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 = 3.62799 3.62799 3.62799 Created orthogonal box = (0 -72.7446 0) to (41.997 72.7446 6.28386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.64139 5.79032 6.28386 Created 1610 atoms create_atoms CPU = 0.00268197 secs 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.64139 5.79032 6.28386 Created 1610 atoms create_atoms CPU = 0.00149107 secs 1610 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXoUFOKU/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 = 7 25 2 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 36 atoms, new total = 3184 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 = 7 25 2 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) = 1211 | 1211 | 1211 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -316188.63 0 -316188.63 -2620.2179 1135 0 -326547.59 0 -326547.59 -79625.45 Loop time of 1634.62 on 1 procs for 1135 steps with 3184 atoms 68.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -316188.631705 -326547.288156 -326547.586849 Force two-norm initial, final = 416.472 8.11431 Force max component initial, final = 65.7258 0.504446 Final line search alpha, max atom move = 0.0865858 0.0436779 Iterations, force evaluations = 1135 1811 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1341.4 | 1341.4 | 1341.4 | 0.0 | 82.06 Neigh | 19.752 | 19.752 | 19.752 | 0.0 | 1.21 Comm | 1.2956 | 1.2956 | 1.2956 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 271.44 | 271.44 | 271.44 | 0.0 | 16.61 Other | | 0.6818 | | | 0.04 Nlocal: 3184 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24948 ave 24948 max 24948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.58096e+06 ave 1.58096e+06 max 1.58096e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1580955 Ave neighs/atom = 496.531 Neighbor list builds = 55 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 : 1135 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 1210 | 1210 | 1210 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1135 0 -326547.59 0 -326547.59 -79625.45 38395.068 1192 0 -328653.61 0 -328653.61 -2691.7351 36488.993 Loop time of 51.3761 on 1 procs for 57 steps with 3184 atoms 63.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -326547.586849 -328653.607265 -328653.609268 Force two-norm initial, final = 76413.4 88.5472 Force max component initial, final = 72569.8 60.2411 Final line search alpha, max atom move = 0.000107199 0.00645776 Iterations, force evaluations = 57 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.51 | 43.51 | 43.51 | 0.0 | 84.69 Neigh | 0.67601 | 0.67601 | 0.67601 | 0.0 | 1.32 Comm | 0.031021 | 0.031021 | 0.031021 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 7.0796 | 7.0796 | 7.0796 | 0.0 | 13.78 Other | | 0.07952 | | | 0.15 Nlocal: 3184 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24864 ave 24864 max 24864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.65815e+06 ave 1.65815e+06 max 1.65815e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1658146 Ave neighs/atom = 520.774 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 = 7 25 2 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) = 1211 | 1211 | 1211 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -328653.61 0 -328653.61 -2691.7351 Loop time of 2.86102e-06 on 1 procs for 0 steps with 3184 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 | | 2.861e-06 | | |100.00 Nlocal: 3184 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24762 ave 24762 max 24762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.65791e+06 ave 1.65791e+06 max 1.65791e+06 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 = 1657907 Ave neighs/atom = 520.699 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) = 1211 | 1211 | 1211 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 -14251.769 -328653.61 39.650179 145.48915 6.325373 -2691.7351 -2727.4006 108.29254 -8398.2462 107.752 2.408446 822.71866 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3184 atoms 209.7% 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 | | 1.907e-06 | | |100.00 Nlocal: 3184 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24762 ave 24762 max 24762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.65791e+06 ave 1.65791e+06 max 1.65791e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.97219e+06 ave 1.97219e+06 max 1.97219e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1972188 Ave neighs/atom = 619.406 Neighbor list builds = 0 Dangerous builds = 0 3184 -14251.7692595873 eV 2.40844595912302 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:28:13