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 -45.9803 0) to (10.8368 45.9803 5.10852) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.02045 5.10852 5.10852 Created 218 atoms create_atoms CPU = 0.000392914 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.02045 5.10852 5.10852 Created 218 atoms create_atoms CPU = 0.000348091 secs 218 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXYuhk5Q/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 = 4 34 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 8 atoms, new total = 428 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 = 4 34 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) = 4.343 | 4.343 | 4.343 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1804.1357 0 -1804.1357 1118.126 65 0 -1817.4317 0 -1817.4317 -10271.566 Loop time of 1.03696 on 1 procs for 65 steps with 428 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1804.13573133 -1817.43026304 -1817.43171664 Force two-norm initial, final = 21.3746 0.120117 Force max component initial, final = 8.02464 0.025674 Final line search alpha, max atom move = 1 0.025674 Iterations, force evaluations = 65 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0338 | 1.0338 | 1.0338 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017457 | 0.0017457 | 0.0017457 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001462 | | | 0.14 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2506 ave 2506 max 2506 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: 22972 ave 22972 max 22972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22972 Ave neighs/atom = 53.6729 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.343 | 4.343 | 4.343 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1817.4317 0 -1817.4317 -10271.566 5090.942 68 0 -1817.4541 0 -1817.4541 -6013.4416 5077.4884 Loop time of 0.055814 on 1 procs for 3 steps with 428 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 = -1817.43171664 -1817.45386234 -1817.45413678 Force two-norm initial, final = 21.842 0.134262 Force max component initial, final = 18.8086 0.0256546 Final line search alpha, max atom move = 0.00060411 1.54982e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055439 | 0.055439 | 0.055439 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.0109e-05 | 8.0109e-05 | 8.0109e-05 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002947 | | | 0.53 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2452 ave 2452 max 2452 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: 23184 ave 23184 max 23184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23184 Ave neighs/atom = 54.1682 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 = 4 34 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) = 3.974 | 3.974 | 3.974 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1817.4541 0 -1817.4541 -6013.4416 Loop time of 2.14577e-06 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2452 ave 2452 max 2452 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: 23184 ave 23184 max 23184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23184 Ave neighs/atom = 54.1682 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) = 3.974 | 3.974 | 3.974 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 -1817.4541 -1817.4541 10.829755 91.960582 5.0983376 -6013.4416 -6013.4416 -3.8477439 -18037.804 1.3268643 2.3870584 158.30855 Loop time of 2.14577e-06 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2452 ave 2452 max 2452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11592 ave 11592 max 11592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23184 ave 23184 max 23184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23184 Ave neighs/atom = 54.1682 Neighbor list builds = 0 Dangerous builds = 0 428 -1817.45413677892 eV 2.38705839977807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01