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 -34.9762 0) to (12.3649 34.9762 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.55551 3.68141 4.01172 Created 153 atoms create_atoms CPU = 0.000253916 secs 153 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.55551 3.68141 4.01172 Created 153 atoms create_atoms CPU = 8.41618e-05 secs 153 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX0Kx0WY/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 12 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 = 300 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 12 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) = 281.1 | 281.1 | 281.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -30339.859 0 -30339.859 -2441.5293 20 0 -30615.943 0 -30615.943 -17043.407 Loop time of 8.88012 on 1 procs for 20 steps with 300 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -30339.8585404 -30615.943254 -30615.943256 Force two-norm initial, final = 339.119 13.7298 Force max component initial, final = 102.817 3.32951 Final line search alpha, max atom move = 1.0325e-10 3.43772e-10 Iterations, force evaluations = 20 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0703 | 8.0703 | 8.0703 | 0.0 | 90.88 Neigh | 0.029403 | 0.029403 | 0.029403 | 0.0 | 0.33 Comm | 0.0047274 | 0.0047274 | 0.0047274 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.77452 | 0.77452 | 0.77452 | 0.0 | 8.72 Other | | 0.001137 | | | 0.01 Nlocal: 300 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7974 ave 7974 max 7974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169661 ave 169661 max 169661 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169661 Ave neighs/atom = 565.537 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 281.1 | 281.1 | 281.1 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -30615.943 0 -30615.943 -17043.413 3469.9649 25 0 -30619.429 0 -30619.429 -6047.2341 3446.7257 Loop time of 5.18611 on 1 procs for 5 steps with 300 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -30615.9434893 -30619.4281206 -30619.4290339 Force two-norm initial, final = 925.511 15.3138 Force max component initial, final = 683.495 5.42514 Final line search alpha, max atom move = 5.05445e-11 2.74211e-10 Iterations, force evaluations = 5 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8372 | 4.8372 | 4.8372 | 0.0 | 93.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023932 | 0.0023932 | 0.0023932 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.341 | 0.341 | 0.341 | 0.0 | 6.58 Other | | 0.005543 | | | 0.11 Nlocal: 300 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8009 ave 8009 max 8009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170172 ave 170172 max 170172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170172 Ave neighs/atom = 567.24 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 12 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) = 281.3 | 281.3 | 281.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -30619.43 0 -30619.43 -6047.2489 Loop time of 9.53674e-07 on 1 procs for 0 steps with 300 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: 300 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8037 ave 8037 max 8037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173203 ave 173203 max 173203 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 = 173203 Ave neighs/atom = 577.343 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) = 281.3 | 281.3 | 281.3 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 -1327.7842 -30619.432 12.326207 69.952371 3.9973745 -6047.2639 -6127.3902 108.96389 -18428.577 -62.557264 2.1473383 176.28129 Loop time of 2.14577e-06 on 1 procs for 0 steps with 300 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: 300 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8037 ave 8037 max 8037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173203 ave 173203 max 173203 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185854 ave 185854 max 185854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185854 Ave neighs/atom = 619.513 Neighbor list builds = 0 Dangerous builds = 0 300 -1327.78423148039 eV 2.14733828788771 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