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 = 4.1668010 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 = 0.002 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1668010 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-XXXXXXqWjADM/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) = 4.317 | 4.317 | 4.317 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1804.406 0 -1804.406 125561.4 44 0 -1976.8808 0 -1976.8808 16656.555 Loop time of 3.59013 on 1 procs for 44 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 = -1804.40598174837 -1976.87898418637 -1976.88083947794 Force two-norm initial, final = 546.24613 0.13123686 Force max component initial, final = 216.01356 0.016380885 Final line search alpha, max atom move = 1.0000000 0.016380885 Iterations, force evaluations = 44 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.583 | 3.583 | 3.583 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032354 | 0.0032354 | 0.0032354 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003903 | | | 0.11 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2392.00 ave 2392 max 2392 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: 26704.0 ave 26704 max 26704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26704 Ave neighs/atom = 58.305677 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) = 4.317 | 4.317 | 4.317 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1976.8808 0 -1976.8808 16656.555 5333.0708 56 0 -1977.4342 0 -1977.4342 -0.14382424 5381.8312 Loop time of 0.656637 on 1 procs for 12 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 = -1976.88083947794 -1977.43407724328 -1977.43420905621 Force two-norm initial, final = 117.55304 0.78337127 Force max component initial, final = 110.79906 0.36885878 Final line search alpha, max atom move = 0.0012873097 0.00047483549 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65321 | 0.65321 | 0.65321 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054739 | 0.00054739 | 0.00054739 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002878 | | | 0.44 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2383.00 ave 2383 max 2383 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: 26468.0 ave 26468 max 26468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26468 Ave neighs/atom = 57.790393 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) = 3.948 | 3.948 | 3.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1977.4342 0 -1977.4342 -0.14382424 Loop time of 2.914e-06 on 1 procs for 0 steps with 458 atoms 137.3% 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 | | 2.914e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2383.00 ave 2383 max 2383 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: 26444.0 ave 26444 max 26444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26444 Ave neighs/atom = 57.737991 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) = 3.948 | 3.948 | 3.948 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 -1977.4342 -1977.4342 21.546038 61.706849 4.0478954 -0.14382424 -0.14382424 42.60683 66.864102 -109.9024 2.2268832 433.7891 Loop time of 2.91e-06 on 1 procs for 0 steps with 458 atoms 137.5% 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 | | 2.91e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2383.00 ave 2383 max 2383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13222.0 ave 13222 max 13222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26444.0 ave 26444 max 26444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26444 Ave neighs/atom = 57.737991 Neighbor list builds = 0 Dangerous builds = 0 458 -1977.43420905621 eV 2.22688323198857 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04