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 -72.425769 0.0000000) to (41.815037 72.425769 6.2566335) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6169453 5.7652354 6.2566335 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.425769 0.0000000) to (41.815037 72.425769 6.2566335) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6169453 5.7652354 6.2566335 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.425769 0.0000000) to (41.815037 72.425769 6.2566335) create_atoms CPU = 0.004 seconds 1610 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXnw6Cp2/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 = 16 54 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 2 atoms, new total = 3216 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 = 16 54 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) = 5.255 | 5.255 | 5.255 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12476.671 0 -12476.671 89417.486 861 0 -13751.711 0 -13751.711 -2881.073 Loop time of 375.665 on 1 procs for 861 steps with 3216 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12476.6714923482 -13751.6970591645 -13751.7107115676 Force two-norm initial, final = 2153.0846 0.38348231 Force max component initial, final = 579.39766 0.092973111 Final line search alpha, max atom move = 0.68767956 0.063935708 Iterations, force evaluations = 861 1704 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 374.87 | 374.87 | 374.87 | 0.0 | 99.79 Neigh | 0.19334 | 0.19334 | 0.19334 | 0.0 | 0.05 Comm | 0.22298 | 0.22298 | 0.22298 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3759 | | | 0.10 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8698.00 ave 8698 max 8698 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: 188696.0 ave 188696 max 188696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188696 Ave neighs/atom = 58.674129 Neighbor list builds = 9 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 : 861 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.265 | 5.265 | 5.265 Mbytes Step Temp E_pair E_mol TotEng Press Volume 861 0 -13751.711 0 -13751.711 -2881.073 37896.257 875 0 -13757.553 0 -13757.553 -2.0600101 37861.18 Loop time of 2.83162 on 1 procs for 14 steps with 3216 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 = -13751.7107115676 -13757.5519586934 -13757.5525439614 Force two-norm initial, final = 714.01011 2.3753574 Force max component initial, final = 502.18745 0.69359516 Final line search alpha, max atom move = 0.00018959649 0.00013150321 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8213 | 2.8213 | 2.8213 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001176 | 0.001176 | 0.001176 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009157 | | | 0.32 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8698.00 ave 8698 max 8698 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: 188648.0 ave 188648 max 188648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188648 Ave neighs/atom = 58.659204 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 = 16 53 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) = 4.894 | 4.894 | 4.894 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13757.553 0 -13757.553 -2.0600101 Loop time of 2.404e-06 on 1 procs for 0 steps with 3216 atoms 166.4% 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 | | 2.404e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8632.00 ave 8632 max 8632 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: 189184.0 ave 189184 max 189184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189184 Ave neighs/atom = 58.825871 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) = 4.894 | 4.894 | 4.894 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 -13757.553 -13757.553 41.464888 144.04658 6.3388532 -2.0600101 -2.0600101 13.350361 10.206272 -29.736664 2.1889474 3715.7606 Loop time of 2.491e-06 on 1 procs for 0 steps with 3216 atoms 200.7% 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 | | 2.491e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8632.00 ave 8632 max 8632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94592.0 ave 94592 max 94592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 189184.0 ave 189184 max 189184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189184 Ave neighs/atom = 58.825871 Neighbor list builds = 0 Dangerous builds = 0 3216 -13757.5525439614 eV 2.18894737943265 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:06:19