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_XuWangQian_2022_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -70.020001 0) to (49.511618 70.020001 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7237999 6.4833334 5.5012908 Created 1294 atoms using lattice units in orthogonal box = (0 -70.020001 0) to (49.511618 70.020001 5.5012908) create_atoms CPU = 0.001 seconds 1294 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7237999 6.4833334 5.5012908 Created 1298 atoms using lattice units in orthogonal box = (0 -70.020001 0) to (49.511618 70.020001 5.5012908) create_atoms CPU = 0.001 seconds 1298 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 12 32 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 8 atoms, new total = 2584 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_559286646876_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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 12 32 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) = 15.04 | 15.04 | 15.04 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7477.8893 0 -7477.8893 117066.33 49 0 -10025.302 0 -10025.302 -1306.3947 Loop time of 1.08586 on 1 procs for 49 steps with 2584 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 = -7477.88925687683 -10025.2935220783 -10025.3024911803 Force two-norm initial, final = 2149.3067 0.37683926 Force max component initial, final = 404.83725 0.059028258 Final line search alpha, max atom move = 1 0.059028258 Iterations, force evaluations = 49 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0665 | 1.0665 | 1.0665 | 0.0 | 98.21 Neigh | 0.01139 | 0.01139 | 0.01139 | 0.0 | 1.05 Comm | 0.0045185 | 0.0045185 | 0.0045185 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003481 | | | 0.32 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14208 ave 14208 max 14208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257286 ave 257286 max 257286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257286 Ave neighs/atom = 99.568885 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 : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.04 | 15.04 | 15.04 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -10025.302 0 -10025.302 -1306.3947 38143.789 52 0 -10025.336 0 -10025.336 10.763505 38118.397 Loop time of 0.0937117 on 1 procs for 3 steps with 2584 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 = -10025.3024911802 -10025.3355792544 -10025.335625604 Force two-norm initial, final = 66.50185 0.59356358 Force max component initial, final = 52.957029 0.31574037 Final line search alpha, max atom move = 0.00087476822 0.00027619964 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.092099 | 0.092099 | 0.092099 | 0.0 | 98.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034831 | 0.00034831 | 0.00034831 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001265 | | | 1.35 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14224 ave 14224 max 14224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257560 ave 257560 max 257560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257560 Ave neighs/atom = 99.674923 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 12 32 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) = 13.92 | 13.92 | 13.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10025.336 0 -10025.336 10.763505 Loop time of 6.72e-07 on 1 procs for 0 steps with 2584 atoms 148.8% 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 | | 6.72e-07 | | |100.00 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14224 ave 14224 max 14224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257580 ave 257580 max 257580 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 = 257580 Ave neighs/atom = 99.682663 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) = 13.92 | 13.92 | 13.92 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 -10025.336 -10025.336 49.545988 139.97867 5.496222 10.763505 10.763505 8.9981228 10.033552 13.258839 2.5951186 1509.0675 Loop time of 9.12e-07 on 1 procs for 0 steps with 2584 atoms 328.9% 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 | | 9.12e-07 | | |100.00 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14224 ave 14224 max 14224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257580 ave 257580 max 257580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 515160 ave 515160 max 515160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 515160 Ave neighs/atom = 199.36533 Neighbor list builds = 0 Dangerous builds = 0 2584 -10025.335625604 eV 2.59511863943856 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01