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 -67.121376 0) to (38.752545 67.121376 6.5817925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.96193 6.0237133 6.5817925 Created 1245 atoms using lattice units in orthogonal box = (0 -67.121376 0) to (38.752545 67.121376 6.5817925) create_atoms CPU = 0.001 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.96193 6.0237133 6.5817925 Created 1249 atoms using lattice units in orthogonal box = (0 -67.121376 0) to (38.752545 67.121376 6.5817925) create_atoms CPU = 0.001 seconds 1249 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 29 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 8 atoms, new total = 2486 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 29 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) = 15.47 | 15.47 | 15.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13173.609 0 -13173.609 77836.72 160 0 -14244.492 0 -14244.492 5269.906 Loop time of 5.72748 on 1 procs for 160 steps with 2486 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 = -13173.6093741042 -14244.4810169051 -14244.4915104302 Force two-norm initial, final = 1198.5709 0.49006036 Force max component initial, final = 327.64779 0.16239008 Final line search alpha, max atom move = 0.6894065 0.11195278 Iterations, force evaluations = 160 300 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6606 | 5.6606 | 5.6606 | 0.0 | 98.83 Neigh | 0.036364 | 0.036364 | 0.036364 | 0.0 | 0.63 Comm | 0.018133 | 0.018133 | 0.018133 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01242 | | | 0.22 Nlocal: 2486 ave 2486 max 2486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14274 ave 14274 max 14274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 305615 ave 305615 max 305615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305615 Ave neighs/atom = 122.93443 Neighbor list builds = 5 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 : 160 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.47 | 15.47 | 15.47 Mbytes Step Temp E_pair E_mol TotEng Press Volume 160 0 -14244.492 0 -14244.492 5269.906 34240.119 164 0 -14244.868 0 -14244.868 -54.801044 34309.323 Loop time of 0.131726 on 1 procs for 4 steps with 2486 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14244.4915104302 -14244.8671969385 -14244.8675247247 Force two-norm initial, final = 279.47372 3.2269172 Force max component initial, final = 271.89035 2.9310212 Final line search alpha, max atom move = 0.00014095905 0.00041315394 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13006 | 0.13006 | 0.13006 | 0.0 | 98.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034305 | 0.00034305 | 0.00034305 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001325 | | | 1.01 Nlocal: 2486 ave 2486 max 2486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14274 ave 14274 max 14274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 305653 ave 305653 max 305653 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305653 Ave neighs/atom = 122.94972 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 29 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) = 14.35 | 14.35 | 14.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14244.868 0 -14244.868 -54.801044 Loop time of 5.51e-07 on 1 procs for 0 steps with 2486 atoms 181.5% 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 | | 5.51e-07 | | |100.00 Nlocal: 2486 ave 2486 max 2486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14226 ave 14226 max 14226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 305381 ave 305381 max 305381 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 = 305381 Ave neighs/atom = 122.84031 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) = 14.35 | 14.35 | 14.35 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 -14244.868 -14244.868 38.74841 134.62103 6.5772654 -54.801044 -54.801044 -136.8582 -50.726313 23.18138 2.450123 1141.1598 Loop time of 1.011e-06 on 1 procs for 0 steps with 2486 atoms 395.6% 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 | | 1.011e-06 | | |100.00 Nlocal: 2486 ave 2486 max 2486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14226 ave 14226 max 14226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 305381 ave 305381 max 305381 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 610762 ave 610762 max 610762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610762 Ave neighs/atom = 245.68061 Neighbor list builds = 0 Dangerous builds = 0 2486 -14244.8675247247 eV 2.45012304560241 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06