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 -32.8604 0) to (23.2338 32.8604 4.04448) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.92837 4.48057 4.04448 Created 266 atoms create_atoms CPU = 0.000465155 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.92837 4.48057 4.04448 Created 266 atoms create_atoms CPU = 0.000283003 secs 266 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXuLLtgT/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 = 9 25 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 8 atoms, new total = 524 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 = 9 25 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) = 4.339 | 4.339 | 4.339 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2234.3912 0 -2234.3912 12377.626 26 0 -2266.5492 0 -2266.5492 -6211.2774 Loop time of 0.603231 on 1 procs for 26 steps with 524 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2234.39116667 -2266.54774113 -2266.54923846 Force two-norm initial, final = 59.9975 0.12587 Force max component initial, final = 17.1729 0.0223536 Final line search alpha, max atom move = 1 0.0223536 Iterations, force evaluations = 26 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60176 | 0.60176 | 0.60176 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082159 | 0.00082159 | 0.00082159 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006449 | | | 0.11 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3088 ave 3088 max 3088 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: 30148 ave 30148 max 30148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30148 Ave neighs/atom = 57.5344 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.339 | 4.339 | 4.339 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -2266.5492 0 -2266.5492 -6211.2774 6175.6721 29 0 -2266.5933 0 -2266.5933 -437.44013 6154.7229 Loop time of 0.0759089 on 1 procs for 3 steps with 524 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 = -2266.54923846 -2266.59333216 -2266.59333978 Force two-norm initial, final = 36.6648 0.175537 Force max component initial, final = 27.1906 0.0674498 Final line search alpha, max atom move = 0.00467359 0.000315233 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075472 | 0.075472 | 0.075472 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.6798e-05 | 9.6798e-05 | 9.6798e-05 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003402 | | | 0.45 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3060 ave 3060 max 3060 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: 30284 ave 30284 max 30284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30284 Ave neighs/atom = 57.7939 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 = 9 25 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) = 3.97 | 3.97 | 3.97 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2266.5933 0 -2266.5933 -437.44013 Loop time of 2.14577e-06 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3076 ave 3076 max 3076 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: 30292 ave 30292 max 30292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30292 Ave neighs/atom = 57.8092 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) = 3.97 | 3.97 | 3.97 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 -2266.5933 -2266.5933 23.193264 65.720712 4.037796 -437.44013 -437.44013 -13.530009 -1316.3197 17.529296 2.2427979 371.79561 Loop time of 2.14577e-06 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3076 ave 3076 max 3076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15146 ave 15146 max 15146 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30292 ave 30292 max 30292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30292 Ave neighs/atom = 57.8092 Neighbor list builds = 0 Dangerous builds = 0 524 -2266.59333978219 eV 2.24279787157902 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00