72 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5106 | 0.5106 | 0.5106 | 0.0 | 98.70 Neigh | 0.0032119 | 0.0032119 | 0.0032119 | 0.0 | 0.62 Comm | 0.0024072 | 0.0024072 | 0.0024072 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001091 | | | 0.21 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5142 ave 5142 max 5142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59104 ave 59104 max 59104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59104 Ave neighs/atom = 123.13333 Neighbor list builds = 2 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 : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.293 | 7.293 | 7.293 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -2745.3325 0 -2745.3325 21116.643 6584.6382 80 0 -2745.8461 0 -2745.8461 -59.138973 6637.3669 Loop time of 0.0427097 on 1 procs for 8 steps with 480 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 = -2745.33245283347 -2745.84586753723 -2745.84606986689 Force two-norm initial, final = 163.68144 1.0064221 Force max component initial, final = 136.9186 0.74773885 Final line search alpha, max atom move = 0.00037395601 0.00027962143 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041865 | 0.041865 | 0.041865 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018913 | 0.00018913 | 0.00018913 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006556 | | | 1.53 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5142 ave 5142 max 5142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59060 ave 59060 max 59060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59060 Ave neighs/atom = 123.04167 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 = 2 18 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) = 6.925 | 6.925 | 6.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2745.8461 0 -2745.8461 -59.138973 Loop time of 5.61e-07 on 1 procs for 0 steps with 480 atoms 178.3% 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 | | 5.61e-07 | | |100.00 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5142 ave 5142 max 5142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58866 ave 58866 max 58866 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 = 58866 Ave neighs/atom = 122.6375 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) = 6.925 | 6.925 | 6.925 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 -2745.8461 -2745.8461 8.5081828 83.831942 9.3057093 -59.138973 -59.138973 -180.73103 -60.504901 63.819015 2.4933152 320.97237 Loop time of 6.31e-07 on 1 procs for 0 steps with 480 atoms 475.4% 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 | | 6.31e-07 | | |100.00 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5142 ave 5142 max 5142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58866 ave 58866 max 58866 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117732 ave 117732 max 117732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117732 Ave neighs/atom = 245.275 Neighbor list builds = 0 Dangerous builds = 0 480 -2745.84606986689 eV 2.4933151903249 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00