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 -47.9258 0) to (16.943 47.9258 5.10852) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.16111 5.4457 5.10852 Created 355 atoms create_atoms CPU = 0.000389814 secs 355 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.16111 5.4457 5.10852 Created 355 atoms create_atoms CPU = 0.000287056 secs 355 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXDkAyyN/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 = 7 36 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 22 atoms, new total = 688 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 = 7 36 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) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2898.8623 0 -2898.8623 -13299.166 52 0 -2922.5343 0 -2922.5343 -32716.115 Loop time of 0.910915 on 1 procs for 52 steps with 688 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 = -2898.86225052 -2922.53138254 -2922.53426023 Force two-norm initial, final = 7.37882 0.144393 Force max component initial, final = 2.0716 0.0140229 Final line search alpha, max atom move = 1 0.0140229 Iterations, force evaluations = 52 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90795 | 0.90795 | 0.90795 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015552 | 0.0015552 | 0.0015552 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001408 | | | 0.15 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3451 ave 3451 max 3451 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: 36448 ave 36448 max 36448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36448 Ave neighs/atom = 52.9767 Neighbor list builds = 0 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -2922.5343 0 -2922.5343 -32716.115 8296.3234 62 0 -2923.6518 0 -2923.6518 -8746.5286 8168.9693 Loop time of 0.117828 on 1 procs for 10 steps with 688 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 = -2922.53426023 -2923.65143863 -2923.65181022 Force two-norm initial, final = 200.853 0.330834 Force max component initial, final = 151.78 0.053577 Final line search alpha, max atom move = 0.000421019 2.25569e-05 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11688 | 0.11688 | 0.11688 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019836 | 0.00019836 | 0.00019836 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007467 | | | 0.63 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3401 ave 3401 max 3401 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: 37056 ave 37056 max 37056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37056 Ave neighs/atom = 53.8605 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 = 7 36 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) = 4.037 | 4.037 | 4.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2923.6518 0 -2923.6518 -8746.5286 Loop time of 1.90735e-06 on 1 procs for 0 steps with 688 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3401 ave 3401 max 3401 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: 37056 ave 37056 max 37056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37056 Ave neighs/atom = 53.8605 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) = 4.037 | 4.037 | 4.037 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 -2923.6518 -2923.6518 16.833796 95.851553 5.062745 -8746.5286 -8746.5286 -7.5790092 -26235.352 3.3454195 2.4737219 104.24374 Loop time of 2.14577e-06 on 1 procs for 0 steps with 688 atoms 93.2% 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 | | 2.146e-06 | | |100.00 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3401 ave 3401 max 3401 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18528 ave 18528 max 18528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37056 ave 37056 max 37056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37056 Ave neighs/atom = 53.8605 Neighbor list builds = 0 Dangerous builds = 0 688 -2923.65181022193 eV 2.4737219106487 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01