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_TersoffZBL_ByggmastarGranberg_2020_Fe__SM_958863895234_000 # For Simulator : LAMMPS 19 Sep 2019 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.6122691 3.6122691 3.6122691 Created orthogonal box = (0.0000000 -71.519278 0.0000000) to (43.796435 71.519278 8.8482160) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0648938 5.1085199 5.8988107 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.519278 0.0000000) to (43.796435 71.519278 8.8482160) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0648938 5.1085199 5.8988107 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.519278 0.0000000) to (43.796435 71.519278 8.8482160) create_atoms CPU = 0.003 seconds 2358 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXiiFLdQ/Fe_Byggmastar.tersoff.zbl with DATE: 2018-09-11 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 = 5.46 ghost atom cutoff = 5.46 binsize = 2.73, bins = 17 53 4 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair tersoff/zbl, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4710 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_958863895234_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 = 5.46 ghost atom cutoff = 5.46 binsize = 2.73, bins = 17 53 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair tersoff/zbl, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.617 | 5.617 | 5.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18967.128 0 -18967.128 63623.378 170 0 -20023.534 0 -20023.534 5153.5849 Loop time of 60.2806 on 1 procs for 170 steps with 4710 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 = -18967.1277425616 -20023.5168431234 -20023.5342370768 Force two-norm initial, final = 1540.7383 0.51840275 Force max component initial, final = 248.46728 0.088203940 Final line search alpha, max atom move = 1.0000000 0.088203940 Iterations, force evaluations = 170 330 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 60.126 | 60.126 | 60.126 | 0.0 | 99.74 Neigh | 0.045937 | 0.045937 | 0.045937 | 0.0 | 0.08 Comm | 0.036926 | 0.036926 | 0.036926 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07141 | | | 0.12 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9415.00 ave 9415 max 9415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257016.0 ave 257016 max 257016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257016 Ave neighs/atom = 54.568153 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 : 170 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.621 | 5.621 | 5.621 Mbytes Step Temp E_pair E_mol TotEng Press Volume 170 0 -20023.534 0 -20023.534 5153.5849 55430.346 174 0 -20023.984 0 -20023.984 -22.651701 55601.101 Loop time of 1.21737 on 1 procs for 4 steps with 4710 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 = -20023.5342370769 -20023.9818678597 -20023.9837505401 Force two-norm initial, final = 339.17358 5.1080893 Force max component initial, final = 289.69192 3.3831165 Final line search alpha, max atom move = 4.9903386e-05 0.00016882897 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.213 | 1.213 | 1.213 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050243 | 0.00050243 | 0.00050243 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003871 | | | 0.32 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9585.00 ave 9585 max 9585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257880.0 ave 257880 max 257880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257880 Ave neighs/atom = 54.751592 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 = 5.46 ghost atom cutoff = 5.46 binsize = 2.73, bins = 17 53 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair tersoff/zbl, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional, half/full from (1) attributes: half, newton on pair build: halffull/newton 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) = 5.253 | 5.253 | 5.253 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20023.984 0 -20023.984 -22.651701 Loop time of 2.051e-06 on 1 procs for 0 steps with 4710 atoms 195.0% 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 | | 2.051e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9578.00 ave 9578 max 9578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257868.0 ave 257868 max 257868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257868 Ave neighs/atom = 54.749045 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) = 5.253 | 5.253 | 5.253 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 -20023.984 -20023.984 43.820647 142.96897 8.8748868 -22.651701 -22.651701 90.380789 -97.43895 -60.896943 2.2179195 2622.4302 Loop time of 2.322e-06 on 1 procs for 0 steps with 4710 atoms 215.3% 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 | | 2.322e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9578.00 ave 9578 max 9578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 128934.0 ave 128934 max 128934 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257868.0 ave 257868 max 257868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257868 Ave neighs/atom = 54.749045 Neighbor list builds = 0 Dangerous builds = 0 4710 -20023.9837505401 eV 2.21791947593413 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:02