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 -78.590435 0) to (39.295218 78.590435 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7397509 5.7397509 4.1652847 Created 712 atoms using lattice units in orthogonal box = (0 -78.590435 0) to (39.295218 78.590435 4.1652847) create_atoms CPU = 0.000 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7397509 5.7397509 4.1652847 Created 714 atoms using lattice units in orthogonal box = (0 -78.590435 0) to (39.295218 78.590435 4.1652847) create_atoms CPU = 0.000 seconds 714 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-XXXXXXHL7BXx/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 = 7 27 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 0 atoms, new total = 1426 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 = 7 27 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) = 604.9 | 604.9 | 604.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -117721.12 0 -117721.12 29288.486 61 0 -122737.6 0 -122737.6 9864.4609 Loop time of 17.7672 on 1 procs for 61 steps with 1426 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 = -117721.120256558 -122737.500470023 -122737.599193784 Force two-norm initial, final = 4244.8067 6.0509662 Force max component initial, final = 767.57198 1.040656 Final line search alpha, max atom move = 0.13421356 0.13967015 Iterations, force evaluations = 61 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.117 | 14.117 | 14.117 | 0.0 | 79.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0089579 | 0.0089579 | 0.0089579 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.6367 | 3.6367 | 3.6367 | 0.0 | 20.47 Other | | 0.004849 | | | 0.03 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17131 ave 17131 max 17131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 484422 ave 484422 max 484422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 484422 Ave neighs/atom = 339.70687 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 604.8 | 604.8 | 604.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -122737.6 0 -122737.6 9864.4609 25726.7 69 0 -122762.12 0 -122762.12 -180.28899 25911.197 Loop time of 1.423 on 1 procs for 8 steps with 1426 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -122737.599193742 -122762.066412483 -122762.122187025 Force two-norm initial, final = 7591.3801 127.76903 Force max component initial, final = 6876.2111 88.375938 Final line search alpha, max atom move = 6.9760372e-06 0.00061651383 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1677 | 1.1677 | 1.1677 | 0.0 | 82.06 Neigh | 0.080044 | 0.080044 | 0.080044 | 0.0 | 5.63 Comm | 0.00071296 | 0.00071296 | 0.00071296 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.17247 | 0.17247 | 0.17247 | 0.0 | 12.12 Other | | 0.002067 | | | 0.15 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15752 ave 15752 max 15752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 481075 ave 481075 max 481075 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 481075 Ave neighs/atom = 337.35975 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 = 7 27 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) = 602 | 602 | 602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -122762.12 0 -122762.12 -180.28899 Loop time of 8.31e-07 on 1 procs for 0 steps with 1426 atoms 361.0% 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 | | 8.31e-07 | | |100.00 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15752 ave 15752 max 15752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 481051 ave 481051 max 481051 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 = 481051 Ave neighs/atom = 337.34292 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) = 602 | 602 | 602 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 -5323.4694 -122762.12 39.280657 158.31046 4.1667663 -180.28899 -182.67781 -236.87887 -79.056761 -232.09781 2.6647886 626.83426 Loop time of 7.31e-07 on 1 procs for 0 steps with 1426 atoms 410.4% 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 | | 7.31e-07 | | |100.00 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15752 ave 15752 max 15752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 481051 ave 481051 max 481051 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 540960 ave 540960 max 540960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 540960 Ave neighs/atom = 379.35484 Neighbor list builds = 0 Dangerous builds = 0 1426 -5323.46942157759 eV 2.66478855362275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20