LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) 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 19 Mar 2020 # Lattice spacing in x,y,z = 3.61227 3.61227 3.61227 Created orthogonal box = (0 -47.3781 0) to (33.4988 47.3781 5.10852) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.23234 6.05952 5.10852 Created 692 atoms create_atoms CPU = 0.000695944 secs 692 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.23234 6.05952 5.10852 Created 692 atoms create_atoms CPU = 0.000531197 secs 692 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXqJyqKO/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 = 13 35 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 14 atoms, new total = 1370 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) 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 = 13 35 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) = 4.535 | 4.535 | 4.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5767.512 0 -5767.512 10528.679 156 0 -5822.8278 0 -5822.8278 -3436.5038 Loop time of 5.22244 on 1 procs for 156 steps with 1370 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 = -5767.51195325 -5822.82275028 -5822.82784635 Force two-norm initial, final = 53.4019 0.246879 Force max component initial, final = 10.1906 0.0477395 Final line search alpha, max atom move = 1 0.0477395 Iterations, force evaluations = 156 268 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1988 | 5.1988 | 5.1988 | 0.0 | 99.55 Neigh | 0.0089791 | 0.0089791 | 0.0089791 | 0.0 | 0.17 Comm | 0.0071247 | 0.0071247 | 0.0071247 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007579 | | | 0.15 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188 ave 5188 max 5188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74866 ave 74866 max 74866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74866 Ave neighs/atom = 54.6467 Neighbor list builds = 4 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 156 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.535 | 4.535 | 4.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 156 0 -5822.8278 0 -5822.8278 -3436.5038 16215.555 159 0 -5822.9111 0 -5822.9111 -4884.5525 16230.477 Loop time of 0.091249 on 1 procs for 3 steps with 1370 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 = -5822.82784635 -5822.90550761 -5822.91107137 Force two-norm initial, final = 56.5632 2.14277 Force max component initial, final = 53.1095 1.57316 Final line search alpha, max atom move = 9.49933e-05 0.00014944 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090708 | 0.090708 | 0.090708 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011539 | 0.00011539 | 0.00011539 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004258 | | | 0.47 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188 ave 5188 max 5188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74876 ave 74876 max 74876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74876 Ave neighs/atom = 54.654 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 = 13 35 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) = 4.166 | 4.166 | 4.166 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5822.9111 0 -5822.9111 -4884.5525 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1370 atoms 314.6% 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 | | 9.537e-07 | | |100.00 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188 ave 5188 max 5188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74882 ave 74882 max 74882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74882 Ave neighs/atom = 54.6584 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) = 4.166 | 4.166 | 4.166 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 -5822.9111 -5822.9111 33.44516 94.756153 5.1214223 -4884.5525 -4884.5525 140.87864 -14950.222 155.68554 2.3376402 901.58372 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1370 atoms 314.6% 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 | | 9.537e-07 | | |100.00 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188 ave 5188 max 5188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37441 ave 37441 max 37441 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74882 ave 74882 max 74882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74882 Ave neighs/atom = 54.6584 Neighbor list builds = 0 Dangerous builds = 0 1370 -5822.91107137319 eV 2.33764020893538 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05