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 -68.4564 0) to (34.2264 68.4564 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.99936 4.99936 3.62799 Created 714 atoms create_atoms CPU = 0.000267029 secs 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.99936 4.99936 3.62799 Created 714 atoms create_atoms CPU = 0.000166893 secs 714 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXTccCq8/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 = 6 23 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 1 atoms, new total = 1427 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 = 6 23 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) = 941.9 | 941.9 | 941.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -140839.81 0 -140839.81 5429.8119 243 0 -142722.07 0 -142722.07 -46393.065 Loop time of 205.326 on 1 procs for 243 steps with 1427 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 = -140839.814293 -142721.928813 -142722.065352 Force two-norm initial, final = 585.222 6.38496 Force max component initial, final = 107.627 0.85424 Final line search alpha, max atom move = 0.0531322 0.0453876 Iterations, force evaluations = 243 427 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 183.35 | 183.35 | 183.35 | 0.0 | 89.30 Neigh | 1.2147 | 1.2147 | 1.2147 | 0.0 | 0.59 Comm | 0.063066 | 0.063066 | 0.063066 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 20.683 | 20.683 | 20.683 | 0.0 | 10.07 Other | | 0.01854 | | | 0.01 Nlocal: 1427 ave 1427 max 1427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21373 ave 21373 max 21373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 778311 ave 778311 max 778311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 778311 Ave neighs/atom = 545.418 Neighbor list builds = 8 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 : 243 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 941.8 | 941.8 | 941.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 243 0 -142722.06 0 -142722.06 -46393.061 17000.854 317 0 -143657.49 0 -143657.49 -39195.202 17000.959 Loop time of 33.5709 on 1 procs for 74 steps with 1427 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 = -142722.062405 -143657.443496 -143657.490027 Force two-norm initial, final = 21989.5 125.171 Force max component initial, final = 21244.8 32.6652 Final line search alpha, max atom move = 3.75849e-06 0.000122772 Iterations, force evaluations = 74 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.915 | 30.915 | 30.915 | 0.0 | 92.09 Neigh | 0.20172 | 0.20172 | 0.20172 | 0.0 | 0.60 Comm | 0.0094736 | 0.0094736 | 0.0094736 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.4192 | 2.4192 | 2.4192 | 0.0 | 7.21 Other | | 0.02545 | | | 0.08 Nlocal: 1427 ave 1427 max 1427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19006 ave 19006 max 19006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 782803 ave 782803 max 782803 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 782803 Ave neighs/atom = 548.566 Neighbor list builds = 2 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 = 6 23 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) = 936 | 936 | 936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -143657.49 0 -143657.49 -39195.194 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1427 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: 1427 ave 1427 max 1427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19006 ave 19006 max 19006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 782800 ave 782800 max 782800 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 = 782800 Ave neighs/atom = 548.563 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) = 936 | 936 | 936 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 -6229.5782 -143657.49 32.213948 136.91276 3.8546553 -39195.175 -39714.511 106.31691 -119108.06 -141.79142 2.1800562 671.45377 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1427 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: 1427 ave 1427 max 1427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19006 ave 19006 max 19006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 782800 ave 782800 max 782800 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 865532 ave 865532 max 865532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 865532 Ave neighs/atom = 606.54 Neighbor list builds = 0 Dangerous builds = 0 1427 -6229.57816270467 eV 2.18005617387348 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:04:02