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 -58.2497 0) to (29.123 58.2497 3.61227) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.03242 4.03242 3.61227 Created 522 atoms create_atoms CPU = 0.000366926 secs 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.03242 4.03242 3.61227 Created 522 atoms create_atoms CPU = 0.000273943 secs 522 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX1ERn6S/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 = 11 43 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 = 1040 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 = 11 43 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) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4363.0583 0 -4363.0583 20829.831 36 0 -4420.5879 0 -4420.5879 1670.5718 Loop time of 1.73822 on 1 procs for 36 steps with 1040 atoms 76.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4363.05829916 -4420.58382628 -4420.58791175 Force two-norm initial, final = 53.2118 0.202681 Force max component initial, final = 10.6011 0.0402827 Final line search alpha, max atom move = 1 0.0402827 Iterations, force evaluations = 36 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7344 | 1.7344 | 1.7344 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022018 | 0.0022018 | 0.0022018 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001647 | | | 0.09 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5966 ave 5966 max 5966 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: 56284 ave 56284 max 56284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56284 Ave neighs/atom = 54.1192 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -4420.5879 0 -4420.5879 1670.5718 12255.769 50 0 -4421.3226 0 -4421.3226 -3108.5584 12289.947 Loop time of 0.518535 on 1 procs for 14 steps with 1040 atoms 69.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4420.58791175 -4421.3222546 -4421.32262966 Force two-norm initial, final = 99.5118 1.76179 Force max component initial, final = 97.732 1.25674 Final line search alpha, max atom move = 0.00367754 0.00462169 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51596 | 0.51596 | 0.51596 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061941 | 0.00061941 | 0.00061941 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001951 | | | 0.38 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6003 ave 6003 max 6003 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: 56924 ave 56924 max 56924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56924 Ave neighs/atom = 54.7346 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 = 11 43 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) = 4.099 | 4.099 | 4.099 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4421.3226 0 -4421.3226 -3108.5584 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1040 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: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4465 ave 4465 max 4465 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: 57000 ave 57000 max 57000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57000 Ave neighs/atom = 54.8077 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) = 4.099 | 4.099 | 4.099 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 -4421.3226 -4421.3226 28.821786 116.4994 3.6602052 -3108.5584 -3108.5584 162.13941 -9361.1404 -126.6742 2.3410752 177.63517 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1040 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: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4465 ave 4465 max 4465 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28500 ave 28500 max 28500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57000 ave 57000 max 57000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57000 Ave neighs/atom = 54.8077 Neighbor list builds = 0 Dangerous builds = 0 1040 -4421.32262965734 eV 2.34107515328657 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02