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 -28.37 0) to (14.1836 28.37 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9714 3.9714 2.83671 Created 101 atoms create_atoms CPU = 0.000198126 secs 101 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9714 3.9714 2.83671 Created 101 atoms create_atoms CPU = 7.29561e-05 secs 101 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXKKTJAs/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 10 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 2 atoms, new total = 200 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 10 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) = 255.7 | 255.7 | 255.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20182.869 0 -20182.869 4339.3562 34 0 -20532.393 0 -20532.393 -3002.4125 Loop time of 6.4081 on 1 procs for 34 steps with 200 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20182.8688437 -20532.3736549 -20532.393154 Force two-norm initial, final = 570.238 2.36241 Force max component initial, final = 200.734 0.376873 Final line search alpha, max atom move = 0.139392 0.052533 Iterations, force evaluations = 34 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8862 | 5.8862 | 5.8862 | 0.0 | 91.86 Neigh | 0.050437 | 0.050437 | 0.050437 | 0.0 | 0.79 Comm | 0.0034964 | 0.0034964 | 0.0034964 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.46706 | 0.46706 | 0.46706 | 0.0 | 7.29 Other | | 0.0008638 | | | 0.01 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7104 ave 7104 max 7104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117756 ave 117756 max 117756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117756 Ave neighs/atom = 588.78 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 255.7 | 255.7 | 255.7 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -20532.393 0 -20532.393 -3002.4125 2282.9148 40 0 -20533.567 0 -20533.567 2679.9133 2275.1867 Loop time of 0.792933 on 1 procs for 6 steps with 200 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 = -20532.393154 -20533.5549104 -20533.5665194 Force two-norm initial, final = 427.074 6.03684 Force max component initial, final = 427.022 3.85087 Final line search alpha, max atom move = 3.55422e-05 0.000136869 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75347 | 0.75347 | 0.75347 | 0.0 | 95.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042152 | 0.00042152 | 0.00042152 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.03816 | 0.03816 | 0.03816 | 0.0 | 4.81 Other | | 0.0008767 | | | 0.11 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7104 ave 7104 max 7104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117315 ave 117315 max 117315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117315 Ave neighs/atom = 586.575 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 10 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) = 255.9 | 255.9 | 255.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20533.567 0 -20533.567 2679.9133 Loop time of 2.14577e-06 on 1 procs for 0 steps with 200 atoms 139.8% 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: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7104 ave 7104 max 7104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118527 ave 118527 max 118527 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 = 118527 Ave neighs/atom = 592.635 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) = 255.9 | 255.9 | 255.9 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 -890.41971 -20533.567 14.212403 56.739937 2.8213741 2679.9133 2715.4221 -112.56282 8375.7867 -116.95755 2.1519466 87.761526 Loop time of 1.19209e-06 on 1 procs for 0 steps with 200 atoms 251.7% 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 | | 1.192e-06 | | |100.00 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7104 ave 7104 max 7104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118527 ave 118527 max 118527 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 124850 ave 124850 max 124850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124850 Ave neighs/atom = 624.25 Neighbor list builds = 0 Dangerous builds = 0 200 -890.419711998723 eV 2.151946617761 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:07