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 -32.8402 0) to (23.2195 32.8402 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.50528 4.90109 4.01172 Created 269 atoms create_atoms CPU = 0.000602961 secs 269 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.50528 4.90109 4.01172 Created 269 atoms create_atoms CPU = 0.000424862 secs 269 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXaTsArU/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 11 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 0 atoms, new total = 538 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 11 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) = 369.9 | 369.9 | 369.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -54203.392 0 -54203.392 9726.6209 42 0 -55220.312 0 -55220.312 1887.42 Loop time of 11.5978 on 1 procs for 42 steps with 538 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 = -54203.392486 -55220.2716961 -55220.3119077 Force two-norm initial, final = 988.291 2.94195 Force max component initial, final = 197.793 0.305154 Final line search alpha, max atom move = 0.165582 0.0505279 Iterations, force evaluations = 42 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.102 | 10.102 | 10.102 | 0.0 | 87.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058277 | 0.0058277 | 0.0058277 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.4883 | 1.4883 | 1.4883 | 0.0 | 12.83 Other | | 0.001871 | | | 0.02 Nlocal: 538 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9934 ave 9934 max 9934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 300894 ave 300894 max 300894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300894 Ave neighs/atom = 559.283 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 369.9 | 369.9 | 369.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -55220.312 0 -55220.312 1887.42 6118.1283 44 0 -55220.569 0 -55220.569 -654.27029 6127.5059 Loop time of 0.54136 on 1 procs for 2 steps with 538 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 = -55220.3119077 -55220.560323 -55220.5694318 Force two-norm initial, final = 421.548 4.19267 Force max component initial, final = 368.411 2.10634 Final line search alpha, max atom move = 2.33709e-05 4.92272e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48949 | 0.48949 | 0.48949 | 0.0 | 90.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021958 | 0.00021958 | 0.00021958 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.051118 | 0.051118 | 0.051118 | 0.0 | 9.44 Other | | 0.0005372 | | | 0.10 Nlocal: 538 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9899 ave 9899 max 9899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302295 ave 302295 max 302295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302295 Ave neighs/atom = 561.887 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 11 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) = 370 | 370 | 370 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -55220.569 0 -55220.569 -654.27029 Loop time of 9.53674e-07 on 1 procs for 0 steps with 538 atoms 314.6% 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: 538 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9899 ave 9899 max 9899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302002 ave 302002 max 302002 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 = 302002 Ave neighs/atom = 561.342 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) = 370 | 370 | 370 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 -2394.5905 -55220.569 23.226965 65.680331 4.0165756 -654.27029 -662.93937 22.773858 -2035.5038 23.911781 2.0552824 360.36196 Loop time of 1.90735e-06 on 1 procs for 0 steps with 538 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: 538 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9899 ave 9899 max 9899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302002 ave 302002 max 302002 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 332044 ave 332044 max 332044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332044 Ave neighs/atom = 617.182 Neighbor list builds = 0 Dangerous builds = 0 538 -2394.59051028996 eV 2.05528235945618 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