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 -44.4372 0) to (5.13075 44.4372 6.28386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.13075 5.92448 6.28386 Created 122 atoms create_atoms CPU = 0.000494957 secs 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.13075 5.92448 6.28386 Created 122 atoms create_atoms CPU = 0.000277042 secs 122 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXxucxAf/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 = 1 15 2 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 5 atoms, new total = 239 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 = 1 15 2 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) = 330.8 | 330.8 | 330.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -23305.932 0 -23305.932 11718.776 296 0 -23987.587 0 -23987.587 -58739.797 Loop time of 97.782 on 1 procs for 296 steps with 239 atoms 74.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -23305.9318548 -23987.5639048 -23987.5872538 Force two-norm initial, final = 493.207 2.50615 Force max component initial, final = 131.684 0.362835 Final line search alpha, max atom move = 0.0758331 0.0275149 Iterations, force evaluations = 296 554 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 90.109 | 90.109 | 90.109 | 0.0 | 92.15 Neigh | 0.59025 | 0.59025 | 0.59025 | 0.0 | 0.60 Comm | 0.041149 | 0.041149 | 0.041149 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 7.0313 | 7.0313 | 7.0313 | 0.0 | 7.19 Other | | 0.01004 | | | 0.01 Nlocal: 239 ave 239 max 239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8042 ave 8042 max 8042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137102 ave 137102 max 137102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137102 Ave neighs/atom = 573.649 Neighbor list builds = 9 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 : 296 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 331.6 | 331.6 | 331.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 296 0 -23987.587 0 -23987.587 -58739.797 2865.3946 317 0 -24017.26 0 -24017.26 -22710.592 2781.26 Loop time of 3.87067 on 1 procs for 21 steps with 239 atoms 74.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -23987.5872538 -24017.239571 -24017.2596513 Force two-norm initial, final = 2650.47 23.3541 Force max component initial, final = 2286 8.77032 Final line search alpha, max atom move = 1.90332e-05 0.000166927 Iterations, force evaluations = 21 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6577 | 3.6577 | 3.6577 | 0.0 | 94.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001687 | 0.001687 | 0.001687 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.20812 | 0.20812 | 0.20812 | 0.0 | 5.38 Other | | 0.00319 | | | 0.08 Nlocal: 239 ave 239 max 239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8059 ave 8059 max 8059 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137050 ave 137050 max 137050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137050 Ave neighs/atom = 573.431 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 = 1 15 2 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) = 331.8 | 331.8 | 331.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -24017.26 0 -24017.26 -22710.592 Loop time of 1.90735e-06 on 1 procs for 0 steps with 239 atoms 367.0% 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 | | 1.907e-06 | | |100.00 Nlocal: 239 ave 239 max 239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8270 ave 8270 max 8270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141589 ave 141589 max 141589 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 = 141589 Ave neighs/atom = 592.423 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) = 331.8 | 331.8 | 331.8 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 -1041.4869 -24017.26 5.0249472 88.874464 6.2277774 -22710.592 -23011.507 214.56812 -69413.765 164.67507 2.2799902 446.67334 Loop time of 2.14577e-06 on 1 procs for 0 steps with 239 atoms 186.4% 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 | | 2.146e-06 | | |100.00 Nlocal: 239 ave 239 max 239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8270 ave 8270 max 8270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141589 ave 141589 max 141589 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 148452 ave 148452 max 148452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148452 Ave neighs/atom = 621.138 Neighbor list builds = 0 Dangerous builds = 0 239 -1041.4869429248 eV 2.27999016060985 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:42