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 -40.12 0) to (20.0586 40.12 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.20937 3.20937 2.83671 Created 202 atoms create_atoms CPU = 0.000319004 secs 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.20937 3.20937 2.83671 Created 202 atoms create_atoms CPU = 0.000145912 secs 202 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXsqqfr9/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 14 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 8 atoms, new total = 396 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 14 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) = 343.1 | 343.1 | 343.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -40514.509 0 -40514.509 -3196.1119 16 0 -40725.528 0 -40725.528 -10836.835 Loop time of 4.65259 on 1 procs for 16 steps with 396 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -40514.5091009 -40725.5025722 -40725.5282484 Force two-norm initial, final = 262.034 2.2416 Force max component initial, final = 58.4812 0.2264 Final line search alpha, max atom move = 0.207535 0.0469859 Iterations, force evaluations = 16 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2374 | 4.2374 | 4.2374 | 0.0 | 91.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020566 | 0.0020566 | 0.0020566 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.41251 | 0.41251 | 0.41251 | 0.0 | 8.87 Other | | 0.0005937 | | | 0.01 Nlocal: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9621 ave 9621 max 9621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224622 ave 224622 max 224622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224622 Ave neighs/atom = 567.227 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 : 16 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 343.1 | 343.1 | 343.1 Mbytes Step Temp E_pair E_mol TotEng Press Volume 16 0 -40725.528 0 -40725.528 -10836.835 4565.6958 20 0 -40727.503 0 -40727.503 -1666.6446 4540.0483 Loop time of 0.978875 on 1 procs for 4 steps with 396 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -40725.5282484 -40727.4865892 -40727.5027911 Force two-norm initial, final = 994.809 29.0867 Force max component initial, final = 779.818 28.4901 Final line search alpha, max atom move = 1.24181e-05 0.000353792 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91595 | 0.91595 | 0.91595 | 0.0 | 93.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047374 | 0.00047374 | 0.00047374 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.061507 | 0.061507 | 0.061507 | 0.0 | 6.28 Other | | 0.0009432 | | | 0.10 Nlocal: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9711 ave 9711 max 9711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 225859 ave 225859 max 225859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225859 Ave neighs/atom = 570.351 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 14 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) = 343.3 | 343.3 | 343.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -40727.503 0 -40727.503 -1666.6446 Loop time of 1.90735e-06 on 1 procs for 0 steps with 396 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: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9711 ave 9711 max 9711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 227811 ave 227811 max 227811 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 = 227811 Ave neighs/atom = 575.28 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) = 343.3 | 343.3 | 343.3 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 -1766.1117 -40727.503 20.013812 80.240038 2.8270893 -1666.6446 -1688.7276 435.01467 -5440.675 -60.522528 2.297107 139.12959 Loop time of 9.53674e-07 on 1 procs for 0 steps with 396 atoms 419.4% 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: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9711 ave 9711 max 9711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 227811 ave 227811 max 227811 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 242776 ave 242776 max 242776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242776 Ave neighs/atom = 613.071 Neighbor list builds = 0 Dangerous builds = 0 396 -1766.11166264366 eV 2.29710703821087 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:06