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 -40.39455 0) to (40.39455 40.39455 3.7999997) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3621085 5.3621085 3.7999997 Created 451 atoms using lattice units in orthogonal box = (0 -40.39455 0) to (40.39455 40.39455 3.7999997) create_atoms CPU = 0.000 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3621085 5.3621085 3.7999997 Created 453 atoms using lattice units in orthogonal box = (0 -40.39455 0) to (40.39455 40.39455 3.7999997) create_atoms CPU = 0.000 seconds 453 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 18 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 0 atoms, new total = 904 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 18 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) = 7.668 | 7.668 | 7.668 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4488.7698 0 -4488.7698 240555.48 69 0 -5178.3823 0 -5178.3823 9410.1359 Loop time of 0.897182 on 1 procs for 69 steps with 904 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4488.76984213632 -5178.3786624549 -5178.38231520515 Force two-norm initial, final = 702.06111 0.31794115 Force max component initial, final = 115.61572 0.13041709 Final line search alpha, max atom move = 1 0.13041709 Iterations, force evaluations = 69 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8886 | 0.8886 | 0.8886 | 0.0 | 99.04 Neigh | 0.00264 | 0.00264 | 0.00264 | 0.0 | 0.29 Comm | 0.0039665 | 0.0039665 | 0.0039665 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001971 | | | 0.22 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8556 ave 8556 max 8556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109991 ave 109991 max 109991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109991 Ave neighs/atom = 121.67146 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.668 | 7.668 | 7.668 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -5178.3823 0 -5178.3823 9410.1359 12401.069 75 0 -5178.806 0 -5178.806 -15.865357 12444.851 Loop time of 0.0650655 on 1 procs for 6 steps with 904 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 = -5178.38231520516 -5178.80584947326 -5178.80598612278 Force two-norm initial, final = 183.1558 0.81473599 Force max component initial, final = 169.41583 0.61819885 Final line search alpha, max atom move = 0.00029486004 0.00018228214 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063916 | 0.063916 | 0.063916 | 0.0 | 98.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024517 | 0.00024517 | 0.00024517 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009048 | | | 1.39 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8072 ave 8072 max 8072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 110359 ave 110359 max 110359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110359 Ave neighs/atom = 122.07854 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 18 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) = 7.293 | 7.293 | 7.293 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5178.806 0 -5178.806 -15.865357 Loop time of 5.71e-07 on 1 procs for 0 steps with 904 atoms 350.3% 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 | | 5.71e-07 | | |100.00 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8055 ave 8055 max 8055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109857 ave 109857 max 109857 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 = 109857 Ave neighs/atom = 121.52323 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) = 7.293 | 7.293 | 7.293 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 -5178.806 -5178.806 40.319528 81.151047 3.8034712 -15.865357 -15.865357 25.790267 6.2746005 -79.66094 2.4473201 177.34364 Loop time of 4.91e-07 on 1 procs for 0 steps with 904 atoms 203.7% 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 | | 4.91e-07 | | |100.00 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8055 ave 8055 max 8055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109857 ave 109857 max 109857 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 219714 ave 219714 max 219714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219714 Ave neighs/atom = 243.04646 Neighbor list builds = 0 Dangerous builds = 0 904 -5178.80598612278 eV 2.44732006837314 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01