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 = 3.62799 3.62799 3.62799 Created orthogonal box = (0 -38.5697 0) to (38.566 38.5697 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.11939 5.11939 3.62799 Created 453 atoms create_atoms CPU = 0.000316858 secs 453 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.11939 5.11939 3.62799 Created 453 atoms create_atoms CPU = 0.000144958 secs 453 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX6PqXTL/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 = 7 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 20 atoms, new total = 886 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 = 7 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) = 564 | 564 | 564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -86770.631 0 -86770.631 -1042.0797 42 0 -87988.674 0 -87988.674 -31828.51 Loop time of 19.1668 on 1 procs for 42 steps with 886 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -86770.6309573 -87988.66349 -87988.6739225 Force two-norm initial, final = 355.381 52.4878 Force max component initial, final = 91.4297 8.1814 Final line search alpha, max atom move = 7.98213e-06 6.5305e-05 Iterations, force evaluations = 42 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.227 | 17.227 | 17.227 | 0.0 | 89.88 Neigh | 0.16359 | 0.16359 | 0.16359 | 0.0 | 0.85 Comm | 0.0060372 | 0.0060372 | 0.0060372 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.768 | 1.768 | 1.768 | 0.0 | 9.22 Other | | 0.001977 | | | 0.01 Nlocal: 886 ave 886 max 886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13238 ave 13238 max 13238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 482620 ave 482620 max 482620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 482620 Ave neighs/atom = 544.718 Neighbor list builds = 2 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 564.8 | 564.8 | 564.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -87988.667 0 -87988.667 -31828.509 10793.12 244 0 -89437.416 0 -89437.416 49849.28 9702.1475 Loop time of 64.5604 on 1 procs for 202 steps with 886 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -87988.6672206 -89437.4195176 -89437.4155783 Force two-norm initial, final = 4294.98 190.078 Force max component initial, final = 3365.66 34.2852 Final line search alpha, max atom move = 1.19545e-07 4.09861e-06 Iterations, force evaluations = 202 210 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 59.964 | 59.964 | 59.964 | 0.0 | 92.88 Neigh | 0.35603 | 0.35603 | 0.35603 | 0.0 | 0.55 Comm | 0.019861 | 0.019861 | 0.019861 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 4.1715 | 4.1715 | 4.1715 | 0.0 | 6.46 Other | | 0.04886 | | | 0.08 Nlocal: 886 ave 886 max 886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15788 ave 15788 max 15788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 536638 ave 536638 max 536638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536638 Ave neighs/atom = 605.686 Neighbor list builds = 4 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 = 8 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) = 579.8 | 579.8 | 579.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -89437.419 0 -89437.419 49849.276 Loop time of 9.53674e-07 on 1 procs for 0 steps with 886 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: 886 ave 886 max 886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16050 ave 16050 max 16050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 536371 ave 536371 max 536371 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 = 536371 Ave neighs/atom = 605.385 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) = 579.8 | 579.8 | 579.8 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 -3878.3735 -89437.417 42.901103 77.139351 2.9317264 49849.292 50509.796 145.69313 151185.28 198.41279 1.9843829 302.02099 Loop time of 9.53674e-07 on 1 procs for 0 steps with 886 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: 886 ave 886 max 886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16050 ave 16050 max 16050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 536371 ave 536371 max 536371 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 580152 ave 580152 max 580152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580152 Ave neighs/atom = 654.799 Neighbor list builds = 0 Dangerous builds = 0 886 -3878.37346041919 eV 1.98438287631716 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:25