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 -48.66374 0) to (24.33187 48.66374 3.7999997) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3411422 5.3411422 3.7999997 Created 328 atoms using lattice units in orthogonal box = (0 -48.66374 0) to (24.33187 48.66374 3.7999997) create_atoms CPU = 0.000 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3411422 5.3411422 3.7999997 Created 330 atoms using lattice units in orthogonal box = (0 -48.66374 0) to (24.33187 48.66374 3.7999997) create_atoms CPU = 0.000 seconds 330 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 = 6 21 1 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 = 656 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 = 6 21 1 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) = 7.206 | 7.206 | 7.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3465.4131 0 -3465.4131 120961.68 33 0 -3757.1823 0 -3757.1823 11415.985 Loop time of 0.305332 on 1 procs for 33 steps with 656 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 = -3465.41313423365 -3757.17947199946 -3757.18234107741 Force two-norm initial, final = 548.99906 0.25695004 Force max component initial, final = 178.13536 0.057494893 Final line search alpha, max atom move = 1 0.057494893 Iterations, force evaluations = 33 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30292 | 0.30292 | 0.30292 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016666 | 0.0016666 | 0.0016666 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007408 | | | 0.24 Nlocal: 656 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7642 ave 7642 max 7642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81368 ave 81368 max 81368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81368 Ave neighs/atom = 124.03659 Neighbor list builds = 0 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 : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.206 | 7.206 | 7.206 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -3757.1823 0 -3757.1823 11415.985 8999.0055 39 0 -3757.5748 0 -3757.5748 210.46442 9036.7835 Loop time of 0.0410339 on 1 procs for 6 steps with 656 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 = -3757.1823410774 -3757.57377183709 -3757.5747976963 Force two-norm initial, final = 152.55675 2.4111378 Force max component initial, final = 142.75786 1.7030404 Final line search alpha, max atom move = 0.0002406438 0.0004098261 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040158 | 0.040158 | 0.040158 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021045 | 0.00021045 | 0.00021045 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006657 | | | 1.62 Nlocal: 656 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7642 ave 7642 max 7642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80600 ave 80600 max 80600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80600 Ave neighs/atom = 122.86585 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 = 6 21 1 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) = 6.837 | 6.837 | 6.837 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3757.5748 0 -3757.5748 210.46442 Loop time of 8.72e-07 on 1 procs for 0 steps with 656 atoms 229.4% 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 | | 8.72e-07 | | |100.00 Nlocal: 656 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7624 ave 7624 max 7624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80296 ave 80296 max 80296 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 = 80296 Ave neighs/atom = 122.40244 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) = 6.837 | 6.837 | 6.837 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 -3757.5748 -3757.5748 24.290928 97.833566 3.8026109 210.46442 210.46442 301.43248 286.02917 43.931609 2.4521516 177.49161 Loop time of 4.8e-07 on 1 procs for 0 steps with 656 atoms 208.3% 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 | | 4.8e-07 | | |100.00 Nlocal: 656 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7624 ave 7624 max 7624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80296 ave 80296 max 80296 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160592 ave 160592 max 160592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160592 Ave neighs/atom = 244.80488 Neighbor list builds = 0 Dangerous builds = 0 656 -3757.5747976963 eV 2.45215160602181 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00