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 -44.473071 0) to (25.67654 44.473071 7.2144848) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7569841 6.2418345 7.2144848 Created 456 atoms using lattice units in orthogonal box = (0 -44.473071 0) to (25.67654 44.473071 7.2144848) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7569841 6.2418345 7.2144848 Created 458 atoms using lattice units in orthogonal box = (0 -44.473071 0) to (25.67654 44.473071 7.2144848) create_atoms CPU = 0.000 seconds 458 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-XXXXXXTykIak/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 = 5 15 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 2 atoms, new total = 912 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 = 5 15 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) = 289.5 | 289.5 | 289.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -73284.456 0 -73284.456 39258.328 60 0 -78192.214 0 -78192.214 16235.891 Loop time of 9.04017 on 1 procs for 60 steps with 912 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 = -73284.4556597094 -78192.1377855594 -78192.2141340479 Force two-norm initial, final = 6067.681 5.032236 Force max component initial, final = 1476.3329 0.58114055 Final line search alpha, max atom move = 0.12951624 0.075267142 Iterations, force evaluations = 60 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8651 | 6.8651 | 6.8651 | 0.0 | 75.94 Neigh | 0.10043 | 0.10043 | 0.10043 | 0.0 | 1.11 Comm | 0.0048369 | 0.0048369 | 0.0048369 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.0666 | 2.0666 | 2.0666 | 0.0 | 22.86 Other | | 0.003217 | | | 0.04 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8679 ave 8679 max 8679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 290561 ave 290561 max 290561 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290561 Ave neighs/atom = 318.59759 Neighbor list builds = 2 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 290.2 | 290.2 | 290.2 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -78192.214 0 -78192.214 16235.891 16476.651 72 0 -78231.66 0 -78231.66 -25.768915 16679.402 Loop time of 1.06342 on 1 procs for 12 steps with 912 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 = -78192.2141339922 -78231.650602595 -78231.6599262299 Force two-norm initial, final = 7794.275 23.32884 Force max component initial, final = 7047.3362 10.89089 Final line search alpha, max atom move = 1.7336287e-05 0.00018880759 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86837 | 0.86837 | 0.86837 | 0.0 | 81.66 Neigh | 0.04909 | 0.04909 | 0.04909 | 0.0 | 4.62 Comm | 0.00055778 | 0.00055778 | 0.00055778 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.14369 | 0.14369 | 0.14369 | 0.0 | 13.51 Other | | 0.001716 | | | 0.16 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8677 ave 8677 max 8677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288795 ave 288795 max 288795 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288795 Ave neighs/atom = 316.66118 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 = 5 15 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) = 290.3 | 290.3 | 290.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -78231.66 0 -78231.66 -25.768915 Loop time of 8.61e-07 on 1 procs for 0 steps with 912 atoms 232.3% 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 | | 8.61e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8689 ave 8689 max 8689 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288822 ave 288822 max 288822 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 = 288822 Ave neighs/atom = 316.69079 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) = 290.3 | 290.3 | 290.3 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 -3392.4458 -78231.66 25.693541 89.937143 7.2180095 -25.768915 -26.110353 -13.004326 -19.939291 -45.387443 2.7339136 801.15872 Loop time of 9.62e-07 on 1 procs for 0 steps with 912 atoms 415.8% 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 | | 9.62e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8689 ave 8689 max 8689 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288822 ave 288822 max 288822 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 345168 ave 345168 max 345168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 345168 Ave neighs/atom = 378.47368 Neighbor list builds = 0 Dangerous builds = 0 912 -3392.4458293491 eV 2.73391364654972 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10