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_XuWangQian_2022_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -57.566744 0) to (47.00305 57.566744 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7948965 5.5200987 6.3523435 Created 1748 atoms using lattice units in orthogonal box = (0 -57.566744 0) to (47.00305 57.566744 9.5285152) create_atoms CPU = 0.001 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7948965 5.5200987 6.3523435 Created 1756 atoms using lattice units in orthogonal box = (0 -57.566744 0) to (47.00305 57.566744 9.5285152) create_atoms CPU = 0.001 seconds 1756 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 11 26 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 2 atoms, new total = 3502 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_559286646876_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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 11 26 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) = 9.273 | 9.273 | 9.273 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9020.3282 0 -9020.3282 181907.77 81 0 -13562.736 0 -13562.736 8751.2297 Loop time of 2.73437 on 1 procs for 81 steps with 3502 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 = -9020.32819357541 -13562.7256743601 -13562.7364749288 Force two-norm initial, final = 2747.9215 0.50376106 Force max component initial, final = 344.48898 0.13785716 Final line search alpha, max atom move = 1 0.13785716 Iterations, force evaluations = 81 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7126 | 2.7126 | 2.7126 | 0.0 | 99.20 Neigh | 0.0081716 | 0.0081716 | 0.0081716 | 0.0 | 0.30 Comm | 0.0064153 | 0.0064153 | 0.0064153 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007231 | | | 0.26 Nlocal: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12367 ave 12367 max 12367 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 348062 ave 348062 max 348062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348062 Ave neighs/atom = 99.389492 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.273 | 9.273 | 9.273 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -13562.736 0 -13562.736 8751.2297 51564.752 88 0 -13563.863 0 -13563.863 -10.449715 51789.812 Loop time of 0.181329 on 1 procs for 7 steps with 3502 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 = -13562.7364749288 -13563.8598540145 -13563.8631558916 Force two-norm initial, final = 524.89713 3.7463213 Force max component initial, final = 439.83779 2.5298378 Final line search alpha, max atom move = 2.5576395e-05 6.4704131e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17874 | 0.17874 | 0.17874 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042565 | 0.00042565 | 0.00042565 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002161 | | | 1.19 Nlocal: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12292 ave 12292 max 12292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 348363 ave 348363 max 348363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348363 Ave neighs/atom = 99.475443 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 11 27 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) = 8.905 | 8.905 | 8.905 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13563.863 0 -13563.863 -10.449715 Loop time of 5.61e-07 on 1 procs for 0 steps with 3502 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: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12292 ave 12292 max 12292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 348053 ave 348053 max 348053 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 = 348053 Ave neighs/atom = 99.386922 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) = 8.905 | 8.905 | 8.905 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 -13563.863 -13563.863 46.946192 115.81347 9.5254367 -10.449715 -10.449715 -71.412217 -38.175038 78.238111 2.5034004 1844.856 Loop time of 5.11e-07 on 1 procs for 0 steps with 3502 atoms 587.1% 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: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12292 ave 12292 max 12292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 348053 ave 348053 max 348053 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 696106 ave 696106 max 696106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 696106 Ave neighs/atom = 198.77384 Neighbor list builds = 0 Dangerous builds = 0 3502 -13563.8631558916 eV 2.50340039880199 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03