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 -46.072547 0) to (37.618077 46.072547 9.3080602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.374011 5.3281177 6.2053735 Created 1176 atoms using lattice units in orthogonal box = (0 -46.072547 0) to (37.618077 46.072547 9.3080602) create_atoms CPU = 0.001 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.374011 5.3281177 6.2053735 Created 1184 atoms using lattice units in orthogonal box = (0 -46.072547 0) to (37.618077 46.072547 9.3080602) create_atoms CPU = 0.001 seconds 1184 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 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 24 atoms, new total = 2336 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 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) = 8.667 | 8.667 | 8.667 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11629.605 0 -11629.605 118518.99 102 0 -13364.945 0 -13364.945 5709.9903 Loop time of 3.37003 on 1 procs for 102 steps with 2336 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 = -11629.6047573736 -13364.9334588196 -13364.944772336 Force two-norm initial, final = 1557.9019 0.47904102 Force max component initial, final = 261.09917 0.059960525 Final line search alpha, max atom move = 1 0.059960525 Iterations, force evaluations = 102 188 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3409 | 3.3409 | 3.3409 | 0.0 | 99.14 Neigh | 0.013733 | 0.013733 | 0.013733 | 0.0 | 0.41 Comm | 0.008123 | 0.008123 | 0.008123 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007234 | | | 0.21 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10381 ave 10381 max 10381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 286232 ave 286232 max 286232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286232 Ave neighs/atom = 122.53082 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 : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.669 | 8.669 | 8.669 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -13364.945 0 -13364.945 5709.9903 32264.727 106 0 -13365.333 0 -13365.333 -137.99519 32337.178 Loop time of 0.105001 on 1 procs for 4 steps with 2336 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13364.944772336 -13365.3324322379 -13365.3331163472 Force two-norm initial, final = 268.4427 5.7980359 Force max component initial, final = 255.41954 5.2461198 Final line search alpha, max atom move = 0.00013930409 0.00073080596 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10388 | 0.10388 | 0.10388 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020607 | 0.00020607 | 0.00020607 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009131 | | | 0.87 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10246 ave 10246 max 10246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 286440 ave 286440 max 286440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286440 Ave neighs/atom = 122.61986 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 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) = 8.299 | 8.299 | 8.299 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13365.333 0 -13365.333 -137.99519 Loop time of 6.81e-07 on 1 procs for 0 steps with 2336 atoms 146.8% 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 | | 6.81e-07 | | |100.00 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10246 ave 10246 max 10246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 286120 ave 286120 max 286120 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 = 286120 Ave neighs/atom = 122.48288 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) = 8.299 | 8.299 | 8.299 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 -13365.333 -13365.333 37.617773 92.429177 9.3003641 -137.99519 -137.99519 -259.92193 -52.41325 -101.65039 2.4529091 1647.2182 Loop time of 1.012e-06 on 1 procs for 0 steps with 2336 atoms 197.6% 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 | | 1.012e-06 | | |100.00 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10246 ave 10246 max 10246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 286120 ave 286120 max 286120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 572240 ave 572240 max 572240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 572240 Ave neighs/atom = 244.96575 Neighbor list builds = 0 Dangerous builds = 0 2336 -13365.3331163472 eV 2.452909091064 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03