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 -48.8075 0) to (24.4023 48.8075 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.95713 3.95713 2.83671 Created 298 atoms create_atoms CPU = 0.000272989 secs 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.95713 3.95713 2.83671 Created 298 atoms create_atoms CPU = 0.000126839 secs 298 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXWyhsxo/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 = 5 17 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 = 588 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 = 5 17 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) = 469.6 | 469.6 | 469.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -59916.223 0 -59916.223 -1427.6773 17 0 -60277.985 0 -60277.985 -11217.779 Loop time of 6.16276 on 1 procs for 17 steps with 588 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -59916.2233295 -60277.9694316 -60277.9848802 Force two-norm initial, final = 373.653 7.61659 Force max component initial, final = 78.3321 0.740854 Final line search alpha, max atom move = 0.067855 0.0502706 Iterations, force evaluations = 17 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5375 | 5.5375 | 5.5375 | 0.0 | 89.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024614 | 0.0024614 | 0.0024614 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.62209 | 0.62209 | 0.62209 | 0.0 | 10.09 Other | | 0.0006828 | | | 0.01 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13225 ave 13225 max 13225 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 333151 ave 333151 max 333151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 333151 Ave neighs/atom = 566.583 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 469.6 | 469.6 | 469.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -60277.985 0 -60277.985 -11217.779 6757.1448 23 0 -60283.202 0 -60283.202 -3568.0285 6726.2663 Loop time of 9.57257 on 1 procs for 6 steps with 588 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -60277.9851357 -60283.2026879 -60283.2018266 Force two-norm initial, final = 1389.47 69.09 Force max component initial, final = 1342.2 63.847 Final line search alpha, max atom move = 2.98732e-11 1.90732e-09 Iterations, force evaluations = 6 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.9175 | 8.9175 | 8.9175 | 0.0 | 93.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035594 | 0.0035594 | 0.0035594 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.64287 | 0.64287 | 0.64287 | 0.0 | 6.72 Other | | 0.008679 | | | 0.09 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13209 ave 13209 max 13209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 335576 ave 335576 max 335576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335576 Ave neighs/atom = 570.707 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 = 5 17 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) = 470.6 | 470.6 | 470.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -60283.203 0 -60283.203 -3568.0142 Loop time of 9.53674e-07 on 1 procs for 0 steps with 588 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: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13233 ave 13233 max 13233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 339460 ave 339460 max 339460 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 = 339460 Ave neighs/atom = 577.313 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) = 470.6 | 470.6 | 470.6 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 -2614.1271 -60283.204 24.412881 97.614991 2.8225296 -3568.0493 -3615.326 659.76626 -11248.596 -257.14778 2.1700903 164.35774 Loop time of 2.14577e-06 on 1 procs for 0 steps with 588 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 | | 2.146e-06 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13233 ave 13233 max 13233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 339460 ave 339460 max 339460 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 363220 ave 363220 max 363220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363220 Ave neighs/atom = 617.721 Neighbor list builds = 0 Dangerous builds = 0 588 -2614.12712319639 eV 2.17009026939524 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:16