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 -36.400304 0.0000000) to (25.738902 36.400304 4.0444782) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7664633 4.9432511 4.0444782 Created 323 atoms using lattice units in orthogonal box = (0.0000000 -36.400304 0.0000000) to (25.738902 36.400304 4.0444782) create_atoms CPU = 0.001 seconds 323 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7664633 4.9432511 4.0444782 Created 325 atoms using lattice units in orthogonal box = (0.0000000 -36.400304 0.0000000) to (25.738902 36.400304 4.0444782) create_atoms CPU = 0.001 seconds 325 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXiIR3Qq/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 = 10 27 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 = 648 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 = 10 27 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) = 4.365 | 4.365 | 4.365 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2711.1865 0 -2711.1865 41980.352 100 0 -2800.2567 0 -2800.2567 7099.4132 Loop time of 5.71995 on 1 procs for 100 steps with 648 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 = -2711.18647629989 -2800.25447294552 -2800.25667868863 Force two-norm initial, final = 125.25671 0.16253143 Force max component initial, final = 45.354985 0.041156116 Final line search alpha, max atom move = 1.0000000 0.041156116 Iterations, force evaluations = 100 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.704 | 5.704 | 5.704 | 0.0 | 99.72 Neigh | 0.0058973 | 0.0058973 | 0.0058973 | 0.0 | 0.10 Comm | 0.0048464 | 0.0048464 | 0.0048464 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005161 | | | 0.09 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3063.00 ave 3063 max 3063 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: 37444.0 ave 37444 max 37444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37444 Ave neighs/atom = 57.783951 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 : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.365 | 4.365 | 4.365 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -2800.2567 0 -2800.2567 7099.4132 7578.5743 105 0 -2800.3791 0 -2800.3791 60.859159 7608.1729 Loop time of 0.245838 on 1 procs for 5 steps with 648 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 = -2800.25667868863 -2800.37908431329 -2800.37912634651 Force two-norm initial, final = 68.665174 0.60240872 Force max component initial, final = 63.148823 0.39462562 Final line search alpha, max atom move = 0.0012970634 0.00051185444 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24477 | 0.24477 | 0.24477 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017964 | 0.00017964 | 0.00017964 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008886 | | | 0.36 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3071.00 ave 3071 max 3071 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: 37480.0 ave 37480 max 37480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37480 Ave neighs/atom = 57.839506 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 = 10 27 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) = 3.996 | 3.996 | 3.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2800.3791 0 -2800.3791 60.859159 Loop time of 1.467e-06 on 1 procs for 0 steps with 648 atoms 136.3% 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 | | 1.467e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3060.00 ave 3060 max 3060 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: 37460.0 ave 37460 max 37460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37460 Ave neighs/atom = 57.808642 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) = 3.996 | 3.996 | 3.996 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 -2800.3791 -2800.3791 25.750816 73.078233 4.0429777 60.859159 60.859159 83.141192 52.868831 46.567455 2.2531783 460.20594 Loop time of 2.973e-06 on 1 procs for 0 steps with 648 atoms 168.2% 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 | | 2.973e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3060.00 ave 3060 max 3060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18730.0 ave 18730 max 18730 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37460.0 ave 37460 max 37460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37460 Ave neighs/atom = 57.808642 Neighbor list builds = 0 Dangerous builds = 0 648 -2800.37912634651 eV 2.25317829818348 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06