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 -79.699551 0.0000000) to (48.805808 79.699551 9.8602623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6442091 5.6928251 6.5735082 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -79.699551 0.0000000) to (48.805808 79.699551 9.8602623) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6442091 5.6928251 6.5735082 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -79.699551 0.0000000) to (48.805808 79.699551 9.8602623) create_atoms CPU = 0.003 seconds 2358 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 = 12 39 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 6 atoms, new total = 4704 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 = 12 39 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) = 15.85 | 15.85 | 15.85 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15506.215 0 -15506.215 12921.355 96 0 -15870.918 0 -15870.918 3958.6598 Loop time of 6.19507 on 1 procs for 96 steps with 4704 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15506.2149720502 -15870.9055031353 -15870.9178495702 Force two-norm initial, final = 268.81961 0.32732428 Force max component initial, final = 40.451429 0.055372979 Final line search alpha, max atom move = 1.0000000 0.055372979 Iterations, force evaluations = 96 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0604 | 6.0604 | 6.0604 | 0.0 | 97.83 Neigh | 0.054284 | 0.054284 | 0.054284 | 0.0 | 0.88 Comm | 0.041086 | 0.041086 | 0.041086 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03926 | | | 0.63 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13754.0 ave 13754 max 13754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327714.0 ave 327714 max 327714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327714 Ave neighs/atom = 69.667092 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 : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.85 | 15.85 | 15.85 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -15870.918 0 -15870.918 3958.6598 76708.916 103 0 -15871.898 0 -15871.898 -73.70233 77104.647 Loop time of 0.321535 on 1 procs for 7 steps with 4704 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 = -15870.9178495702 -15871.8967264171 -15871.8983242581 Force two-norm initial, final = 375.03631 6.3485651 Force max component initial, final = 334.48326 4.6224932 Final line search alpha, max atom move = 0.00010432010 0.00048221896 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29625 | 0.29625 | 0.29625 | 0.0 | 92.14 Neigh | 0.017661 | 0.017661 | 0.017661 | 0.0 | 5.49 Comm | 0.0012609 | 0.0012609 | 0.0012609 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006359 | | | 1.98 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13702.0 ave 13702 max 13702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327708.0 ave 327708 max 327708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327708 Ave neighs/atom = 69.665816 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 = 12 40 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) = 14.74 | 14.74 | 14.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15871.898 0 -15871.898 -73.70233 Loop time of 2.042e-06 on 1 procs for 0 steps with 4704 atoms 195.9% 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 | | 2.042e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13702.0 ave 13702 max 13702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327708.0 ave 327708 max 327708 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 = 327708 Ave neighs/atom = 69.665816 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) = 14.74 | 14.74 | 14.74 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 -15871.898 -15871.898 48.803617 160.39988 9.8497341 -73.70233 -73.70233 -96.047615 -50.451539 -74.607837 2.5352733 2148.8078 Loop time of 2.07e-06 on 1 procs for 0 steps with 4704 atoms 241.5% 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 | | 2.07e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13702.0 ave 13702 max 13702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327708.0 ave 327708 max 327708 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 655416.0 ave 655416 max 655416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 655416 Ave neighs/atom = 139.33163 Neighbor list builds = 0 Dangerous builds = 0 4704 -15871.8983242581 eV 2.53527329382596 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07