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 -45.615788 0) to (22.347081 45.615788 9.9939184) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9592216 5.4738945 6.6626122 Created 600 atoms using lattice units in orthogonal box = (0 -45.615788 0) to (22.347081 45.615788 9.9939184) create_atoms CPU = 0.000 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9592216 5.4738945 6.6626122 Created 612 atoms using lattice units in orthogonal box = (0 -45.615788 0) to (22.347081 45.615788 9.9939184) create_atoms CPU = 0.000 seconds 612 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 = 5 20 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 = 1188 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 = 5 20 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) = 7.817 | 7.817 | 7.817 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4328.6567 0 -4328.6567 38660.984 35 0 -4508.2681 0 -4508.2681 -8128.9722 Loop time of 0.397393 on 1 procs for 35 steps with 1188 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 = -4328.65667137941 -4508.26384941873 -4508.26809455461 Force two-norm initial, final = 337.57214 0.19930609 Force max component initial, final = 66.57861 0.025422412 Final line search alpha, max atom move = 1 0.025422412 Iterations, force evaluations = 35 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39491 | 0.39491 | 0.39491 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013843 | 0.0013843 | 0.0013843 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001095 | | | 0.28 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6214 ave 6214 max 6214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117696 ave 117696 max 117696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117696 Ave neighs/atom = 99.070707 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.817 | 7.817 | 7.817 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -4508.2681 0 -4508.2681 -8128.9722 20375.195 39 0 -4508.5163 0 -4508.5163 -20.333677 20282.084 Loop time of 0.0428644 on 1 procs for 4 steps with 1188 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 = -4508.26809455461 -4508.51614000826 -4508.51628016171 Force two-norm initial, final = 179.46706 0.56248234 Force max component initial, final = 110.28437 0.41452772 Final line search alpha, max atom move = 0.00087388787 0.00036225075 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042139 | 0.042139 | 0.042139 | 0.0 | 98.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014668 | 0.00014668 | 0.00014668 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005782 | | | 1.35 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6226 ave 6226 max 6226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117852 ave 117852 max 117852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117852 Ave neighs/atom = 99.20202 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 = 5 20 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) = 7.449 | 7.449 | 7.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4508.5163 0 -4508.5163 -20.333677 Loop time of 5.41e-07 on 1 procs for 0 steps with 1188 atoms 184.8% 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 | | 5.41e-07 | | |100.00 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6240 ave 6240 max 6240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117876 ave 117876 max 117876 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 = 117876 Ave neighs/atom = 99.222222 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) = 7.449 | 7.449 | 7.449 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 -4508.5163 -4508.5163 22.290076 91.206632 9.9764171 -20.333677 -20.333677 -23.76571 -4.5471845 -32.688137 2.6222534 812.52869 Loop time of 4.61e-07 on 1 procs for 0 steps with 1188 atoms 216.9% 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 | | 4.61e-07 | | |100.00 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6240 ave 6240 max 6240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117876 ave 117876 max 117876 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235752 ave 235752 max 235752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235752 Ave neighs/atom = 198.44444 Neighbor list builds = 0 Dangerous builds = 0 1188 -4508.51628016171 eV 2.62225341384842 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00