LAMMPS (30 Jul 2021) 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_StarikovGordeevLysogorskiy_2020_SiAuAl__SM_113843830602_000 # For Simulator : LAMMPS 3 Mar 2020 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 4.0254352 4.0254352 4.0254352 Created orthogonal box = (0.0000000 -42.979887 0.0000000) to (30.391369 42.979887 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9313649 6.7862979 5.6928251 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -42.979887 0.0000000) to (30.391369 42.979887 5.6928251) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9313649 6.7862979 5.6928251 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -42.979887 0.0000000) to (30.391369 42.979887 5.6928251) create_atoms CPU = 0.001 seconds 458 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 = 8 21 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 6 atoms, new total = 908 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_113843830602_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:189) 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 = 8 21 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) = 7.250 | 7.250 | 7.250 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2931.8286 0 -2931.8286 19333.515 77 0 -3061.1006 0 -3061.1006 1673.499 Loop time of 1.08293 on 1 procs for 77 steps with 908 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2931.82858162541 -3061.09789314684 -3061.10061535589 Force two-norm initial, final = 176.78381 0.12808692 Force max component initial, final = 54.929518 0.027231475 Final line search alpha, max atom move = 1.0000000 0.027231475 Iterations, force evaluations = 77 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0546 | 1.0546 | 1.0546 | 0.0 | 97.38 Neigh | 0.011212 | 0.011212 | 0.011212 | 0.0 | 1.04 Comm | 0.0091674 | 0.0091674 | 0.0091674 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007951 | | | 0.73 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5748.00 ave 5748 max 5748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63216.0 ave 63216 max 63216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63216 Ave neighs/atom = 69.621145 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.253 | 7.253 | 7.253 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -3061.1006 0 -3061.1006 1673.499 14872.137 81 0 -3061.1384 0 -3061.1384 -1.7212495 14905.126 Loop time of 0.0535554 on 1 procs for 4 steps with 908 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3061.10061535589 -3061.13777653421 -3061.13844002489 Force two-norm initial, final = 31.826819 0.23054530 Force max component initial, final = 29.409716 0.12932661 Final line search alpha, max atom move = 0.00019064189 2.4655069e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051589 | 0.051589 | 0.051589 | 0.0 | 96.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003592 | 0.0003592 | 0.0003592 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001607 | | | 3.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5756.00 ave 5756 max 5756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63208.0 ave 63208 max 63208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63208 Ave neighs/atom = 69.612335 Neighbor list builds = 0 Dangerous builds = 0 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 = 8 22 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) = 6.885 | 6.885 | 6.885 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3061.1384 0 -3061.1384 -1.7212495 Loop time of 2.239e-06 on 1 procs for 0 steps with 908 atoms 178.7% 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 | | 2.239e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5748.00 ave 5748 max 5748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63166.0 ave 63166 max 63166 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63166 Ave neighs/atom = 69.566079 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.885 | 6.885 | 6.885 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 -3061.1384 -3061.1384 30.383673 86.195003 5.6913239 -1.7212495 -1.7212495 13.047954 -4.3138388 -13.897863 2.6738649 923.37427 Loop time of 2.717e-06 on 1 procs for 0 steps with 908 atoms 220.8% 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 | | 2.717e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5748.00 ave 5748 max 5748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63166.0 ave 63166 max 63166 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126332.0 ave 126332 max 126332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126332 Ave neighs/atom = 139.13216 Neighbor list builds = 0 Dangerous builds = 0 908 -3061.13844002489 eV 2.67386487324191 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01