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 -48.1343 0) to (17.0168 48.1343 5.13075) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.18792 5.4694 5.13075 Created 359 atoms create_atoms CPU = 0.00037694 secs 359 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.18792 5.4694 5.13075 Created 359 atoms create_atoms CPU = 0.000132084 secs 359 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXTzzZ2L/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 17 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 22 atoms, new total = 696 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 = 3 17 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) = 489.1 | 489.1 | 489.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -68509.445 0 -68509.445 366.57471 317 0 -70019.165 0 -70019.165 -76614.659 Loop time of 116.919 on 1 procs for 317 steps with 696 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -68509.4445242 -70019.0928003 -70019.1648638 Force two-norm initial, final = 338.178 4.46752 Force max component initial, final = 77.145 0.459046 Final line search alpha, max atom move = 0.0646877 0.0296946 Iterations, force evaluations = 317 577 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 104.35 | 104.35 | 104.35 | 0.0 | 89.25 Neigh | 0.62767 | 0.62767 | 0.62767 | 0.0 | 0.54 Comm | 0.047547 | 0.047547 | 0.047547 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 11.884 | 11.884 | 11.884 | 0.0 | 10.16 Other | | 0.01371 | | | 0.01 Nlocal: 696 ave 696 max 696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11307 ave 11307 max 11307 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 370860 ave 370860 max 370860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370860 Ave neighs/atom = 532.845 Neighbor list builds = 10 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 : 317 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 489.1 | 489.1 | 489.1 Mbytes Step Temp E_pair E_mol TotEng Press Volume 317 0 -70019.165 0 -70019.165 -76614.658 8405.1049 358 0 -70631.06 0 -70631.06 28520.497 7808.0681 Loop time of 15.3553 on 1 procs for 41 steps with 696 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 = -70019.1654126 -70631.0621293 -70631.06024 Force two-norm initial, final = 22039.7 323.48 Force max component initial, final = 16491.6 259.926 Final line search alpha, max atom move = 6.42241e-10 1.66935e-07 Iterations, force evaluations = 41 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.164 | 14.164 | 14.164 | 0.0 | 92.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0053654 | 0.0053654 | 0.0053654 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.1732 | 1.1732 | 1.1732 | 0.0 | 7.64 Other | | 0.01296 | | | 0.08 Nlocal: 696 ave 696 max 696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11286 ave 11286 max 11286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 370957 ave 370957 max 370957 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370957 Ave neighs/atom = 532.984 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 17 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) = 491.2 | 491.2 | 491.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -70631.063 0 -70631.063 28520.504 Loop time of 1.19209e-06 on 1 procs for 0 steps with 696 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 | | 1.192e-06 | | |100.00 Nlocal: 696 ave 696 max 696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11780 ave 11780 max 11780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 401421 ave 401421 max 401421 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 = 401421 Ave neighs/atom = 576.754 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) = 491.2 | 491.2 | 491.2 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 -3062.8527 -70631.062 16.334452 96.268671 4.9653977 28520.488 28898.385 1473.582 87459.895 -2238.3222 2.2452232 1063.5027 Loop time of 1.90735e-06 on 1 procs for 0 steps with 696 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 | | 1.907e-06 | | |100.00 Nlocal: 696 ave 696 max 696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11780 ave 11780 max 11780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 401421 ave 401421 max 401421 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 445242 ave 445242 max 445242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 445242 Ave neighs/atom = 639.716 Neighbor list builds = 0 Dangerous builds = 0 696 -3062.85270480103 eV 2.24522319321332 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:02:13