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 = 2.85988 2.85988 2.85988 Created orthogonal box = (0 -30.538 0) to (21.5916 30.538 4.04448) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9244 4.82134 4.04448 Created 230 atoms create_atoms CPU = 0.000307083 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9244 4.82134 4.04448 Created 230 atoms create_atoms CPU = 0.000231981 secs 230 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXcNu1Qz/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 = 8 23 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 = 456 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 = 8 23 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) = 4.317 | 4.317 | 4.317 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1902.4984 0 -1902.4984 46089.831 46 0 -1971.1217 0 -1971.1217 4789.1237 Loop time of 0.78163 on 1 procs for 46 steps with 456 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 = -1902.49844815 -1971.11977501 -1971.12173718 Force two-norm initial, final = 106.49 0.155755 Force max component initial, final = 35.1292 0.0273033 Final line search alpha, max atom move = 1 0.0273033 Iterations, force evaluations = 46 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77873 | 0.77873 | 0.77873 | 0.0 | 99.63 Neigh | 0.00092721 | 0.00092721 | 0.00092721 | 0.0 | 0.12 Comm | 0.00098634 | 0.00098634 | 0.00098634 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009849 | | | 0.13 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2373 ave 2373 max 2373 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: 26452 ave 26452 max 26452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26452 Ave neighs/atom = 58.0088 Neighbor list builds = 1 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.317 | 4.317 | 4.317 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1971.1217 0 -1971.1217 4789.1237 5333.5703 48 0 -1971.1326 0 -1971.1326 2095.3606 5341.6627 Loop time of 0.0514691 on 1 procs for 2 steps with 456 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 = -1971.12173718 -1971.13170664 -1971.13263484 Force two-norm initial, final = 16.3215 1.15285 Force max component initial, final = 15.5815 1.00312 Final line search alpha, max atom move = 0.000293072 0.000293985 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051244 | 0.051244 | 0.051244 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.4121e-05 | 5.4121e-05 | 5.4121e-05 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001707 | | | 0.33 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2363 ave 2363 max 2363 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: 26460 ave 26460 max 26460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26460 Ave neighs/atom = 58.0263 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 = 8 23 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) = 3.949 | 3.949 | 3.949 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1971.1326 0 -1971.1326 2095.3606 Loop time of 2.14577e-06 on 1 procs for 0 steps with 456 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: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2363 ave 2363 max 2363 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: 26440 ave 26440 max 26440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26440 Ave neighs/atom = 57.9825 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) = 3.949 | 3.949 | 3.949 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 -1971.1326 -1971.1326 21.622451 61.076001 4.0448362 2095.3606 2095.3606 -162.73733 6749.7199 -300.90069 2.2451625 326.27165 Loop time of 1.90735e-06 on 1 procs for 0 steps with 456 atoms 104.9% 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: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2363 ave 2363 max 2363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13220 ave 13220 max 13220 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26440 ave 26440 max 26440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26440 Ave neighs/atom = 57.9825 Neighbor list builds = 0 Dangerous builds = 0 456 -1971.1326348405 eV 2.24516245054835 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00