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 = 3.62799 3.62799 3.62799 Created orthogonal box = (0 -44.8794 0) to (14.9586 44.8794 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.39958 4.39958 3.62799 Created 206 atoms create_atoms CPU = 0.000277042 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.39958 4.39958 3.62799 Created 206 atoms create_atoms CPU = 0.000109196 secs 206 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXHMTfnK/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 = 3 15 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 5 atoms, new total = 407 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 = 3 15 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) = 442.6 | 442.6 | 442.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -40105.035 0 -40105.035 4701.2884 142 0 -40695.518 0 -40695.518 -47033.496 Loop time of 46.4674 on 1 procs for 142 steps with 407 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 = -40105.0346843 -40695.4787305 -40695.5183912 Force two-norm initial, final = 420.978 3.09821 Force max component initial, final = 86.7437 0.38659 Final line search alpha, max atom move = 0.106239 0.041071 Iterations, force evaluations = 142 267 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42.109 | 42.109 | 42.109 | 0.0 | 90.62 Neigh | 0.18381 | 0.18381 | 0.18381 | 0.0 | 0.40 Comm | 0.023545 | 0.023545 | 0.023545 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 4.1456 | 4.1456 | 4.1456 | 0.0 | 8.92 Other | | 0.005961 | | | 0.01 Nlocal: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10369 ave 10369 max 10369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 227038 ave 227038 max 227038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227038 Ave neighs/atom = 557.833 Neighbor list builds = 3 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 : 142 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 442.6 | 442.6 | 442.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 142 0 -40695.518 0 -40695.518 -47033.496 4871.1669 439 0 -41264.116 0 -41264.116 -18533.977 4715.8769 Loop time of 45.3255 on 1 procs for 297 steps with 407 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 = -40695.5183912 -41264.0812022 -41264.1159319 Force two-norm initial, final = 5458.78 91.4591 Force max component initial, final = 5381.32 45.168 Final line search alpha, max atom move = 1.71885e-05 0.000776371 Iterations, force evaluations = 297 309 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 41.937 | 41.937 | 41.937 | 0.0 | 92.52 Neigh | 0.055912 | 0.055912 | 0.055912 | 0.0 | 0.12 Comm | 0.017064 | 0.017064 | 0.017064 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.2652 | 3.2652 | 3.2652 | 0.0 | 7.20 Other | | 0.05032 | | | 0.11 Nlocal: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9435 ave 9435 max 9435 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 232297 ave 232297 max 232297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232297 Ave neighs/atom = 570.754 Neighbor list builds = 1 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 = 3 15 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) = 442.1 | 442.1 | 442.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -41264.116 0 -41264.116 -18533.977 Loop time of 1.90735e-06 on 1 procs for 0 steps with 407 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: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9750 ave 9750 max 9750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 233391 ave 233391 max 233391 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 = 233391 Ave neighs/atom = 573.442 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) = 442.1 | 442.1 | 442.1 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 -1789.3814 -41264.116 13.260382 89.758737 3.9621389 -18533.977 -18779.553 589.89484 -57641.692 713.13949 2.1704019 629.45471 Loop time of 1.90735e-06 on 1 procs for 0 steps with 407 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: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9750 ave 9750 max 9750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 233391 ave 233391 max 233391 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 251254 ave 251254 max 251254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251254 Ave neighs/atom = 617.332 Neighbor list builds = 0 Dangerous builds = 0 407 -1789.38141063693 eV 2.17040188312537 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:32