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 -29.165147 0.0000000) to (14.582574 29.165147 2.8598780) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.3652093 3.3652093 2.8598780 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -29.165147 0.0000000) to (14.582574 29.165147 2.8598780) create_atoms CPU = 0.002 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.3652093 3.3652093 2.8598780 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -29.165147 0.0000000) to (14.582574 29.165147 2.8598780) create_atoms CPU = 0.001 seconds 106 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXs11MmW/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 = 6 22 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 2 atoms, new total = 208 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 = 6 22 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) = 4.256 | 4.256 | 4.256 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -879.37674 0 -879.37674 31799.201 30 0 -898.29718 0 -898.29718 10814.843 Loop time of 1.6324 on 1 procs for 30 steps with 208 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 = -879.376744601115 -898.29651977202 -898.29718467697 Force two-norm initial, final = 45.984975 0.073582411 Force max component initial, final = 16.290566 0.011195242 Final line search alpha, max atom move = 1.0000000 0.011195242 Iterations, force evaluations = 30 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6278 | 1.6278 | 1.6278 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025859 | 0.0025859 | 0.0025859 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002061 | | | 0.13 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 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: 12088.0 ave 12088 max 12088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12088 Ave neighs/atom = 58.115385 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 : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.256 | 4.256 | 4.256 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -898.29718 0 -898.29718 10814.843 2432.6288 45 0 -898.51356 0 -898.51356 91.341576 2447.077 Loop time of 0.487042 on 1 procs for 15 steps with 208 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 = -898.29718467697 -898.513112892077 -898.513564062686 Force two-norm initial, final = 36.127586 1.0643859 Force max component initial, final = 34.232900 0.65207920 Final line search alpha, max atom move = 0.0082251052 0.0053634201 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4837 | 0.4837 | 0.4837 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073049 | 0.00073049 | 0.00073049 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00261 | | | 0.54 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 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: 11976.0 ave 11976 max 11976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11976 Ave neighs/atom = 57.576923 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 = 6 22 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) = 3.888 | 3.888 | 3.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -898.51356 0 -898.51356 91.341576 Loop time of 6.705e-06 on 1 procs for 0 steps with 208 atoms 193.9% 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 | | 6.705e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 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: 11960.0 ave 11960 max 11960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11960 Ave neighs/atom = 57.500000 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) = 3.888 | 3.888 | 3.888 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 -898.51356 -898.51356 14.584322 59.127474 2.8377366 91.341576 91.341576 -426.98747 370.24267 330.76953 2.3734689 106.14559 Loop time of 7.217e-06 on 1 procs for 0 steps with 208 atoms 221.7% 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 | | 7.217e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5980.00 ave 5980 max 5980 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11960.0 ave 11960 max 11960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11960 Ave neighs/atom = 57.500000 Neighbor list builds = 0 Dangerous builds = 0 208 -898.513564062686 eV 2.373468857556 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02