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 -40.654903 0.0000000) to (28.747357 40.654903 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0730631 6.3772397 5.6928251 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.654903 0.0000000) to (28.747357 40.654903 5.6928251) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0730631 6.3772397 5.6928251 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.654903 0.0000000) to (28.747357 40.654903 5.6928251) create_atoms CPU = 0.001 seconds 410 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 20 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 = 812 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 20 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) = 7.222 | 7.222 | 7.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2600.7521 0 -2600.7521 22717.147 74 0 -2735.3765 0 -2735.3765 3366.2597 Loop time of 0.804521 on 1 procs for 74 steps with 812 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2600.7521167659 -2735.37399270565 -2735.37647631608 Force two-norm initial, final = 181.14441 0.13070735 Force max component initial, final = 49.537339 0.025906035 Final line search alpha, max atom move = 1.0000000 0.025906035 Iterations, force evaluations = 74 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78793 | 0.78793 | 0.78793 | 0.0 | 97.94 Neigh | 0.0054442 | 0.0054442 | 0.0054442 | 0.0 | 0.68 Comm | 0.006302 | 0.006302 | 0.006302 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004842 | | | 0.60 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5312.00 ave 5312 max 5312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56382.0 ave 56382 max 56382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56382 Ave neighs/atom = 69.435961 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) = 7.222 | 7.222 | 7.222 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -2735.3765 0 -2735.3765 3366.2597 13306.649 82 0 -2735.5922 0 -2735.5922 -67.522753 13366.639 Loop time of 0.0628022 on 1 procs for 8 steps with 812 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2735.37647631609 -2735.59155867191 -2735.59220230307 Force two-norm initial, final = 65.825934 1.0611747 Force max component initial, final = 64.162936 0.77250077 Final line search alpha, max atom move = 0.00052176496 0.00040306383 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060316 | 0.060316 | 0.060316 | 0.0 | 96.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042795 | 0.00042795 | 0.00042795 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002059 | | | 3.28 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5284.00 ave 5284 max 5284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56306.0 ave 56306 max 56306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56306 Ave neighs/atom = 69.342365 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 20 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) = 6.853 | 6.853 | 6.853 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2735.5922 0 -2735.5922 -67.522753 Loop time of 1.884e-06 on 1 procs for 0 steps with 812 atoms 159.2% 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 | | 1.884e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5284.00 ave 5284 max 5284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56238.0 ave 56238 max 56238 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 = 56238 Ave neighs/atom = 69.258621 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) = 6.853 | 6.853 | 6.853 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 -2735.5922 -2735.5922 28.703327 81.909329 5.6853422 -67.522753 -67.522753 -92.453076 -72.783751 -37.331431 2.5931226 585.16658 Loop time of 1.847e-06 on 1 procs for 0 steps with 812 atoms 162.4% 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 | | 1.847e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5284.00 ave 5284 max 5284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56238.0 ave 56238 max 56238 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112476.0 ave 112476 max 112476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112476 Ave neighs/atom = 138.51724 Neighbor list builds = 0 Dangerous builds = 0 812 -2735.59220230307 eV 2.59312259435546 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01