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 -52.616 0) to (18.6016 52.616 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.75854 4.89425 4.01172 Created 345 atoms create_atoms CPU = 0.00089407 secs 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.75854 4.89425 4.01172 Created 345 atoms create_atoms CPU = 0.000714064 secs 345 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXVVL9Nw/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 18 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 = 690 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 18 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) = 476.2 | 476.2 | 476.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -70090.417 0 -70090.417 7735.8045 52 0 -71029.441 0 -71029.441 2182.448 Loop time of 17.8747 on 1 procs for 52 steps with 690 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 = -70090.4173822 -71029.3834656 -71029.4414543 Force two-norm initial, final = 925.501 3.73605 Force max component initial, final = 188.577 0.421089 Final line search alpha, max atom move = 0.13958 0.0587756 Iterations, force evaluations = 52 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.538 | 15.538 | 15.538 | 0.0 | 86.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0093513 | 0.0093513 | 0.0093513 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.325 | 2.325 | 2.325 | 0.0 | 13.01 Other | | 0.002795 | | | 0.02 Nlocal: 690 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12939 ave 12939 max 12939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 385884 ave 385884 max 385884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 385884 Ave neighs/atom = 559.252 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 476.2 | 476.2 | 476.2 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -71029.441 0 -71029.441 2182.448 7852.865 54 0 -71029.622 0 -71029.622 168.62587 7862.2918 Loop time of 0.940211 on 1 procs for 2 steps with 690 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 = -71029.4414543 -71029.6199706 -71029.6218102 Force two-norm initial, final = 410.544 3.82521 Force max component initial, final = 331.456 0.432926 Final line search alpha, max atom move = 4.40831e-05 1.90847e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85257 | 0.85257 | 0.85257 | 0.0 | 90.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038576 | 0.00038576 | 0.00038576 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.086323 | 0.086323 | 0.086323 | 0.0 | 9.18 Other | | 0.0009353 | | | 0.10 Nlocal: 690 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11893 ave 11893 max 11893 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387235 ave 387235 max 387235 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 387235 Ave neighs/atom = 561.21 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 18 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) = 474.1 | 474.1 | 474.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -71029.622 0 -71029.622 168.62586 Loop time of 9.53674e-07 on 1 procs for 0 steps with 690 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: 690 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11893 ave 11893 max 11893 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387074 ave 387074 max 387074 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 = 387074 Ave neighs/atom = 560.977 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) = 474.1 | 474.1 | 474.1 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 -3080.1359 -71029.622 18.616099 105.23206 4.0133998 168.62587 170.86016 -3.6734807 512.9545 3.2994501 2.0448864 269.85019 Loop time of 1.90735e-06 on 1 procs for 0 steps with 690 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: 690 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11893 ave 11893 max 11893 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387074 ave 387074 max 387074 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 423916 ave 423916 max 423916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423916 Ave neighs/atom = 614.371 Neighbor list builds = 0 Dangerous builds = 0 690 -3080.13590019563 eV 2.04488642663427 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:20