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 -58.5032 0) to (29.2498 58.5032 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.94996 4.94996 3.62799 Created 522 atoms create_atoms CPU = 0.0245731 secs 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.94996 4.94996 3.62799 Created 522 atoms create_atoms CPU = 0.000351906 secs 522 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXi1TUpq/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 20 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 2 atoms, new total = 1042 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 = 5 20 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) = 760.6 | 760.6 | 760.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -103073.97 0 -103073.97 5129.3912 186 0 -104496.13 0 -104496.13 -50458.515 Loop time of 169.97 on 1 procs for 186 steps with 1042 atoms 70.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -103073.972733 -104496.030978 -104496.128206 Force two-norm initial, final = 589.415 4.84653 Force max component initial, final = 115.854 0.45995 Final line search alpha, max atom move = 0.077598 0.0356912 Iterations, force evaluations = 186 335 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 150.16 | 150.16 | 150.16 | 0.0 | 88.34 Neigh | 1.0772 | 1.0772 | 1.0772 | 0.0 | 0.63 Comm | 0.072382 | 0.072382 | 0.072382 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 18.646 | 18.646 | 18.646 | 0.0 | 10.97 Other | | 0.01531 | | | 0.01 Nlocal: 1042 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17214 ave 17214 max 17214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 569913 ave 569913 max 569913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 569913 Ave neighs/atom = 546.941 Neighbor list builds = 6 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 : 186 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 760.6 | 760.6 | 760.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 186 0 -104496.13 0 -104496.13 -50458.515 12416.466 273 0 -105328.1 0 -105328.1 -39446.666 12355.853 Loop time of 40.2145 on 1 procs for 87 steps with 1042 atoms 71.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -104496.128206 -105328.056362 -105328.104234 Force two-norm initial, final = 16597.1 172.057 Force max component initial, final = 16128.2 102.27 Final line search alpha, max atom move = 1.02491e-05 0.00104818 Iterations, force evaluations = 87 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.688 | 36.688 | 36.688 | 0.0 | 91.23 Neigh | 0.10179 | 0.10179 | 0.10179 | 0.0 | 0.25 Comm | 0.022782 | 0.022782 | 0.022782 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.3559 | 3.3559 | 3.3559 | 0.0 | 8.35 Other | | 0.04643 | | | 0.12 Nlocal: 1042 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15177 ave 15177 max 15177 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 578156 ave 578156 max 578156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578156 Ave neighs/atom = 554.852 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 = 5 20 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) = 756.4 | 756.4 | 756.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -105328.1 0 -105328.1 -39446.666 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1042 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: 1042 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15464 ave 15464 max 15464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 575456 ave 575456 max 575456 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 = 575456 Ave neighs/atom = 552.261 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) = 756.4 | 756.4 | 756.4 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 -4567.4589 -105328.1 27.26772 117.00637 3.8727047 -39446.666 -39969.334 -432.00292 -118862.14 -613.85636 2.1602023 662.79742 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1042 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: 1042 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15464 ave 15464 max 15464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 575456 ave 575456 max 575456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 633784 ave 633784 max 633784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 633784 Ave neighs/atom = 608.238 Neighbor list builds = 0 Dangerous builds = 0 1042 -4567.45885563473 eV 2.16020229101853 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:03:33