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 = 2.85988 2.85988 2.85988 Created orthogonal box = (0 -37.4006 0) to (17.6295 37.4006 4.04448) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.71147 4.59271 4.04448 Created 229 atoms create_atoms CPU = 0.000298977 secs 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.71147 4.59271 4.04448 Created 229 atoms create_atoms CPU = 0.000185966 secs 229 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXWMERK6/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 = 7 28 2 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 3 atoms, new total = 455 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 = 7 28 2 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) = 4.325 | 4.325 | 4.325 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1922.3828 0 -1922.3828 29843.049 28 0 -1965.7298 0 -1965.7298 3607.0926 Loop time of 0.42504 on 1 procs for 28 steps with 455 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 = -1922.38284806 -1965.72792146 -1965.7297972 Force two-norm initial, final = 84.7703 0.161659 Force max component initial, final = 26.2747 0.0420746 Final line search alpha, max atom move = 1 0.0420746 Iterations, force evaluations = 28 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42373 | 0.42373 | 0.42373 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072598 | 0.00072598 | 0.00072598 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000581 | | | 0.14 Nlocal: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889 ave 2889 max 2889 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: 26384 ave 26384 max 26384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26384 Ave neighs/atom = 57.9868 Neighbor list builds = 0 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.325 | 4.325 | 4.325 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -1965.7298 0 -1965.7298 3607.0926 5333.4786 30 0 -1965.733 0 -1965.733 2654.5342 5336.4927 Loop time of 0.046397 on 1 procs for 2 steps with 455 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 = -1965.7297972 -1965.73229111 -1965.73295386 Force two-norm initial, final = 7.63465 0.164288 Force max component initial, final = 7.5015 0.0404366 Final line search alpha, max atom move = 0.000413368 1.67152e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04613 | 0.04613 | 0.04613 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.1049e-05 | 7.1049e-05 | 7.1049e-05 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000196 | | | 0.42 Nlocal: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889 ave 2889 max 2889 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: 26318 ave 26318 max 26318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26318 Ave neighs/atom = 57.8418 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 = 7 28 2 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) = 3.957 | 3.957 | 3.957 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1965.733 0 -1965.733 2654.5342 Loop time of 2.14577e-06 on 1 procs for 0 steps with 455 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889 ave 2889 max 2889 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: 26318 ave 26318 max 26318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26318 Ave neighs/atom = 57.8418 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) = 3.957 | 3.957 | 3.957 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 -1965.733 -1965.733 17.623467 74.801234 4.0481428 2654.5342 2654.5342 0.59008363 7967.5099 -4.4973636 2.2153405 321.15316 Loop time of 2.14577e-06 on 1 procs for 0 steps with 455 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889 ave 2889 max 2889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13159 ave 13159 max 13159 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26318 ave 26318 max 26318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26318 Ave neighs/atom = 57.8418 Neighbor list builds = 0 Dangerous builds = 0 455 -1965.73295385545 eV 2.21534048474071 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00