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 -37.6361 0) to (13.3054 37.6361 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.83831 4.27651 4.01172 Created 178 atoms create_atoms CPU = 0.000269175 secs 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.83831 4.27651 4.01172 Created 178 atoms create_atoms CPU = 0.000120163 secs 178 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXgViw3e/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 = 3 13 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 6 atoms, new total = 350 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 = 3 13 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) = 310.9 | 310.9 | 310.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -35419.287 0 -35419.287 1327.5615 38 0 -35774.946 0 -35774.946 -4492.7304 Loop time of 14.6631 on 1 procs for 38 steps with 350 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -35419.2869622 -35774.9207221 -35774.9460746 Force two-norm initial, final = 557.716 7.93647 Force max component initial, final = 215.221 1.19901 Final line search alpha, max atom move = 0.0402249 0.0482299 Iterations, force evaluations = 38 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.274 | 13.274 | 13.274 | 0.0 | 90.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0071776 | 0.0071776 | 0.0071776 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.3801 | 1.3801 | 1.3801 | 0.0 | 9.41 Other | | 0.001841 | | | 0.01 Nlocal: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8659 ave 8659 max 8659 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 197523 ave 197523 max 197523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197523 Ave neighs/atom = 564.351 Neighbor list builds = 0 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 310.9 | 310.9 | 310.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -35774.946 0 -35774.946 -4492.7274 4017.8311 41 0 -35776.055 0 -35776.055 304.3126 4006.2831 Loop time of 0.642084 on 1 procs for 3 steps with 350 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 = -35774.9458088 -35776.0511775 -35776.0548827 Force two-norm initial, final = 477.688 25.1068 Force max component initial, final = 346.631 17.4185 Final line search alpha, max atom move = 0.000509829 0.00888048 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59438 | 0.59438 | 0.59438 | 0.0 | 92.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.046845 | 0.046845 | 0.046845 | 0.0 | 7.30 Other | | 0.0005836 | | | 0.09 Nlocal: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8729 ave 8729 max 8729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198322 ave 198322 max 198322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198322 Ave neighs/atom = 566.634 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 = 3 13 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) = 311 | 311 | 311 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -35776.054 0 -35776.054 304.31835 Loop time of 1.90735e-06 on 1 procs for 0 steps with 350 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 | | 1.907e-06 | | |100.00 Nlocal: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8729 ave 8729 max 8729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198874 ave 198874 max 198874 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 = 198874 Ave neighs/atom = 568.211 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) = 311 | 311 | 311 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 -1551.3965 -35776.054 13.2837 75.272179 4.0067116 304.29301 308.32489 281.12404 945.56044 -301.7098 2.1267456 293.34121 Loop time of 1.90735e-06 on 1 procs for 0 steps with 350 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 | | 1.907e-06 | | |100.00 Nlocal: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8729 ave 8729 max 8729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198874 ave 198874 max 198874 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 214480 ave 214480 max 214480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214480 Ave neighs/atom = 612.8 Neighbor list builds = 0 Dangerous builds = 0 350 -1551.39653466374 eV 2.12674557205126 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:16