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 = 2.83671 2.83671 2.83671 Created orthogonal box = (0 -28.9317 0) to (25.0532 28.9317 4.91333) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.49672 4.4506 4.91333 Created 315 atoms create_atoms CPU = 0.000226021 secs 315 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.49672 4.4506 4.91333 Created 316 atoms create_atoms CPU = 0.000139952 secs 316 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXHnST14/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 = 5 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 9 atoms, new total = 622 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 = 5 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) = 349.5 | 349.5 | 349.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -62477.629 0 -62477.629 5437.3459 46 0 -63400.768 0 -63400.768 -5883.532 Loop time of 14.9419 on 1 procs for 46 steps with 622 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -62477.6288674 -63400.7341005 -63400.7684669 Force two-norm initial, final = 773.906 4.25251 Force max component initial, final = 193.753 0.511228 Final line search alpha, max atom move = 0.128497 0.0656913 Iterations, force evaluations = 46 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.232 | 13.232 | 13.232 | 0.0 | 88.55 Neigh | 0.06665 | 0.06665 | 0.06665 | 0.0 | 0.45 Comm | 0.0061803 | 0.0061803 | 0.0061803 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.6354 | 1.6354 | 1.6354 | 0.0 | 10.94 Other | | 0.001929 | | | 0.01 Nlocal: 622 ave 622 max 622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9465 ave 9465 max 9465 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 342182 ave 342182 max 342182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 342182 Ave neighs/atom = 550.132 Neighbor list builds = 1 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 349.6 | 349.6 | 349.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -63400.768 0 -63400.768 -5883.5338 7122.6803 48 0 -63401.192 0 -63401.192 -5673.8935 7121.7332 Loop time of 0.641665 on 1 procs for 2 steps with 622 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -63400.7677866 -63401.1628058 -63401.192064 Force two-norm initial, final = 483.791 5.34009 Force max component initial, final = 358.787 2.14085 Final line search alpha, max atom move = 7.88866e-06 1.68884e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58588 | 0.58588 | 0.58588 | 0.0 | 91.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026298 | 0.00026298 | 0.00026298 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.055118 | 0.055118 | 0.055118 | 0.0 | 8.59 Other | | 0.0004089 | | | 0.06 Nlocal: 622 ave 622 max 622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9445 ave 9445 max 9445 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 342590 ave 342590 max 342590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 342590 Ave neighs/atom = 550.788 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 = 5 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) = 349.7 | 349.7 | 349.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -63401.192 0 -63401.192 -5673.8868 Loop time of 2.14577e-06 on 1 procs for 0 steps with 622 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 | | 2.146e-06 | | |100.00 Nlocal: 622 ave 622 max 622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9439 ave 9439 max 9439 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 342713 ave 342713 max 342713 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 = 342713 Ave neighs/atom = 550.986 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) = 349.7 | 349.7 | 349.7 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 -2749.3359 -63401.193 25.01434 57.863497 4.9203045 -5673.9128 -5749.0921 17.73944 -17285.902 20.886005 2.1414569 480.58534 Loop time of 1.90735e-06 on 1 procs for 0 steps with 622 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: 622 ave 622 max 622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9439 ave 9439 max 9439 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 342713 ave 342713 max 342713 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 383856 ave 383856 max 383856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383856 Ave neighs/atom = 617.132 Neighbor list builds = 0 Dangerous builds = 0 622 -2749.33592867101 eV 2.14145689317756 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:16