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 -36.1083 0) to (8.51014 36.1083 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.72786 4.01172 4.01172 Created 110 atoms create_atoms CPU = 0.000356913 secs 110 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.72786 4.01172 4.01172 Created 110 atoms create_atoms CPU = 0.000215054 secs 110 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXb52t4j/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 = 2 13 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 = 216 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 = 2 13 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) = 264.7 | 264.7 | 264.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -21912.666 0 -21912.666 1467.5216 15 0 -22168.323 0 -22168.323 -2544.8449 Loop time of 3.08303 on 1 procs for 15 steps with 216 atoms 86.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -21912.6656039 -22168.3089106 -22168.3230062 Force two-norm initial, final = 477.799 1.80258 Force max component initial, final = 99.6544 0.368043 Final line search alpha, max atom move = 0.213584 0.0786079 Iterations, force evaluations = 15 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8155 | 2.8155 | 2.8155 | 0.0 | 91.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018015 | 0.0018015 | 0.0018015 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.26521 | 0.26521 | 0.26521 | 0.0 | 8.60 Other | | 0.0004923 | | | 0.02 Nlocal: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7456 ave 7456 max 7456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125550 ave 125550 max 125550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125550 Ave neighs/atom = 581.25 Neighbor list builds = 0 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 : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 264.8 | 264.8 | 264.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -22168.323 0 -22168.323 -2544.8449 2465.4951 18 0 -22168.63 0 -22168.63 -3588.2071 2467.0332 Loop time of 0.614377 on 1 procs for 3 steps with 216 atoms 80.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -22168.3230062 -22168.6256251 -22168.6304084 Force two-norm initial, final = 227.386 4.08069 Force max component initial, final = 197.539 2.65806 Final line search alpha, max atom move = 4.42185e-05 0.000117535 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57524 | 0.57524 | 0.57524 | 0.0 | 93.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.038299 | 0.038299 | 0.038299 | 0.0 | 6.23 Other | | 0.000617 | | | 0.10 Nlocal: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7456 ave 7456 max 7456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126302 ave 126302 max 126302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126302 Ave neighs/atom = 584.731 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 = 2 13 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) = 264.9 | 264.9 | 264.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -22168.63 0 -22168.63 -3588.2071 Loop time of 9.53674e-07 on 1 procs for 0 steps with 216 atoms 314.6% 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: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7456 ave 7456 max 7456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126274 ave 126274 max 126274 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 = 126274 Ave neighs/atom = 584.602 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) = 264.9 | 264.9 | 264.9 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 -961.32279 -22168.63 8.4967431 72.216602 4.0205498 -3588.2071 -3635.7508 61.098534 -11043.372 75.021432 2.0924682 171.08063 Loop time of 1.90735e-06 on 1 procs for 0 steps with 216 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: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7456 ave 7456 max 7456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126274 ave 126274 max 126274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132956 ave 132956 max 132956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132956 Ave neighs/atom = 615.537 Neighbor list builds = 0 Dangerous builds = 0 216 -961.322792363922 eV 2.09246815336925 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:04