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 -45.915571 0) to (56.23486 45.915571 9.3080602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3923838 5.6608238 6.2053735 Created 1751 atoms using lattice units in orthogonal box = (0 -45.915571 0) to (56.23486 45.915571 9.3080602) create_atoms CPU = 0.001 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3923838 5.6608238 6.2053735 Created 1757 atoms using lattice units in orthogonal box = (0 -45.915571 0) to (56.23486 45.915571 9.3080602) create_atoms CPU = 0.001 seconds 1757 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 = 13 20 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 16 atoms, new total = 3492 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 = 13 20 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) = 16.18 | 16.18 | 16.18 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15580.381 0 -15580.381 182811.73 82 0 -20001.946 0 -20001.946 2324.4405 Loop time of 3.93754 on 1 procs for 82 steps with 3492 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 = -15580.3805117994 -20001.9287657845 -20001.9457379596 Force two-norm initial, final = 2595.5018 0.56448077 Force max component initial, final = 322.43857 0.056122532 Final line search alpha, max atom move = 1 0.056122532 Iterations, force evaluations = 82 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9018 | 3.9018 | 3.9018 | 0.0 | 99.09 Neigh | 0.020468 | 0.020468 | 0.020468 | 0.0 | 0.52 Comm | 0.0074196 | 0.0074196 | 0.0074196 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007904 | | | 0.20 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13327 ave 13327 max 13327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 428156 ave 428156 max 428156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428156 Ave neighs/atom = 122.61054 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 : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.18 | 16.18 | 16.18 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -20001.946 0 -20001.946 2324.4405 48067.859 84 0 -20001.977 0 -20001.977 -12.371041 48110.39 Loop time of 0.133415 on 1 procs for 2 steps with 3492 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 = -20001.9457379596 -20001.9766797555 -20001.9768593508 Force two-norm initial, final = 121.14676 1.0105789 Force max component initial, final = 74.917463 0.75786169 Final line search alpha, max atom move = 0.00020818671 0.00015777673 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13225 | 0.13225 | 0.13225 | 0.0 | 99.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022183 | 0.00022183 | 0.00022183 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009413 | | | 0.71 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13314 ave 13314 max 13314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 428675 ave 428675 max 428675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428675 Ave neighs/atom = 122.75916 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 = 13 20 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) = 15.06 | 15.06 | 15.06 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20001.977 0 -20001.977 -12.371041 Loop time of 6.01e-07 on 1 procs for 0 steps with 3492 atoms 166.4% 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 | | 6.01e-07 | | |100.00 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13311 ave 13311 max 13311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 428550 ave 428550 max 428550 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 = 428550 Ave neighs/atom = 122.72337 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) = 15.06 | 15.06 | 15.06 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 -20001.977 -20001.977 56.246848 91.861087 9.311274 -12.371041 -12.371041 -11.867108 0.0010770477 -25.247092 2.4977326 1870.3028 Loop time of 1.703e-06 on 1 procs for 0 steps with 3492 atoms 234.9% 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 | | 1.703e-06 | | |100.00 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13311 ave 13311 max 13311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 428550 ave 428550 max 428550 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 857100 ave 857100 max 857100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 857100 Ave neighs/atom = 245.44674 Neighbor list builds = 0 Dangerous builds = 0 3492 -20001.9768593508 eV 2.49773257407528 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04