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 -57.494715 0.0000000) to (40.654903 57.494715 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3772397 5.0730631 5.6928251 Created 815 atoms using lattice units in orthogonal box = (0.0000000 -57.494715 0.0000000) to (40.654903 57.494715 5.6928251) create_atoms CPU = 0.002 seconds 815 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3772397 5.0730631 5.6928251 Created 823 atoms using lattice units in orthogonal box = (0.0000000 -57.494715 0.0000000) to (40.654903 57.494715 5.6928251) create_atoms CPU = 0.001 seconds 823 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 = 10 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 6 atoms, new total = 1632 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 = 10 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) = 7.895 | 7.895 | 7.895 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5327.542 0 -5327.542 18165.585 74 0 -5505.0167 0 -5505.0167 4074.9749 Loop time of 1.69363 on 1 procs for 74 steps with 1632 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 = -5327.54200968325 -5505.01126963626 -5505.01667020751 Force two-norm initial, final = 160.06403 0.19357694 Force max component initial, final = 22.699556 0.021184850 Final line search alpha, max atom move = 1.0000000 0.021184850 Iterations, force evaluations = 74 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6546 | 1.6546 | 1.6546 | 0.0 | 97.70 Neigh | 0.012282 | 0.012282 | 0.012282 | 0.0 | 0.73 Comm | 0.014137 | 0.014137 | 0.014137 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01259 | | | 0.74 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8207.00 ave 8207 max 8207 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113692.0 ave 113692 max 113692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113692 Ave neighs/atom = 69.664216 Neighbor list builds = 2 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.895 | 7.895 | 7.895 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5505.0167 0 -5505.0167 4074.9749 26613.297 81 0 -5505.3548 0 -5505.3548 76.031706 26749.106 Loop time of 0.129908 on 1 procs for 7 steps with 1632 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 = -5505.01667020752 -5505.35250881885 -5505.35480187812 Force two-norm initial, final = 129.60084 2.2239899 Force max component initial, final = 112.50987 1.4441336 Final line search alpha, max atom move = 0.00020161722 0.00029116220 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12549 | 0.12549 | 0.12549 | 0.0 | 96.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066727 | 0.00066727 | 0.00066727 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003755 | | | 2.89 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8156.00 ave 8156 max 8156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113678.0 ave 113678 max 113678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113678 Ave neighs/atom = 69.655637 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 = 10 29 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) = 7.522 | 7.522 | 7.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5505.3548 0 -5505.3548 76.031706 Loop time of 2.187e-06 on 1 procs for 0 steps with 1632 atoms 182.9% 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 | | 2.187e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8156.00 ave 8156 max 8156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113622.0 ave 113622 max 113622 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 = 113622 Ave neighs/atom = 69.621324 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) = 7.522 | 7.522 | 7.522 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 -5505.3548 -5505.3548 40.613221 115.73965 5.6906209 76.031706 76.031706 72.040827 87.062818 68.991473 2.6747426 1185.1655 Loop time of 2.37e-06 on 1 procs for 0 steps with 1632 atoms 464.1% 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 | | 2.37e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8156.00 ave 8156 max 8156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113622.0 ave 113622 max 113622 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227244.0 ave 227244 max 227244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227244 Ave neighs/atom = 139.24265 Neighbor list builds = 0 Dangerous builds = 0 1632 -5505.35480187812 eV 2.67474262737727 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02