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 -33.0843 0) to (16.5407 33.0843 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.89194 3.89194 2.83671 Created 138 atoms create_atoms CPU = 0.000249863 secs 138 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.89194 3.89194 2.83671 Created 138 atoms create_atoms CPU = 8.70228e-05 secs 138 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXlLi3oK/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 12 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 4 atoms, new total = 272 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 12 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) = 299 | 299 | 299 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -27495.284 0 -27495.284 4102.5473 27 0 -27911.978 0 -27911.978 -2198.843 Loop time of 6.25871 on 1 procs for 27 steps with 272 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -27495.2836407 -27911.9532264 -27911.97826 Force two-norm initial, final = 592.85 2.56097 Force max component initial, final = 162.738 0.380142 Final line search alpha, max atom move = 0.132197 0.0502536 Iterations, force evaluations = 27 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7282 | 5.7282 | 5.7282 | 0.0 | 91.52 Neigh | 0.050586 | 0.050586 | 0.050586 | 0.0 | 0.81 Comm | 0.0037053 | 0.0037053 | 0.0037053 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.47532 | 0.47532 | 0.47532 | 0.0 | 7.59 Other | | 0.0009441 | | | 0.02 Nlocal: 272 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8322 ave 8322 max 8322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 158449 ave 158449 max 158449 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158449 Ave neighs/atom = 582.533 Neighbor list builds = 1 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 299 | 299 | 299 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -27911.978 0 -27911.978 -2198.843 3104.7199 33 0 -27913.475 0 -27913.475 3889.1422 3093.5077 Loop time of 0.968957 on 1 procs for 6 steps with 272 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -27911.97826 -27913.4687339 -27913.4748052 Force two-norm initial, final = 582.138 6.71949 Force max component initial, final = 580.559 4.31757 Final line search alpha, max atom move = 4.06582e-05 0.000175545 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9145 | 0.9145 | 0.9145 | 0.0 | 94.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051355 | 0.00051355 | 0.00051355 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.052796 | 0.052796 | 0.052796 | 0.0 | 5.45 Other | | 0.001146 | | | 0.12 Nlocal: 272 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8301 ave 8301 max 8301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 158211 ave 158211 max 158211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158211 Ave neighs/atom = 581.658 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 = 3 12 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) = 299.2 | 299.2 | 299.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -27913.475 0 -27913.475 3889.1422 Loop time of 1.90735e-06 on 1 procs for 0 steps with 272 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: 272 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8307 ave 8307 max 8307 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160435 ave 160435 max 160435 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 = 160435 Ave neighs/atom = 589.835 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) = 299.2 | 299.2 | 299.2 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 -1210.4428 -27913.475 16.567795 66.168625 2.8218529 3889.1422 3940.6733 -88.045696 12006.526 -96.460159 2.1577439 159.75817 Loop time of 1.90735e-06 on 1 procs for 0 steps with 272 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: 272 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8307 ave 8307 max 8307 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160435 ave 160435 max 160435 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 169836 ave 169836 max 169836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169836 Ave neighs/atom = 624.397 Neighbor list builds = 0 Dangerous builds = 0 272 -1210.44282167961 eV 2.15774386050001 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:08