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 -45.9803 0) to (32.5104 45.9803 5.10852) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.02045 6.24375 5.10852 Created 649 atoms create_atoms CPU = 0.000660896 secs 649 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.02045 6.24375 5.10852 Created 649 atoms create_atoms CPU = 0.000525951 secs 649 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXFgMfeI/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 = 12 34 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 = 1284 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 = 12 34 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) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5420.9651 0 -5420.9651 2275.383 151 0 -5458.4195 0 -5458.4195 -11872.398 Loop time of 5.02548 on 1 procs for 151 steps with 1284 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 = -5420.96514401 -5458.41516136 -5458.4194978 Force two-norm initial, final = 38.7409 0.275517 Force max component initial, final = 13.7247 0.114532 Final line search alpha, max atom move = 0.911879 0.104439 Iterations, force evaluations = 151 278 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0085 | 5.0085 | 5.0085 | 0.0 | 99.66 Neigh | 0.0038352 | 0.0038352 | 0.0038352 | 0.0 | 0.08 Comm | 0.0059822 | 0.0059822 | 0.0059822 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007181 | | | 0.14 Nlocal: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4527 ave 4527 max 4527 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: 69590 ave 69590 max 69590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69590 Ave neighs/atom = 54.1978 Neighbor list builds = 2 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 : 151 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press Volume 151 0 -5458.4195 0 -5458.4195 -11872.398 15272.826 155 0 -5458.597 0 -5458.597 -5291.0111 15211.419 Loop time of 0.137345 on 1 procs for 4 steps with 1284 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 = -5458.4194978 -5458.59384942 -5458.59700292 Force two-norm initial, final = 109.985 0.463795 Force max component initial, final = 94.3959 0.29313 Final line search alpha, max atom move = 9.98297e-05 2.92631e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13667 | 0.13667 | 0.13667 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013256 | 0.00013256 | 0.00013256 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005434 | | | 0.40 Nlocal: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4534 ave 4534 max 4534 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: 69782 ave 69782 max 69782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69782 Ave neighs/atom = 54.3474 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 = 12 34 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) = 4.143 | 4.143 | 4.143 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5458.597 0 -5458.597 -5291.0111 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1284 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: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4535 ave 4535 max 4535 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: 69802 ave 69802 max 69802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69802 Ave neighs/atom = 54.3629 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) = 4.143 | 4.143 | 4.143 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 -5458.597 -5458.597 32.48692 91.960582 5.0916608 -5291.0111 -5291.0111 -19.467604 -15822.793 -30.772678 2.2210278 558.42129 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1284 atoms 139.8% 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: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4535 ave 4535 max 4535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34901 ave 34901 max 34901 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69802 ave 69802 max 69802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69802 Ave neighs/atom = 54.3629 Neighbor list builds = 0 Dangerous builds = 0 1284 -5458.59700292412 eV 2.22102776360672 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05