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 -48.805808 0.0000000) to (39.849775 48.805808 9.8602623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6928251 5.6442091 6.5735082 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -48.805808 0.0000000) to (39.849775 48.805808 9.8602623) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6928251 5.6442091 6.5735082 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -48.805808 0.0000000) to (39.849775 48.805808 9.8602623) create_atoms CPU = 0.001 seconds 1184 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 24 3 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 8 atoms, new total = 2352 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 24 3 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) = 8.004 | 8.004 | 8.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7633.3544 0 -7633.3544 21661.934 59 0 -7924.3148 0 -7924.3148 6541.3027 Loop time of 1.92631 on 1 procs for 59 steps with 2352 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 = -7633.35435839424 -7924.30696777798 -7924.31479329006 Force two-norm initial, final = 213.90176 0.20982223 Force max component initial, final = 25.694060 0.013795494 Final line search alpha, max atom move = 1.0000000 0.013795494 Iterations, force evaluations = 59 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8879 | 1.8879 | 1.8879 | 0.0 | 98.01 Neigh | 0.018587 | 0.018587 | 0.018587 | 0.0 | 0.96 Comm | 0.0084097 | 0.0084097 | 0.0084097 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01139 | | | 0.59 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7860.00 ave 7860 max 7860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163504.0 ave 163504 max 163504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163504 Ave neighs/atom = 69.517007 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.007 | 8.007 | 8.007 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -7924.3148 0 -7924.3148 6541.3027 38354.458 70 0 -7925.6268 0 -7925.6268 76.509482 38669.687 Loop time of 0.232304 on 1 procs for 11 steps with 2352 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 = -7924.31479329006 -7925.62561894809 -7925.62683442105 Force two-norm initial, final = 309.87825 3.2961661 Force max component initial, final = 276.99680 2.1618794 Final line search alpha, max atom move = 0.00023712678 0.00051263951 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2172 | 0.2172 | 0.2172 | 0.0 | 93.50 Neigh | 0.0089445 | 0.0089445 | 0.0089445 | 0.0 | 3.85 Comm | 0.0010088 | 0.0010088 | 0.0010088 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005155 | | | 2.22 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7930.00 ave 7930 max 7930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163344.0 ave 163344 max 163344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163344 Ave neighs/atom = 69.448980 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 = 10 25 3 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) = 7.638 | 7.638 | 7.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7925.6268 0 -7925.6268 76.509482 Loop time of 1.844e-06 on 1 procs for 0 steps with 2352 atoms 162.7% 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 | | 1.844e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7930.00 ave 7930 max 7930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163336.0 ave 163336 max 163336 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 = 163336 Ave neighs/atom = 69.445578 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) = 7.638 | 7.638 | 7.638 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 -7925.6268 -7925.6268 39.835668 98.613739 9.8437625 76.509482 76.509482 57.483187 90.491355 81.553905 2.5731257 1725.5379 Loop time of 1.948e-06 on 1 procs for 0 steps with 2352 atoms 205.3% 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 | | 1.948e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7930.00 ave 7930 max 7930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163336.0 ave 163336 max 163336 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 326672.0 ave 326672 max 326672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326672 Ave neighs/atom = 138.89116 Neighbor list builds = 0 Dangerous builds = 0 2352 -7925.62683442105 eV 2.5731257031074 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02