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_StarikovLopanitsynaSmirnova_2018_SiAu__SM_985135773293_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.1820496 4.1820496 4.1820496 Created orthogonal box = (0 -75.276893 0) to (53.228801 75.276893 5.9143112) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.2286026 6.9700826 5.9143112 Created 1296 atoms using lattice units in orthogonal box = (0 -75.276893 0) to (53.228801 75.276893 5.9143112) create_atoms CPU = 0.001 seconds 1296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.2286026 6.9700826 5.9143112 Created 1300 atoms using lattice units in orthogonal box = (0 -75.276893 0) to (53.228801 75.276893 5.9143112) create_atoms CPU = 0.001 seconds 1300 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 = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 13 37 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 12 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_985135773293_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 = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 13 37 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) = 8.204 | 8.204 | 8.204 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9634.8244 0 -9634.8244 16445.078 96 0 -10075.188 0 -10075.188 -512.31487 Loop time of 1.43267 on 1 procs for 96 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 = -9634.82443922272 -10075.1791618575 -10075.1880652023 Force two-norm initial, final = 375.32374 0.26422578 Force max component initial, final = 82.99213 0.03620689 Final line search alpha, max atom move = 1 0.03620689 Iterations, force evaluations = 96 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4139 | 1.4139 | 1.4139 | 0.0 | 98.69 Neigh | 0.0043783 | 0.0043783 | 0.0043783 | 0.0 | 0.31 Comm | 0.0075821 | 0.0075821 | 0.0075821 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006785 | | | 0.47 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11414 ave 11414 max 11414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171876 ave 171876 max 171876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171876 Ave neighs/atom = 66.51548 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 : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.204 | 8.204 | 8.204 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -10075.188 0 -10075.188 -512.31487 47396.093 98 0 -10075.208 0 -10075.208 1.4631986 47334.939 Loop time of 0.0407181 on 1 procs for 2 steps with 2584 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 = -10075.1880652023 -10075.2048528813 -10075.2082023683 Force two-norm initial, final = 31.231097 0.74131974 Force max component initial, final = 28.065956 0.51733702 Final line search alpha, max atom move = 0.00011631409 6.0173584e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039769 | 0.039769 | 0.039769 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019715 | 0.00019715 | 0.00019715 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000752 | | | 1.85 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11406 ave 11406 max 11406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172220 ave 172220 max 172220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172220 Ave neighs/atom = 66.648607 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 = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 13 37 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) = 7.835 | 7.835 | 7.835 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10075.208 0 -10075.208 1.4631986 Loop time of 6.01e-07 on 1 procs for 0 steps with 2584 atoms 332.8% 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 | | 6.01e-07 | | |100.00 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11406 ave 11406 max 11406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172268 ave 172268 max 172268 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 = 172268 Ave neighs/atom = 66.667183 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) = 7.835 | 7.835 | 7.835 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 -10075.208 -10075.208 53.213379 150.34777 5.9164882 1.4631986 1.4631986 -17.50557 10.599607 11.295559 2.8134032 1829.8123 Loop time of 5.01e-07 on 1 procs for 0 steps with 2584 atoms 199.6% 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 | | 5.01e-07 | | |100.00 Nlocal: 2584 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11406 ave 11406 max 11406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172268 ave 172268 max 172268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 344536 ave 344536 max 344536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344536 Ave neighs/atom = 133.33437 Neighbor list builds = 0 Dangerous builds = 0 2584 -10075.2082023683 eV 2.81340324049623 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01