LAMMPS (23 Jun 2022) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_001 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.1652847 4.1652847 4.1652847 Created orthogonal box = (0 -53.988261 0) to (31.170137 53.988261 7.2144848) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.679315 6.4271739 7.2144848 Created 672 atoms using lattice units in orthogonal box = (0 -53.988261 0) to (31.170137 53.988261 7.2144848) create_atoms CPU = 0.001 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.679315 6.4271739 7.2144848 Created 676 atoms using lattice units in orthogonal box = (0 -53.988261 0) to (31.170137 53.988261 7.2144848) create_atoms CPU = 0.001 seconds 676 atoms in group lower Displacing atoms ... WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:98) Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXX8vn1ql/ffield.reax.AuO 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 18 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: full/ghost/bin/3d bin: standard (3) fix qeq/reax, perpetual, copy from (2) attributes: half, newton off pair build: copy stencil: none bin: none Deleted 4 atoms, new total = 1344 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_974345878378_001#item-citation - pair reaxff command: - fix qeq/reaxff command: The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) 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 18 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: full/ghost/bin/3d bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off 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) = 376.4 | 376.4 | 376.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -111341.37 0 -111341.37 28544.692 66 0 -115381.2 0 -115381.2 13933.731 Loop time of 15.6061 on 1 procs for 66 steps with 1344 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -111341.370041927 -115381.108611843 -115381.199906239 Force two-norm initial, final = 3725.0209 5.3197393 Force max component initial, final = 496.51634 0.82072595 Final line search alpha, max atom move = 0.16773826 0.13766714 Iterations, force evaluations = 66 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.091 | 12.091 | 12.091 | 0.0 | 77.48 Neigh | 0.06775 | 0.06775 | 0.06775 | 0.0 | 0.43 Comm | 0.0083287 | 0.0083287 | 0.0083287 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.4333 | 3.4333 | 3.4333 | 0.0 | 22.00 Other | | 0.005792 | | | 0.04 Nlocal: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11083 ave 11083 max 11083 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 423031 ave 423031 max 423031 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423031 Ave neighs/atom = 314.75521 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : real Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 377.1 | 377.1 | 377.1 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -115381.2 0 -115381.2 13933.731 24281.38 77 0 -115425.4 0 -115425.4 -27.38693 24524.364 Loop time of 1.50378 on 1 procs for 11 steps with 1344 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 = -115381.199906212 -115425.401152715 -115425.404016163 Force two-norm initial, final = 10036.893 30.629687 Force max component initial, final = 9190.6261 17.715302 Final line search alpha, max atom move = 1.5348458e-05 0.00027190256 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2199 | 1.2199 | 1.2199 | 0.0 | 81.12 Neigh | 0.064555 | 0.064555 | 0.064555 | 0.0 | 4.29 Comm | 0.00072797 | 0.00072797 | 0.00072797 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.21625 | 0.21625 | 0.21625 | 0.0 | 14.38 Other | | 0.002362 | | | 0.16 Nlocal: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11001 ave 11001 max 11001 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 421291 ave 421291 max 421291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421291 Ave neighs/atom = 313.46057 Neighbor list builds = 1 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 19 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: full/ghost/bin/3d 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 bin: standard (4) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off 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) = 377.2 | 377.2 | 377.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -115425.4 0 -115425.4 -27.38693 Loop time of 1.303e-06 on 1 procs for 0 steps with 1344 atoms 153.5% 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 | | 1.303e-06 | | |100.00 Nlocal: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10980 ave 10980 max 10980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 421292 ave 421292 max 421292 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 = 421292 Ave neighs/atom = 313.46131 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 377.2 | 377.2 | 377.2 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 -5005.3192 -115425.4 31.181501 109.02369 7.2140617 -27.386931 -27.749808 -50.205332 -41.383078 8.3389845 2.7429688 1017.0884 Loop time of 1.412e-06 on 1 procs for 0 steps with 1344 atoms 212.5% 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 | | 1.412e-06 | | |100.00 Nlocal: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10980 ave 10980 max 10980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 421292 ave 421292 max 421292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 508816 ave 508816 max 508816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508816 Ave neighs/atom = 378.58333 Neighbor list builds = 0 Dangerous builds = 0 1344 -5005.31921249743 eV 2.74296884584003 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17