LAMMPS (24 Jan 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_ReaxFF_AryanpourVanDuinKubicki_2010_FeHO__SM_222964216001_001 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 24 Jan 2020 # Lattice spacing in x,y,z = 2.83671 2.83671 2.83671 Created orthogonal box = (0 -46.094 0) to (16.2957 46.094 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.44428 4.88845 4.01172 Created 265 atoms create_atoms CPU = 0.00078702 secs 265 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.44428 4.88845 4.01172 Created 265 atoms create_atoms CPU = 0.000576973 secs 265 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXQ73qoH/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 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 3 atoms, new total = 527 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) 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 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) = 398.3 | 398.3 | 398.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -53622.58 0 -53622.58 3474.8379 59 0 -54212.328 0 -54212.328 -5387.2849 Loop time of 16.9122 on 1 procs for 59 steps with 527 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 = -53622.5796742 -54212.2831834 -54212.3284407 Force two-norm initial, final = 650.222 3.26725 Force max component initial, final = 169.444 0.454228 Final line search alpha, max atom move = 0.0998045 0.045334 Iterations, force evaluations = 59 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.819 | 14.819 | 14.819 | 0.0 | 87.62 Neigh | 0.077417 | 0.077417 | 0.077417 | 0.0 | 0.46 Comm | 0.0088351 | 0.0088351 | 0.0088351 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.0045 | 2.0045 | 2.0045 | 0.0 | 11.85 Other | | 0.002654 | | | 0.02 Nlocal: 527 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10967 ave 10967 max 10967 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296617 ave 296617 max 296617 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296617 Ave neighs/atom = 562.841 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : real Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 398.3 | 398.3 | 398.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -54212.328 0 -54212.328 -5387.2849 6026.6633 61 0 -54212.451 0 -54212.451 -4172.2022 6022.3013 Loop time of 0.751128 on 1 procs for 2 steps with 527 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 = -54212.3284407 -54212.4367617 -54212.4513044 Force two-norm initial, final = 245.925 3.26105 Force max component initial, final = 245.451 0.462798 Final line search alpha, max atom move = 1.25295e-05 5.79861e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68939 | 0.68939 | 0.68939 | 0.0 | 91.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029206 | 0.00029206 | 0.00029206 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.060766 | 0.060766 | 0.060766 | 0.0 | 8.09 Other | | 0.000679 | | | 0.09 Nlocal: 527 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10981 ave 10981 max 10981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296787 ave 296787 max 296787 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296787 Ave neighs/atom = 563.163 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 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) = 398.4 | 398.4 | 398.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -54212.451 0 -54212.451 -4172.2022 Loop time of 1.90735e-06 on 1 procs for 0 steps with 527 atoms 157.3% 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: 527 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11037 ave 11037 max 11037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296880 ave 296880 max 296880 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 = 296880 Ave neighs/atom = 563.34 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) = 398.4 | 398.4 | 398.4 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 -2350.8744 -54212.451 16.279086 92.18794 4.0129002 -4172.2022 -4227.4839 0.70241109 -12681.621 -1.5330152 2.0621617 250.92107 Loop time of 1.90735e-06 on 1 procs for 0 steps with 527 atoms 157.3% 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: 527 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11037 ave 11037 max 11037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296880 ave 296880 max 296880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 323258 ave 323258 max 323258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323258 Ave neighs/atom = 613.393 Neighbor list builds = 0 Dangerous builds = 0 527 -2350.87437106916 eV 2.0621616607714 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:18