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 -45.7435 0) to (22.8703 45.7435 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.16666 3.16666 2.83671 Created 261 atoms create_atoms CPU = 0.000174046 secs 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.16666 3.16666 2.83671 Created 261 atoms create_atoms CPU = 4.79221e-05 secs 261 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXaZ4QhU/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 16 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 = 516 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 16 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) = 429.9 | 429.9 | 429.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -52613.417 0 -52613.417 -527.23951 10 0 -52884.649 0 -52884.649 -6499.476 Loop time of 12.2686 on 1 procs for 10 steps with 516 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -52613.4166958 -52884.6293614 -52884.649168 Force two-norm initial, final = 320.564 22.2913 Force max component initial, final = 88.747 4.41163 Final line search alpha, max atom move = 8.06578e-11 3.55832e-10 Iterations, force evaluations = 10 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.079 | 11.079 | 11.079 | 0.0 | 90.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050614 | 0.0050614 | 0.0050614 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.1831 | 1.1831 | 1.1831 | 0.0 | 9.64 Other | | 0.001114 | | | 0.01 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12148 ave 12148 max 12148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 292497 ave 292497 max 292497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292497 Ave neighs/atom = 566.855 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 : 10 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 430.6 | 430.6 | 430.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 10 0 -52884.65 0 -52884.65 -6499.4659 5935.353 13 0 -52886.65 0 -52886.65 -1070.2733 5916.054 Loop time of 1.09016 on 1 procs for 3 steps with 516 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 = -52884.6496113 -52886.644326 -52886.6496106 Force two-norm initial, final = 782.246 24.5941 Force max component initial, final = 623.033 8.21046 Final line search alpha, max atom move = 2.71073e-05 0.000222563 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0113 | 1.0113 | 1.0113 | 0.0 | 92.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047374 | 0.00047374 | 0.00047374 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.077502 | 0.077502 | 0.077502 | 0.0 | 7.11 Other | | 0.0009074 | | | 0.08 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12178 ave 12178 max 12178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 293554 ave 293554 max 293554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293554 Ave neighs/atom = 568.903 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 16 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) = 430.8 | 430.8 | 430.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -52886.649 0 -52886.649 -1070.2541 Loop time of 9.53674e-07 on 1 procs for 0 steps with 516 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: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12198 ave 12198 max 12198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 294081 ave 294081 max 294081 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 = 294081 Ave neighs/atom = 569.924 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) = 430.8 | 430.8 | 430.8 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 -2293.3822 -52886.65 22.846428 91.486924 2.8304455 -1070.2748 -1084.4559 -96.314195 -3237.245 80.191517 2.2408278 131.83906 Loop time of 9.53674e-07 on 1 procs for 0 steps with 516 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: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12198 ave 12198 max 12198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 294081 ave 294081 max 294081 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 314352 ave 314352 max 314352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314352 Ave neighs/atom = 609.209 Neighbor list builds = 0 Dangerous builds = 0 516 -2293.38219851122 eV 2.24082784530278 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:14