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 = 3.62799 3.62799 3.62799 Created orthogonal box = (0 -36.2835 0) to (18.1399 36.2835 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.07918 5.07918 3.62799 Created 202 atoms create_atoms CPU = 0.000185966 secs 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.07918 5.07918 3.62799 Created 202 atoms create_atoms CPU = 5.6982e-05 secs 202 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX4I3eHY/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 13 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 14 atoms, new total = 390 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 13 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) = 357.3 | 357.3 | 357.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -38113.155 0 -38113.155 -3895.9884 46 0 -38606.975 0 -38606.975 -43447.945 Loop time of 20.8492 on 1 procs for 46 steps with 390 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -38113.1551125 -38606.944886 -38606.9749892 Force two-norm initial, final = 174.203 21.4032 Force max component initial, final = 46.3592 3.87501 Final line search alpha, max atom move = 0.000158254 0.000613238 Iterations, force evaluations = 46 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.027 | 19.027 | 19.027 | 0.0 | 91.26 Neigh | 0.091666 | 0.091666 | 0.091666 | 0.0 | 0.44 Comm | 0.0082786 | 0.0082786 | 0.0082786 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.7203 | 1.7203 | 1.7203 | 0.0 | 8.25 Other | | 0.001996 | | | 0.01 Nlocal: 390 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8619 ave 8619 max 8619 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 214675 ave 214675 max 214675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214675 Ave neighs/atom = 550.449 Neighbor list builds = 2 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 357.4 | 357.4 | 357.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -38606.975 0 -38606.975 -43447.951 4775.7453 274 0 -39259.537 0 -39259.537 44550.009 4275.5009 Loop time of 43.4711 on 1 procs for 228 steps with 390 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -38606.975167 -39259.5345755 -39259.5369454 Force two-norm initial, final = 3018.02 182.999 Force max component initial, final = 2651.18 104.956 Final line search alpha, max atom move = 1.81726e-11 1.90732e-09 Iterations, force evaluations = 228 266 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.734 | 40.734 | 40.734 | 0.0 | 93.70 Neigh | 0.099979 | 0.099979 | 0.099979 | 0.0 | 0.23 Comm | 0.015493 | 0.015493 | 0.015493 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.583 | 2.583 | 2.583 | 0.0 | 5.94 Other | | 0.03889 | | | 0.09 Nlocal: 390 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10131 ave 10131 max 10131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 238546 ave 238546 max 238546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238546 Ave neighs/atom = 611.656 Neighbor list builds = 2 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 13 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) = 362.4 | 362.4 | 362.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -39259.534 0 -39259.534 44549.988 Loop time of 9.53674e-07 on 1 procs for 0 steps with 390 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: 390 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10200 ave 10200 max 10200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 238640 ave 238640 max 238640 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 = 238640 Ave neighs/atom = 611.897 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) = 362.4 | 362.4 | 362.4 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 -1702.4545 -39259.534 20.100991 72.567028 2.931097 44549.985 45140.272 835.90363 133207 1377.9103 2.0743035 328.38027 Loop time of 9.53674e-07 on 1 procs for 0 steps with 390 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: 390 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10200 ave 10200 max 10200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 238640 ave 238640 max 238640 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 254788 ave 254788 max 254788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254788 Ave neighs/atom = 653.303 Neighbor list builds = 0 Dangerous builds = 0 390 -1702.45451792661 eV 2.0743034920502 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:05