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 -45.7435 0) to (22.8703 45.7435 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.87036 3.87036 2.83671 Created 261 atoms create_atoms CPU = 0.000169992 secs 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.87036 3.87036 2.83671 Created 261 atoms create_atoms CPU = 5.98431e-05 secs 261 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXYGmdAO/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 = 4 16 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 = 518 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 = 4 16 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) = 434.8 | 434.8 | 434.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -52614.942 0 -52614.942 832.45056 19 0 -53020.613 0 -53020.613 -6229.6408 Loop time of 26.7616 on 1 procs for 19 steps with 518 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -52614.9416332 -53020.6132058 -53020.6133257 Force two-norm initial, final = 514.542 7.50696 Force max component initial, final = 149.182 1.05781 Final line search alpha, max atom move = 1.78707e-10 1.89039e-10 Iterations, force evaluations = 19 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.207 | 24.207 | 24.207 | 0.0 | 90.45 Neigh | 0.087959 | 0.087959 | 0.087959 | 0.0 | 0.33 Comm | 0.011134 | 0.011134 | 0.011134 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.4535 | 2.4535 | 2.4535 | 0.0 | 9.17 Other | | 0.002331 | | | 0.01 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12187 ave 12187 max 12187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296740 ave 296740 max 296740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296740 Ave neighs/atom = 572.857 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 434.8 | 434.8 | 434.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -53020.614 0 -53020.614 -6229.6476 5935.353 24 0 -53024.075 0 -53024.075 -437.01866 5914.9646 Loop time of 1.44927 on 1 procs for 5 steps with 518 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -53020.6136311 -53024.0462377 -53024.0754184 Force two-norm initial, final = 1013.31 29.7981 Force max component initial, final = 996.994 22.8975 Final line search alpha, max atom move = 9.79913e-06 0.000224376 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3507 | 1.3507 | 1.3507 | 0.0 | 93.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052881 | 0.00052881 | 0.00052881 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.096951 | 0.096951 | 0.096951 | 0.0 | 6.69 Other | | 0.001136 | | | 0.08 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12187 ave 12187 max 12187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296625 ave 296625 max 296625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296625 Ave neighs/atom = 572.635 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 = 4 16 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) = 435 | 435 | 435 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -53024.075 0 -53024.075 -437.00998 Loop time of 9.53674e-07 on 1 procs for 0 steps with 518 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 | | 9.537e-07 | | |100.00 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12197 ave 12197 max 12197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 300111 ave 300111 max 300111 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 = 300111 Ave neighs/atom = 579.365 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) = 435 | 435 | 435 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 -2299.3415 -53024.075 22.89411 91.486924 2.8240304 -437.01177 -442.80218 -203.92555 -856.72531 -267.75568 2.1131592 228.81251 Loop time of 9.53674e-07 on 1 procs for 0 steps with 518 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 | | 9.537e-07 | | |100.00 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12197 ave 12197 max 12197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 300111 ave 300111 max 300111 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320624 ave 320624 max 320624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320624 Ave neighs/atom = 618.965 Neighbor list builds = 0 Dangerous builds = 0 518 -2299.34151717037 eV 2.11315919778168 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:29