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 -36.1083 0) to (25.5304 36.1083 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.72786 4.90321 4.01172 Created 326 atoms create_atoms CPU = 0.000675917 secs 326 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.72786 4.90321 4.01172 Created 326 atoms create_atoms CPU = 0.00051403 secs 326 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXyWQCfS/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 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 0 atoms, new total = 652 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 = 5 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) = 415.3 | 415.3 | 415.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -65580.535 0 -65580.535 12853.466 35 0 -66969.831 0 -66969.831 5950.2737 Loop time of 10.7848 on 1 procs for 35 steps with 652 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 = -65580.5346831 -66969.7754585 -66969.8313961 Force two-norm initial, final = 1182.63 3.58209 Force max component initial, final = 210.839 0.278026 Final line search alpha, max atom move = 0.0869862 0.0241844 Iterations, force evaluations = 35 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3814 | 9.3814 | 9.3814 | 0.0 | 86.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0054057 | 0.0054057 | 0.0054057 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.3963 | 1.3963 | 1.3963 | 0.0 | 12.95 Other | | 0.00177 | | | 0.02 Nlocal: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11136 ave 11136 max 11136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 363941 ave 363941 max 363941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363941 Ave neighs/atom = 558.192 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 415.4 | 415.4 | 415.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -66969.831 0 -66969.831 5950.2737 7396.4854 37 0 -66970.539 0 -66970.539 1751.1726 7415.0041 Loop time of 0.619584 on 1 procs for 2 steps with 652 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 = -66969.8313961 -66970.4887705 -66970.539059 Force two-norm initial, final = 797.302 20.5626 Force max component initial, final = 610.362 16.9807 Final line search alpha, max atom move = 5.69162e-06 9.66475e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55787 | 0.55787 | 0.55787 | 0.0 | 90.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024676 | 0.00024676 | 0.00024676 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.060868 | 0.060868 | 0.060868 | 0.0 | 9.82 Other | | 0.0006025 | | | 0.10 Nlocal: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11150 ave 11150 max 11150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 365168 ave 365168 max 365168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 365168 Ave neighs/atom = 560.074 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 = 5 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) = 415.5 | 415.5 | 415.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -66970.539 0 -66970.539 1751.1726 Loop time of 9.53674e-07 on 1 procs for 0 steps with 652 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: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11136 ave 11136 max 11136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 364707 ave 364707 max 364707 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 = 364707 Ave neighs/atom = 559.367 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) = 415.5 | 415.5 | 415.5 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 -2904.1174 -66970.539 25.566106 72.216602 4.0161484 1751.1726 1774.3756 102.84779 5379.5599 -159.2808 2.0573509 380.69809 Loop time of 1.90735e-06 on 1 procs for 0 steps with 652 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: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11136 ave 11136 max 11136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 364707 ave 364707 max 364707 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 402416 ave 402416 max 402416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402416 Ave neighs/atom = 617.202 Neighbor list builds = 0 Dangerous builds = 0 652 -2904.11741403131 eV 2.05735085414556 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:12