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 = 4.0800001 4.0800001 4.0800001 Created orthogonal box = (0 -49.467372 0) to (40.38994 49.467372 9.9939184) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7699915 5.7207165 6.6626122 Created 1176 atoms using lattice units in orthogonal box = (0 -49.467372 0) to (40.38994 49.467372 9.9939184) create_atoms CPU = 0.001 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7699915 5.7207165 6.6626122 Created 1184 atoms using lattice units in orthogonal box = (0 -49.467372 0) to (40.38994 49.467372 9.9939184) 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 22 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 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 22 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) = 8.606 | 8.606 | 8.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7627.1556 0 -7627.1556 83065.596 85 0 -8867.4036 0 -8867.4036 -3410.9142 Loop time of 2.03096 on 1 procs for 85 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 = -7627.15556882331 -8867.39523357213 -8867.40355615069 Force two-norm initial, final = 1214.8871 0.25926188 Force max component initial, final = 196.01431 0.022721315 Final line search alpha, max atom move = 1 0.022721315 Iterations, force evaluations = 85 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.013 | 2.013 | 2.013 | 0.0 | 99.12 Neigh | 0.0064995 | 0.0064995 | 0.0064995 | 0.0 | 0.32 Comm | 0.0058049 | 0.0058049 | 0.0058049 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005663 | | | 0.28 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9448 ave 9448 max 9448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231776 ave 231776 max 231776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231776 Ave neighs/atom = 99.219178 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.606 | 8.606 | 8.606 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -8867.4036 0 -8867.4036 -3410.9142 39935.382 89 0 -8867.5892 0 -8867.5892 238.62936 39853.427 Loop time of 0.073234 on 1 procs for 4 steps with 2336 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 = -8867.40355615074 -8867.58472743398 -8867.58916418125 Force two-norm initial, final = 158.76763 13.414825 Force max component initial, final = 121.06184 12.83725 Final line search alpha, max atom move = 4.5476028e-05 0.00058378713 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07221 | 0.07221 | 0.07221 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018742 | 0.00018742 | 0.00018742 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008366 | | | 1.14 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9165 ave 9165 max 9165 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 232376 ave 232376 max 232376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232376 Ave neighs/atom = 99.476027 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 22 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) = 8.237 | 8.237 | 8.237 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8867.5892 0 -8867.5892 238.62936 Loop time of 6.51e-07 on 1 procs for 0 steps with 2336 atoms 153.6% 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 | | 6.51e-07 | | |100.00 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9313 ave 9313 max 9313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 232360 ave 232360 max 232360 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 = 232360 Ave neighs/atom = 99.469178 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) = 8.237 | 8.237 | 8.237 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 -8867.5892 -8867.5892 40.333501 99.111026 9.9696011 238.62936 238.62936 53.075415 516.99913 145.81353 2.6214343 1710.7978 Loop time of 6.82e-07 on 1 procs for 0 steps with 2336 atoms 293.3% 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 | | 6.82e-07 | | |100.00 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9313 ave 9313 max 9313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 232360 ave 232360 max 232360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 464720 ave 464720 max 464720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 464720 Ave neighs/atom = 198.93836 Neighbor list builds = 0 Dangerous builds = 0 2336 -8867.58916418125 eV 2.62143430506575 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02