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 -59.161574 0.0000000) to (20.916775 59.161574 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4228676 6.5735082 5.6928251 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.161574 0.0000000) to (20.916775 59.161574 5.6928251) create_atoms CPU = 0.002 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4228676 6.5735082 5.6928251 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.161574 0.0000000) to (20.916775 59.161574 5.6928251) create_atoms CPU = 0.001 seconds 434 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 = 6 29 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 0 atoms, new total = 866 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 = 6 29 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) = 7.272 | 7.272 | 7.272 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2859.5784 0 -2859.5784 16203.29 67 0 -2920.1441 0 -2920.1441 7169.9401 Loop time of 0.805041 on 1 procs for 67 steps with 866 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 = -2859.57842762297 -2920.1416208298 -2920.14411134327 Force two-norm initial, final = 82.759666 0.12488141 Force max component initial, final = 28.409957 0.026805791 Final line search alpha, max atom move = 1.0000000 0.026805791 Iterations, force evaluations = 67 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79079 | 0.79079 | 0.79079 | 0.0 | 98.23 Neigh | 0.0030356 | 0.0030356 | 0.0030356 | 0.0 | 0.38 Comm | 0.0064282 | 0.0064282 | 0.0064282 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004785 | | | 0.59 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6134.00 ave 6134 max 6134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60312.0 ave 60312 max 60312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60312 Ave neighs/atom = 69.644342 Neighbor list builds = 1 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -2920.1441 0 -2920.1441 7169.9401 14089.393 76 0 -2920.6047 0 -2920.6047 20.315877 14217.47 Loop time of 0.0764163 on 1 procs for 9 steps with 866 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 = -2920.14411134327 -2920.6018499719 -2920.6047319282 Force two-norm initial, final = 120.53166 0.71093253 Force max component initial, final = 103.17670 0.58102074 Final line search alpha, max atom move = 0.00019963769 0.00011599364 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069852 | 0.069852 | 0.069852 | 0.0 | 91.41 Neigh | 0.0032099 | 0.0032099 | 0.0032099 | 0.0 | 4.20 Comm | 0.00078616 | 0.00078616 | 0.00078616 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002569 | | | 3.36 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6126.00 ave 6126 max 6126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60254.0 ave 60254 max 60254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60254 Ave neighs/atom = 69.577367 Neighbor list builds = 1 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 = 6 30 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) = 6.903 | 6.903 | 6.903 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2920.6047 0 -2920.6047 20.315877 Loop time of 1.623e-06 on 1 procs for 0 steps with 866 atoms 123.2% 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 | | 1.623e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6126.00 ave 6126 max 6126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60254.0 ave 60254 max 60254 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 = 60254 Ave neighs/atom = 69.577367 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) = 6.903 | 6.903 | 6.903 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 -2920.6047 -2920.6047 20.94363 119.35845 5.6874449 20.315877 20.315877 -28.895345 24.429226 65.41375 2.6483051 600.15735 Loop time of 1.842e-06 on 1 procs for 0 steps with 866 atoms 162.9% 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 | | 1.842e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6126.00 ave 6126 max 6126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60254.0 ave 60254 max 60254 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120508.0 ave 120508 max 120508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120508 Ave neighs/atom = 139.15473 Neighbor list builds = 0 Dangerous builds = 0 866 -2920.6047319282 eV 2.64830513791692 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01