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 -38.5721 0) to (22.2675 38.5721 6.25663) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.85987 5.41312 6.25663 Created 458 atoms create_atoms CPU = 0.000375032 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.85987 5.41312 6.25663 Created 458 atoms create_atoms CPU = 0.00026083 secs 458 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXIKByj6/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 = 9 29 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 17 atoms, new total = 899 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 = 9 29 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) = 4.393 | 4.393 | 4.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3769.1851 0 -3769.1851 2051.2082 517 0 -3837.4218 0 -3837.4218 -23703.553 Loop time of 14.8625 on 1 procs for 517 steps with 899 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 = -3769.18505123 -3837.41798775 -3837.42177046 Force two-norm initial, final = 40.7993 0.184555 Force max component initial, final = 14.178 0.0585316 Final line search alpha, max atom move = 1 0.0585316 Iterations, force evaluations = 517 1008 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.817 | 14.817 | 14.817 | 0.0 | 99.70 Neigh | 0.0093238 | 0.0093238 | 0.0093238 | 0.0 | 0.06 Comm | 0.01589 | 0.01589 | 0.01589 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01998 | | | 0.13 Nlocal: 899 ave 899 max 899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3306 ave 3306 max 3306 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: 52110 ave 52110 max 52110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52110 Ave neighs/atom = 57.9644 Neighbor list builds = 6 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 : 517 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.396 | 4.396 | 4.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 517 0 -3837.4218 0 -3837.4218 -23703.553 10747.706 529 0 -3838.4402 0 -3838.4402 -13089.413 10687.564 Loop time of 0.250456 on 1 procs for 12 steps with 899 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 = -3837.42177046 -3838.43993973 -3838.44021417 Force two-norm initial, final = 178.347 2.67334 Force max component initial, final = 177.749 2.29569 Final line search alpha, max atom move = 0.0012585 0.00288912 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24918 | 0.24918 | 0.24918 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002079 | 0.0002079 | 0.0002079 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00107 | | | 0.43 Nlocal: 899 ave 899 max 899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3306 ave 3306 max 3306 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: 52066 ave 52066 max 52066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52066 Ave neighs/atom = 57.9155 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 = 9 29 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) = 4.026 | 4.026 | 4.026 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3838.4402 0 -3838.4402 -13089.413 Loop time of 1.90735e-06 on 1 procs for 0 steps with 899 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: 899 ave 899 max 899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3309 ave 3309 max 3309 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: 52270 ave 52270 max 52270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52270 Ave neighs/atom = 58.1424 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) = 4.026 | 4.026 | 4.026 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 -3838.4402 -3838.4402 22.021283 77.144183 6.2911917 -13089.413 -13089.413 340.3421 -39667.972 59.389499 2.2428894 1980.8624 Loop time of 1.90735e-06 on 1 procs for 0 steps with 899 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 899 ave 899 max 899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3309 ave 3309 max 3309 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26135 ave 26135 max 26135 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52270 ave 52270 max 52270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52270 Ave neighs/atom = 58.1424 Neighbor list builds = 0 Dangerous builds = 0 899 -3838.44021416888 eV 2.24288943014382 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15