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 -28.883352 0.0000000) to (20.423614 28.883352 4.0444782) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6041671 4.5307218 4.0444782 Created 203 atoms using lattice units in orthogonal box = (0.0000000 -28.883352 0.0000000) to (20.423614 28.883352 4.0444782) create_atoms CPU = 0.001 seconds 203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6041671 4.5307218 4.0444782 Created 205 atoms using lattice units in orthogonal box = (0.0000000 -28.883352 0.0000000) to (20.423614 28.883352 4.0444782) create_atoms CPU = 0.000 seconds 205 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXNC0Tb3/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 = 8 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 4 atoms, new total = 404 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 = 8 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) = 4.305 | 4.305 | 4.305 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1524.1394 0 -1524.1394 144933.49 89 0 -1742.5604 0 -1742.5604 -5924.132 Loop time of 3.19001 on 1 procs for 89 steps with 404 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 = -1524.13937451134 -1742.55885297571 -1742.56038986723 Force two-norm initial, final = 793.08692 0.14138771 Force max component initial, final = 275.82477 0.028341295 Final line search alpha, max atom move = 1.0000000 0.028341295 Iterations, force evaluations = 89 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1813 | 3.1813 | 3.1813 | 0.0 | 99.73 Neigh | 0.0021211 | 0.0021211 | 0.0021211 | 0.0 | 0.07 Comm | 0.003228 | 0.003228 | 0.003228 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003325 | | | 0.10 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2195.00 ave 2195 max 2195 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: 23360.0 ave 23360 max 23360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23360 Ave neighs/atom = 57.821782 Neighbor list builds = 1 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.305 | 4.305 | 4.305 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -1742.5604 0 -1742.5604 -5924.132 4771.6949 92 0 -1742.593 0 -1742.593 -15.612311 4755.2129 Loop time of 0.11238 on 1 procs for 3 steps with 404 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 = -1742.56038986723 -1742.59223004451 -1742.59296173199 Force two-norm initial, final = 30.813972 0.96028751 Force max component initial, final = 20.722343 0.81025482 Final line search alpha, max atom move = 0.00051491934 0.00041721588 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11184 | 0.11184 | 0.11184 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010305 | 0.00010305 | 0.00010305 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004393 | | | 0.39 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2195.00 ave 2195 max 2195 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: 23316.0 ave 23316 max 23316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23316 Ave neighs/atom = 57.712871 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 = 8 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) = 3.937 | 3.937 | 3.937 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1742.593 0 -1742.593 -15.612311 Loop time of 1.578e-06 on 1 procs for 0 steps with 404 atoms 126.7% 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 | | 1.578e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2195.00 ave 2195 max 2195 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: 23336.0 ave 23336 max 23336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23336 Ave neighs/atom = 57.762376 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) = 3.937 | 3.937 | 3.937 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 -1742.593 -1742.593 20.415232 57.658042 4.0397617 -15.612311 -15.612311 85.881136 139.96318 -272.68125 2.2681441 343.80677 Loop time of 1.386e-06 on 1 procs for 0 steps with 404 atoms 144.3% 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 | | 1.386e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2195.00 ave 2195 max 2195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11668.0 ave 11668 max 11668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23336.0 ave 23336 max 23336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23336 Ave neighs/atom = 57.762376 Neighbor list builds = 0 Dangerous builds = 0 404 -1742.59296173199 eV 2.268144084792 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03