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 = 2.8598780 2.8598780 2.8598780 Created orthogonal box = (0.0000000 -30.535141 0.0000000) to (21.591605 30.535141 4.0444782) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9244012 4.8213380 4.0444782 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.535141 0.0000000) to (21.591605 30.535141 4.0444782) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9244012 4.8213380 4.0444782 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.535141 0.0000000) to (21.591605 30.535141 4.0444782) create_atoms CPU = 0.001 seconds 230 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXProREP/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 = 8 23 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 0 atoms, new total = 458 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 = 8 23 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) = 4.320 | 4.320 | 4.320 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1894.3284 0 -1894.3284 61801.867 44 0 -1979.5566 0 -1979.5566 13893.36 Loop time of 2.26032 on 1 procs for 44 steps with 458 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1894.32843585524 -1979.55477451063 -1979.5565941914 Force two-norm initial, final = 139.36592 0.12462665 Force max component initial, final = 36.802685 0.026550746 Final line search alpha, max atom move = 1.0000000 0.026550746 Iterations, force evaluations = 44 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2552 | 2.2552 | 2.2552 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026038 | 0.0026038 | 0.0026038 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002493 | | | 0.11 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2802.00 ave 2802 max 2802 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: 26668.0 ave 26668 max 26668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26668 Ave neighs/atom = 58.227074 Neighbor list builds = 0 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.320 | 4.320 | 4.320 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1979.5566 0 -1979.5566 13893.36 5333.0708 52 0 -1979.8486 0 -1979.8486 -46.078437 5374.5505 Loop time of 0.234294 on 1 procs for 8 steps with 458 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 = -1979.55659419139 -1979.84848107754 -1979.84855761209 Force two-norm initial, final = 89.873113 0.56850689 Force max component initial, final = 78.127384 0.28920514 Final line search alpha, max atom move = 0.00083541627 0.00024160668 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23301 | 0.23301 | 0.23301 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023659 | 0.00023659 | 0.00023659 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001048 | | | 0.45 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2798.00 ave 2798 max 2798 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: 26612.0 ave 26612 max 26612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26612 Ave neighs/atom = 58.104803 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 = 8 23 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) = 3.951 | 3.951 | 3.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1979.8486 0 -1979.8486 -46.078437 Loop time of 1.407e-06 on 1 procs for 0 steps with 458 atoms 142.1% 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 | | 1.407e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2798.00 ave 2798 max 2798 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: 26564.0 ave 26564 max 26564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26564 Ave neighs/atom = 58.000000 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) = 3.951 | 3.951 | 3.951 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 -1979.8486 -1979.8486 21.631867 61.493431 4.040354 -46.078437 -46.078437 26.649184 -86.810652 -78.073845 2.2669457 363.52786 Loop time of 1.281e-06 on 1 procs for 0 steps with 458 atoms 156.1% 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 | | 1.281e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2798.00 ave 2798 max 2798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13282.0 ave 13282 max 13282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26564.0 ave 26564 max 26564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26564 Ave neighs/atom = 58.000000 Neighbor list builds = 0 Dangerous builds = 0 458 -1979.84855761209 eV 2.26694565268767 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02