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 -56.6746 0) to (28.3355 56.6746 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.10968 5.10968 3.62799 Created 490 atoms create_atoms CPU = 0.000316143 secs 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.10968 5.10968 3.62799 Created 490 atoms create_atoms CPU = 0.000175953 secs 490 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXXcWDni/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 = 5 19 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 1 atoms, new total = 979 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 = 5 19 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) = 721.9 | 721.9 | 721.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -96451.548 0 -96451.548 5724.0876 366 0 -98106.985 0 -98106.985 -46980.637 Loop time of 237.259 on 1 procs for 366 steps with 979 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -96451.547729 -98106.9168925 -98106.9854256 Force two-norm initial, final = 512.518 5.32131 Force max component initial, final = 101.277 0.547604 Final line search alpha, max atom move = 0.0569221 0.0311708 Iterations, force evaluations = 366 692 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 213.04 | 213.04 | 213.04 | 0.0 | 89.79 Neigh | 0.81977 | 0.81977 | 0.81977 | 0.0 | 0.35 Comm | 0.079661 | 0.079661 | 0.079661 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 23.299 | 23.299 | 23.299 | 0.0 | 9.82 Other | | 0.02202 | | | 0.01 Nlocal: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16453 ave 16453 max 16453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 536660 ave 536660 max 536660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536660 Ave neighs/atom = 548.172 Neighbor list builds = 7 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 : 366 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 721.8 | 721.8 | 721.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 366 0 -98106.983 0 -98106.983 -46980.624 11652.399 434 0 -98670.996 0 -98670.996 -42363.661 11699.018 Loop time of 22.7255 on 1 procs for 68 steps with 979 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -98106.983471 -98670.9521039 -98670.9964005 Force two-norm initial, final = 14442.2 223.765 Force max component initial, final = 13806.9 185.806 Final line search alpha, max atom move = 1.04603e-06 0.000194358 Iterations, force evaluations = 68 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.094 | 21.094 | 21.094 | 0.0 | 92.82 Neigh | 0.082875 | 0.082875 | 0.082875 | 0.0 | 0.36 Comm | 0.0069809 | 0.0069809 | 0.0069809 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.5226 | 1.5226 | 1.5226 | 0.0 | 6.70 Other | | 0.01888 | | | 0.08 Nlocal: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14526 ave 14526 max 14526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 541361 ave 541361 max 541361 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 541361 Ave neighs/atom = 552.973 Neighbor list builds = 1 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 = 5 19 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) = 716.7 | 716.7 | 716.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -98670.994 0 -98670.994 -42363.638 Loop time of 1.90735e-06 on 1 procs for 0 steps with 979 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 | | 1.907e-06 | | |100.00 Nlocal: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14638 ave 14638 max 14638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 537016 ave 537016 max 537016 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 = 537016 Ave neighs/atom = 548.535 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) = 716.7 | 716.7 | 716.7 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 -4278.7792 -98670.994 26.881914 113.34924 3.8394639 -42363.659 -42924.977 -616.05398 -129326.63 1167.7511 2.1667122 243.00428 Loop time of 9.53674e-07 on 1 procs for 0 steps with 979 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: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14638 ave 14638 max 14638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 537016 ave 537016 max 537016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 590422 ave 590422 max 590422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 590422 Ave neighs/atom = 603.087 Neighbor list builds = 0 Dangerous builds = 0 979 -4278.77924900752 eV 2.16671216943689 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:04:22