LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) 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 19 Mar 2020 # Lattice spacing in x,y,z = 3.61227 3.61227 3.61227 Created orthogonal box = (0 -46.824 0) to (27.0317 46.824 6.25663) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.79252 5.57385 6.25663 Created 676 atoms create_atoms CPU = 0.000552893 secs 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.79252 5.57385 6.25663 Created 676 atoms create_atoms CPU = 0.000399113 secs 676 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXJMTg7S/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 = 10 35 3 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 27 atoms, new total = 1325 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) 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 = 10 35 3 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) = 4.48 | 4.48 | 4.48 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5559.0345 0 -5559.0345 1972.6213 111 0 -5629.7631 0 -5629.7631 -19784.537 Loop time of 3.39215 on 1 procs for 111 steps with 1325 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 = -5559.03453885 -5629.75752621 -5629.7630649 Force two-norm initial, final = 57.0605 0.288648 Force max component initial, final = 14.4597 0.0772518 Final line search alpha, max atom move = 1 0.0772518 Iterations, force evaluations = 111 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3769 | 3.3769 | 3.3769 | 0.0 | 99.55 Neigh | 0.0064063 | 0.0064063 | 0.0064063 | 0.0 | 0.19 Comm | 0.0037704 | 0.0037704 | 0.0037704 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005091 | | | 0.15 Nlocal: 1325 ave 1325 max 1325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4259 ave 4259 max 4259 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72350 ave 72350 max 72350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72350 Ave neighs/atom = 54.6038 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -5629.7631 0 -5629.7631 -19784.537 15838.464 119 0 -5630.4934 0 -5630.4934 -7568.3425 15720.872 Loop time of 0.18086 on 1 procs for 8 steps with 1325 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 = -5629.7630649 -5630.49215904 -5630.49339057 Force two-norm initial, final = 213.905 3.02768 Force max component initial, final = 197.986 2.82881 Final line search alpha, max atom move = 0.000134083 0.000379296 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17985 | 0.17985 | 0.17985 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018644 | 0.00018644 | 0.00018644 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008252 | | | 0.46 Nlocal: 1325 ave 1325 max 1325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4267 ave 4267 max 4267 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72588 ave 72588 max 72588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72588 Ave neighs/atom = 54.7834 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 = 10 35 3 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) = 4.112 | 4.112 | 4.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5630.4934 0 -5630.4934 -7568.3425 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1325 atoms 104.9% 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 | | 1.907e-06 | | |100.00 Nlocal: 1325 ave 1325 max 1325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4276 ave 4276 max 4276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72684 ave 72684 max 72684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72684 Ave neighs/atom = 54.8558 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) = 4.112 | 4.112 | 4.112 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 -5630.4934 -5630.4934 26.840508 93.647941 6.254429 -7568.3425 -7568.3425 -286.25605 -22339.9 -78.871607 2.24964 1027.9444 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1325 atoms 104.9% 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 | | 1.907e-06 | | |100.00 Nlocal: 1325 ave 1325 max 1325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4276 ave 4276 max 4276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36342 ave 36342 max 36342 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72684 ave 72684 max 72684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72684 Ave neighs/atom = 54.8558 Neighbor list builds = 0 Dangerous builds = 0 1325 -5630.49339056595 eV 2.24963998152747 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03