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 -39.2463 0) to (13.0809 39.2463 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.03111 5.03111 3.62799 Created 158 atoms create_atoms CPU = 0.000313044 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.03111 5.03111 3.62799 Created 158 atoms create_atoms CPU = 0.000134945 secs 158 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXeATOo4/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 14 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 1 atoms, new total = 315 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 14 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) = 375.5 | 375.5 | 375.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -30912.737 0 -30912.737 12054.353 281 0 -31629.361 0 -31629.361 -55861.299 Loop time of 114.355 on 1 procs for 281 steps with 315 atoms 70.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -30912.7374847 -31629.3322341 -31629.3610875 Force two-norm initial, final = 492.542 2.7054 Force max component initial, final = 104.485 0.414718 Final line search alpha, max atom move = 0.116551 0.0483359 Iterations, force evaluations = 281 516 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 104.48 | 104.48 | 104.48 | 0.0 | 91.36 Neigh | 0.53698 | 0.53698 | 0.53698 | 0.0 | 0.47 Comm | 0.054874 | 0.054874 | 0.054874 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 9.1843 | 9.1843 | 9.1843 | 0.0 | 8.03 Other | | 0.1027 | | | 0.09 Nlocal: 315 ave 315 max 315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8909 ave 8909 max 8909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 177911 ave 177911 max 177911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177911 Ave neighs/atom = 564.797 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 : 281 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 376.2 | 376.2 | 376.2 Mbytes Step Temp E_pair E_mol TotEng Press Volume 281 0 -31629.361 0 -31629.361 -55861.299 3725.0532 377 0 -31949.168 0 -31949.168 -42497.426 3724.7828 Loop time of 22.0609 on 1 procs for 96 steps with 315 atoms 66.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -31629.3610875 -31949.1427899 -31949.1675097 Force two-norm initial, final = 6623.3 80.4763 Force max component initial, final = 6352.23 56.1206 Final line search alpha, max atom move = 3.75021e-05 0.00210464 Iterations, force evaluations = 96 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.781 | 20.781 | 20.781 | 0.0 | 94.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064662 | 0.0064662 | 0.0064662 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.2188 | 1.2188 | 1.2188 | 0.0 | 5.52 Other | | 0.05492 | | | 0.25 Nlocal: 315 ave 315 max 315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8973 ave 8973 max 8973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 177845 ave 177845 max 177845 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177845 Ave neighs/atom = 564.587 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 14 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) = 374.1 | 374.1 | 374.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -31949.168 0 -31949.168 -42497.426 Loop time of 9.53674e-07 on 1 procs for 0 steps with 315 atoms 419.4% 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: 315 ave 315 max 315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8183 ave 8183 max 8183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178923 ave 178923 max 178923 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 = 178923 Ave neighs/atom = 568.01 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) = 374.1 | 374.1 | 374.1 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 -1385.447 -31949.168 12.219667 78.492649 3.8834043 -42497.426 -43060.517 977.87653 -130829.81 670.38177 2.1711778 178.8018 Loop time of 1.90735e-06 on 1 procs for 0 steps with 315 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: 315 ave 315 max 315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8183 ave 8183 max 8183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178923 ave 178923 max 178923 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191290 ave 191290 max 191290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191290 Ave neighs/atom = 607.27 Neighbor list builds = 0 Dangerous builds = 0 315 -1385.44701942859 eV 2.17117782313507 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:02:18