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 -28.6522 0) to (20.2582 28.6522 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.57497 4.49402 4.01172 Created 206 atoms create_atoms CPU = 0.000414133 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.57497 4.49402 4.01172 Created 206 atoms create_atoms CPU = 0.000261068 secs 206 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXVvc1zR/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 10 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 = 408 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 10 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) = 308.6 | 308.6 | 308.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -41104.423 0 -41104.423 5136.8601 15 0 -41806.995 0 -41806.995 -1608.1876 Loop time of 3.13641 on 1 procs for 15 steps with 408 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -41104.4234806 -41806.965631 -41806.9951697 Force two-norm initial, final = 920.952 2.47357 Force max component initial, final = 198.726 0.26729 Final line search alpha, max atom move = 0.140786 0.0376306 Iterations, force evaluations = 15 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7555 | 2.7555 | 2.7555 | 0.0 | 87.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017147 | 0.0017147 | 0.0017147 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.37861 | 0.37861 | 0.37861 | 0.0 | 12.07 Other | | 0.0005691 | | | 0.02 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8398 ave 8398 max 8398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228796 ave 228796 max 228796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228796 Ave neighs/atom = 560.775 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 : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 308.7 | 308.7 | 308.7 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -41806.995 0 -41806.995 -1608.1876 4657.1416 16 0 -41807.027 0 -41807.027 -1012.6423 4655.4185 Loop time of 0.35834 on 1 procs for 1 steps with 408 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 = -41806.9951697 -41806.9951697 -41807.0265562 Force two-norm initial, final = 91.492 29.3416 Force max component initial, final = 84.4666 27.0142 Final line search alpha, max atom move = 1.1839e-05 0.000319821 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32739 | 0.32739 | 0.32739 | 0.0 | 91.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013804 | 0.00013804 | 0.00013804 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.030485 | 0.030485 | 0.030485 | 0.0 | 8.51 Other | | 0.00033 | | | 0.09 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8398 ave 8398 max 8398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230523 ave 230523 max 230523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230523 Ave neighs/atom = 565.007 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 10 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) = 308.8 | 308.8 | 308.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -41807.027 0 -41807.027 -1012.6423 Loop time of 1.19209e-06 on 1 procs for 0 steps with 408 atoms 251.7% 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 | | 1.192e-06 | | |100.00 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8405 ave 8405 max 8405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230564 ave 230564 max 230564 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 = 230564 Ave neighs/atom = 565.108 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) = 308.8 | 308.8 | 308.8 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 -1812.9242 -41807.027 20.245373 57.304471 4.0127717 -1012.6423 -1026.0598 166.84579 -3648.2883 403.26302 2.1229687 319.88624 Loop time of 1.90735e-06 on 1 procs for 0 steps with 408 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 | | 1.907e-06 | | |100.00 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8405 ave 8405 max 8405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230564 ave 230564 max 230564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 252060 ave 252060 max 252060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252060 Ave neighs/atom = 617.794 Neighbor list builds = 0 Dangerous builds = 0 408 -1812.92424335755 eV 2.12296870872202 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:04