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 -45.054443 0) to (15.018148 45.054443 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7762107 5.7762107 4.1652847 Created 156 atoms using lattice units in orthogonal box = (0 -45.054443 0) to (15.018148 45.054443 4.1652847) create_atoms CPU = 0.000 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7762107 5.7762107 4.1652847 Created 158 atoms using lattice units in orthogonal box = (0 -45.054443 0) to (15.018148 45.054443 4.1652847) create_atoms CPU = 0.000 seconds 158 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-XXXXXXomJoI7/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 = 3 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: 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 = 312 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 = 3 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: 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) = 226.6 | 226.6 | 226.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -25605.14 0 -25605.14 30870.265 19 0 -26778.194 0 -26778.194 12298.69 Loop time of 1.65547 on 1 procs for 19 steps with 312 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 = -25605.1397350119 -26778.1753577816 -26778.1939590289 Force two-norm initial, final = 2510.7551 2.2460957 Force max component initial, final = 880.66674 0.35935432 Final line search alpha, max atom move = 0.23738481 0.085305256 Iterations, force evaluations = 19 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4062 | 1.4062 | 1.4062 | 0.0 | 84.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001181 | 0.001181 | 0.001181 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.24728 | 0.24728 | 0.24728 | 0.0 | 14.94 Other | | 0.0007679 | | | 0.05 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6793 ave 6793 max 6793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109754 ave 109754 max 109754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109754 Ave neighs/atom = 351.77564 Neighbor list builds = 0 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 226.6 | 226.6 | 226.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -26778.194 0 -26778.194 12298.69 5636.7489 29 0 -26787.379 0 -26787.379 15.508471 5686.3124 Loop time of 0.524226 on 1 procs for 10 steps with 312 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -26778.1939590492 -26787.3586156186 -26787.3791489437 Force two-norm initial, final = 2149.605 17.383271 Force max component initial, final = 1974.2969 12.690588 Final line search alpha, max atom move = 2.1896024e-05 0.00027787341 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47734 | 0.47734 | 0.47734 | 0.0 | 91.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032532 | 0.00032532 | 0.00032532 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.045532 | 0.045532 | 0.045532 | 0.0 | 8.69 Other | | 0.001033 | | | 0.20 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6793 ave 6793 max 6793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109000 ave 109000 max 109000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109000 Ave neighs/atom = 349.35897 Neighbor list builds = 0 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 = 3 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: 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) = 226.7 | 226.7 | 226.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -26787.379 0 -26787.379 15.508471 Loop time of 1.032e-06 on 1 procs for 0 steps with 312 atoms 290.7% 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 | | 1.032e-06 | | |100.00 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6793 ave 6793 max 6793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108622 ave 108622 max 108622 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 = 108622 Ave neighs/atom = 348.14744 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) = 226.7 | 226.7 | 226.7 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 -1161.6107 -26787.379 15.000626 90.956869 4.1675982 15.508471 15.713958 154.87622 -100.03882 -7.6955298 2.6799344 214.27335 Loop time of 7.81e-07 on 1 procs for 0 steps with 312 atoms 512.2% 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 | | 7.81e-07 | | |100.00 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6793 ave 6793 max 6793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108622 ave 108622 max 108622 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118336 ave 118336 max 118336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118336 Ave neighs/atom = 379.28205 Neighbor list builds = 0 Dangerous builds = 0 312 -1161.61069263699 eV 2.67993437575233 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02