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 -31.974408 0.0000000) to (6.3948815 31.974408 2.8598780) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8369289 3.8369289 2.8598780 Created 50 atoms using lattice units in orthogonal box = (0.0000000 -31.974408 0.0000000) to (6.3948815 31.974408 2.8598780) create_atoms CPU = 0.001 seconds 50 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8369289 3.8369289 2.8598780 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -31.974408 0.0000000) to (6.3948815 31.974408 2.8598780) create_atoms CPU = 0.000 seconds 51 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXsIfpUn/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 = 3 24 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 1 atoms, new total = 100 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 = 3 24 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) = 4.235 | 4.235 | 4.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -425.34442 0 -425.34442 23798.058 42 0 -431.7636 0 -431.7636 8824.079 Loop time of 1.12271 on 1 procs for 42 steps with 100 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 = -425.344418527742 -431.763230547641 -431.763601239053 Force two-norm initial, final = 19.016398 0.075061351 Force max component initial, final = 7.5735127 0.021042856 Final line search alpha, max atom move = 1.0000000 0.021042856 Iterations, force evaluations = 42 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1178 | 1.1178 | 1.1178 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002814 | 0.002814 | 0.002814 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002136 | | | 0.19 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1485.00 ave 1485 max 1485 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: 5808.00 ave 5808 max 5808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5808 Ave neighs/atom = 58.080000 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.236 | 4.236 | 4.236 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -431.7636 0 -431.7636 8824.079 1169.5331 56 0 -431.86179 0 -431.86179 -582.01369 1175.4162 Loop time of 0.216758 on 1 procs for 14 steps with 100 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 = -431.763601239053 -431.86166798532 -431.861787989274 Force two-norm initial, final = 17.175693 0.77767358 Force max component initial, final = 17.103279 0.52973583 Final line search alpha, max atom move = 0.018364702 0.0097284407 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2146 | 0.2146 | 0.2146 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049128 | 0.00049128 | 0.00049128 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001667 | | | 0.77 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1505.00 ave 1505 max 1505 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: 5756.00 ave 5756 max 5756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5756 Ave neighs/atom = 57.560000 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 = 3 24 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) = 3.867 | 3.867 | 3.867 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -431.86179 0 -431.86179 -582.01369 Loop time of 6.134e-06 on 1 procs for 0 steps with 100 atoms 163.0% 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 | | 6.134e-06 | | |100.00 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1505.00 ave 1505 max 1505 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: 5756.00 ave 5756 max 5756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5756 Ave neighs/atom = 57.560000 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) = 3.867 | 3.867 | 3.867 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 -431.86179 -431.86179 6.394637 64.732456 2.8395772 -582.01369 -582.01369 -605.10567 -730.91628 -410.01912 2.3975862 66.400408 Loop time of 5.984e-06 on 1 procs for 0 steps with 100 atoms 200.5% 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 | | 5.984e-06 | | |100.00 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1505.00 ave 1505 max 1505 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2878.00 ave 2878 max 2878 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5756.00 ave 5756 max 5756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5756 Ave neighs/atom = 57.560000 Neighbor list builds = 0 Dangerous builds = 0 100 -431.861787989274 eV 2.39758616023793 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01