LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_AryanpourVanDuinKubicki_2010_FeHO__SM_222964216001_000 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 2.83671 2.83671 2.83671 Created orthogonal box = (0 -30.2906 0) to (21.4167 30.2906 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.88451 4.78229 4.01172 Created 230 atoms create_atoms CPU = 0.000236988 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.88451 4.78229 4.01172 Created 230 atoms create_atoms CPU = 0.000100851 secs 230 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXxm90L6/ffield.reax.Fe_O_C_H with DATE: 2011-02-18 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 4 11 1 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (3) fix qeq/reax, perpetual, copy from (2) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Deleted 0 atoms, new total = 460 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 4 11 1 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 338.5 | 338.5 | 338.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -45646.173 0 -45646.173 19576.66 31 0 -47021.952 0 -47021.952 12405.579 Loop time of 9.23201 on 1 procs for 31 steps with 460 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -45646.1732285 -47021.9503858 -47021.9522793 Force two-norm initial, final = 1017.66 8.49947 Force max component initial, final = 174.231 0.76906 Final line search alpha, max atom move = 1.95041e-05 1.49998e-05 Iterations, force evaluations = 31 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2144 | 8.2144 | 8.2144 | 0.0 | 88.98 Neigh | 0.040818 | 0.040818 | 0.040818 | 0.0 | 0.44 Comm | 0.0041397 | 0.0041397 | 0.0041397 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.97146 | 0.97146 | 0.97146 | 0.0 | 10.52 Other | | 0.001225 | | | 0.01 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9102 ave 9102 max 9102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262522 ave 262522 max 262522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262522 Ave neighs/atom = 570.7 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : real Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 338.5 | 338.5 | 338.5 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -47021.951 0 -47021.951 12405.593 5205.0127 34 0 -47022.404 0 -47022.404 9941.0235 5212.6085 Loop time of 1.36472 on 1 procs for 3 steps with 460 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -47021.9514106 -47022.3816829 -47022.4040664 Force two-norm initial, final = 1025.06 698.625 Force max component initial, final = 798.623 554.042 Final line search alpha, max atom move = 1.09103e-07 6.04475e-05 Iterations, force evaluations = 3 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2524 | 1.2524 | 1.2524 | 0.0 | 91.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053453 | 0.00053453 | 0.00053453 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.11057 | 0.11057 | 0.11057 | 0.0 | 8.10 Other | | 0.001217 | | | 0.09 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9102 ave 9102 max 9102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261799 ave 261799 max 261799 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261799 Ave neighs/atom = 569.128 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 4 11 1 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (4) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 338.7 | 338.7 | 338.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -47022.406 0 -47022.406 9941.0457 Loop time of 9.53674e-07 on 1 procs for 0 steps with 460 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9102 ave 9102 max 9102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261397 ave 261397 max 261397 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261397 Ave neighs/atom = 568.254 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 338.7 | 338.7 | 338.7 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 -2039.0845 -47022.406 21.434116 60.58129 4.014311 9941.0452 10072.764 7390.6338 17152.77 5674.8882 2.1146114 278.0704 Loop time of 2.14577e-06 on 1 procs for 0 steps with 460 atoms 0.0% 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9102 ave 9102 max 9102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261397 ave 261397 max 261397 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 286520 ave 286520 max 286520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286520 Ave neighs/atom = 622.87 Neighbor list builds = 0 Dangerous builds = 0 460 -2039.08449557788 eV 2.1146113665851 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:11