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 -53.456700 0.0000000) to (43.647213 53.456700 8.8482160) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3811632 5.1259850 5.8988107 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -53.456700 0.0000000) to (43.647213 53.456700 8.8482160) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3811632 5.1259850 5.8988107 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -53.456700 0.0000000) to (43.647213 53.456700 8.8482160) create_atoms CPU = 0.002 seconds 1757 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXp64U72/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 40 4 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 = 3504 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 40 4 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12114.362 0 -12114.362 169297.7 106 0 -14879.921 0 -14879.921 3159.3586 Loop time of 25.5096 on 1 procs for 106 steps with 3504 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 = -12114.3622831674 -14879.9068555946 -14879.921032296 Force two-norm initial, final = 3648.6361 0.36158716 Force max component initial, final = 537.22470 0.094023996 Final line search alpha, max atom move = 0.68276173 0.064195987 Iterations, force evaluations = 106 192 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.431 | 25.431 | 25.431 | 0.0 | 99.69 Neigh | 0.036548 | 0.036548 | 0.036548 | 0.0 | 0.14 Comm | 0.013492 | 0.013492 | 0.013492 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0283 | | | 0.11 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7151.00 ave 7151 max 7151 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: 193462.0 ave 193462 max 193462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193462 Ave neighs/atom = 55.211758 Neighbor list builds = 2 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 : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.067 | 5.067 | 5.067 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -14879.921 0 -14879.921 3159.3586 41289.952 116 0 -14882.973 0 -14882.973 3.1807236 41376.753 Loop time of 1.61244 on 1 procs for 10 steps with 3504 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 = -14879.921032296 -14882.9685824292 -14882.972600622 Force two-norm initial, final = 512.61359 2.5867596 Force max component initial, final = 416.07037 1.5219537 Final line search alpha, max atom move = 7.6210284e-05 0.00011598852 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6066 | 1.6066 | 1.6066 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065009 | 0.00065009 | 0.00065009 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005229 | | | 0.32 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7181.00 ave 7181 max 7181 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: 193560.0 ave 193560 max 193560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193560 Ave neighs/atom = 55.239726 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 = 17 39 4 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) = 4.699 | 4.699 | 4.699 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14882.973 0 -14882.973 3.1807236 Loop time of 1.988e-06 on 1 procs for 0 steps with 3504 atoms 201.2% 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 | | 1.988e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7096.00 ave 7096 max 7096 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: 193572.0 ave 193572 max 193572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193572 Ave neighs/atom = 55.243151 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) = 4.699 | 4.699 | 4.699 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 -14882.973 -14882.973 43.756144 105.99159 8.9216659 3.1807236 3.1807236 49.131888 19.83206 -59.421777 2.2612638 2260.8918 Loop time of 2.288e-06 on 1 procs for 0 steps with 3504 atoms 174.8% 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 | | 2.288e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7096.00 ave 7096 max 7096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96786.0 ave 96786 max 96786 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193572.0 ave 193572 max 193572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193572 Ave neighs/atom = 55.243151 Neighbor list builds = 0 Dangerous builds = 0 3504 -14882.972600622 eV 2.26126380037514 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27