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 = 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 = 0.000205994 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 = 6.91414e-05 secs 206 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXWZPM4j/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: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 = 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) = 307.8 | 307.8 | 307.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -40984.677 0 -40984.677 5213.3713 20 0 -41585.015 0 -41585.015 -850.11352 Loop time of 3.38316 on 1 procs for 20 steps with 408 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 = -40984.6766305 -41585.0046329 -41585.0151573 Force two-norm initial, final = 808.91 8.89669 Force max component initial, final = 233.47 1.14487 Final line search alpha, max atom move = 0.0506192 0.0579525 Iterations, force evaluations = 20 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9892 | 2.9892 | 2.9892 | 0.0 | 88.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015037 | 0.0015037 | 0.0015037 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.39194 | 0.39194 | 0.39194 | 0.0 | 11.59 Other | | 0.000494 | | | 0.01 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8440 ave 8440 max 8440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228882 ave 228882 max 228882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228882 Ave neighs/atom = 560.985 Neighbor list builds = 0 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 307.8 | 307.8 | 307.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -41585.016 0 -41585.016 -850.11608 4657.1416 21 0 -41585.013 0 -41585.013 -850.12775 4657.1416 Loop time of 3.55412 on 1 procs for 1 steps with 408 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 = -41585.0162425 -41585.0162425 -41585.0125613 Force two-norm initial, final = 158.213 158.212 Force max component initial, final = 157.808 157.807 Final line search alpha, max atom move = 4.83461e-11 7.62934e-09 Iterations, force evaluations = 1 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2505 | 3.2505 | 3.2505 | 0.0 | 91.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014398 | 0.0014398 | 0.0014398 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.29876 | 0.29876 | 0.29876 | 0.0 | 8.41 Other | | 0.003437 | | | 0.10 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8419 ave 8419 max 8419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230502 ave 230502 max 230502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230502 Ave neighs/atom = 564.956 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 | 308 | 308 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -41585.017 0 -41585.017 -850.12867 Loop time of 9.53674e-07 on 1 procs for 0 steps with 408 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: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8419 ave 8419 max 8419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230502 ave 230502 max 230502 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 = 230502 Ave neighs/atom = 564.956 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 | 308 | 308 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 -1803.2969 -41585.016 20.258184 57.304471 4.0117183 -850.11178 -861.37576 104.22576 -5042.596 2354.2429 2.1160435 314.52328 Loop time of 9.53674e-07 on 1 procs for 0 steps with 408 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: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8419 ave 8419 max 8419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230502 ave 230502 max 230502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 252000 ave 252000 max 252000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252000 Ave neighs/atom = 617.647 Neighbor list builds = 0 Dangerous builds = 0 408 -1803.29693645814 eV 2.11604348633697 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:07