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 = 3.6122691 3.6122691 3.6122691 Created orthogonal box = (0.0000000 -51.593522 0.0000000) to (36.482129 51.593522 5.1085199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7226869 4.5523696 5.1085199 Created 816 atoms using lattice units in orthogonal box = (0.0000000 -51.593522 0.0000000) to (36.482129 51.593522 5.1085199) create_atoms CPU = 0.001 seconds 816 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7226869 4.5523696 5.1085199 Created 824 atoms using lattice units in orthogonal box = (0.0000000 -51.593522 0.0000000) to (36.482129 51.593522 5.1085199) create_atoms CPU = 0.001 seconds 824 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXkOmC7k/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 = 14 38 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 = 1640 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 = 14 38 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6426.5873 0 -6426.5873 104668.55 62 0 -6972.544 0 -6972.544 9797.8751 Loop time of 7.6439 on 1 procs for 62 steps with 1640 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 = -6426.58732751738 -6972.53923894496 -6972.54399918505 Force two-norm initial, final = 1014.9997 0.24397571 Force max component initial, final = 209.60145 0.024584465 Final line search alpha, max atom move = 1.0000000 0.024584465 Iterations, force evaluations = 62 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6266 | 7.6266 | 7.6266 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0075202 | 0.0075202 | 0.0075202 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009749 | | | 0.13 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5994.00 ave 5994 max 5994 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: 89376.0 ave 89376 max 89376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89376 Ave neighs/atom = 54.497561 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -6972.544 0 -6972.544 9797.8751 19230.937 67 0 -6972.9197 0 -6972.9197 214.31714 19336.514 Loop time of 0.497593 on 1 procs for 5 steps with 1640 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 = -6972.54399918506 -6972.91899787262 -6972.91971635818 Force two-norm initial, final = 206.29643 5.4577552 Force max component initial, final = 144.17121 5.0968243 Final line search alpha, max atom move = 0.00020255656 0.0010323952 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49502 | 0.49502 | 0.49502 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039591 | 0.00039591 | 0.00039591 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002175 | | | 0.44 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5939.00 ave 5939 max 5939 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: 90192.0 ave 90192 max 90192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90192 Ave neighs/atom = 54.995122 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 = 14 38 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) = 4.226 | 4.226 | 4.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6972.9197 0 -6972.9197 214.31714 Loop time of 1.93e-06 on 1 procs for 0 steps with 1640 atoms 155.4% 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 | | 1.93e-06 | | |100.00 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5939.00 ave 5939 max 5939 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: 90096.0 ave 90096 max 90096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90096 Ave neighs/atom = 54.936585 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) = 4.226 | 4.226 | 4.226 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 -6972.9197 -6972.9197 36.506234 103.60018 5.1127038 214.31714 214.31714 125.4144 424.00131 93.535718 2.3241634 1180.5729 Loop time of 2.013e-06 on 1 procs for 0 steps with 1640 atoms 198.7% 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 | | 2.013e-06 | | |100.00 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5939.00 ave 5939 max 5939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45048.0 ave 45048 max 45048 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90096.0 ave 90096 max 90096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90096 Ave neighs/atom = 54.936585 Neighbor list builds = 0 Dangerous builds = 0 1640 -6972.91971635818 eV 2.32416342995071 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08