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 -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 = 0.000332117 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 = 0.000161886 secs 261 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX4H9L7E/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 4 atoms, new total = 518 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 = 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) = 413.7 | 413.7 | 413.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -52980.588 0 -52980.588 -63.025106 32 0 -53327.827 0 -53327.827 -2459.2774 Loop time of 11.6128 on 1 procs for 32 steps with 518 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 = -52980.5883457 -53327.7785169 -53327.8266604 Force two-norm initial, final = 435.536 3.3583 Force max component initial, final = 136.856 0.420385 Final line search alpha, max atom move = 0.104321 0.0438549 Iterations, force evaluations = 32 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.477 | 10.477 | 10.477 | 0.0 | 90.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050325 | 0.0050325 | 0.0050325 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.1296 | 1.1296 | 1.1296 | 0.0 | 9.73 Other | | 0.001456 | | | 0.01 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11524 ave 11524 max 11524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 294725 ave 294725 max 294725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294725 Ave neighs/atom = 568.967 Neighbor list builds = 0 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 413.7 | 413.7 | 413.7 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -53327.827 0 -53327.827 -2459.2774 5935.353 34 0 -53328.215 0 -53328.215 1137.2606 5922.5887 Loop time of 0.769068 on 1 procs for 2 steps with 518 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -53327.8266603 -53328.1909572 -53328.2151738 Force two-norm initial, final = 500.108 38.8972 Force max component initial, final = 416.906 38.0301 Final line search alpha, max atom move = 8.8065e-06 0.000334912 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71814 | 0.71814 | 0.71814 | 0.0 | 93.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003171 | 0.0003171 | 0.0003171 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.049997 | 0.049997 | 0.049997 | 0.0 | 6.50 Other | | 0.0006101 | | | 0.08 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11578 ave 11578 max 11578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 295786 ave 295786 max 295786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295786 Ave neighs/atom = 571.015 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) = 413.9 | 413.9 | 413.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -53328.215 0 -53328.215 1137.2606 Loop time of 9.53674e-07 on 1 procs for 0 steps with 518 atoms 209.7% 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: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11578 ave 11578 max 11578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296274 ave 296274 max 296274 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 = 296274 Ave neighs/atom = 571.958 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) = 413.9 | 413.9 | 413.9 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 -2312.5303 -53328.215 22.853359 91.486924 2.8327125 1137.2606 1152.3293 445.79463 3097.2676 -86.074357 2.260704 121.03841 Loop time of 2.14577e-06 on 1 procs for 0 steps with 518 atoms 139.8% 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: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11578 ave 11578 max 11578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296274 ave 296274 max 296274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316952 ave 316952 max 316952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316952 Ave neighs/atom = 611.876 Neighbor list builds = 0 Dangerous builds = 0 518 -2312.53026362865 eV 2.26070395967515 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:13