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 -51.014111 0) to (5.8906022 51.014111 7.2144848) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8906022 6.8018815 7.2144848 Created 120 atoms using lattice units in orthogonal box = (0 -51.014111 0) to (5.8906022 51.014111 7.2144848) create_atoms CPU = 0.000 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8906022 6.8018815 7.2144848 Created 122 atoms using lattice units in orthogonal box = (0 -51.014111 0) to (5.8906022 51.014111 7.2144848) create_atoms CPU = 0.000 seconds 122 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-XXXXXXWnEdKE/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 = 1 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 2 atoms, new total = 240 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 = 1 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) = 199.2 | 199.2 | 199.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20749.881 0 -20749.881 -0.042688965 1 0 -20749.881 0 -20749.881 -0.042688965 Loop time of 0.106743 on 1 procs for 1 steps with 240 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 = -20749.8809630343 -20749.8809630343 -20749.8809630333 Force two-norm initial, final = 3.4541242e-06 1.2040433e-06 Force max component initial, final = 1.099318e-06 4.0444665e-07 Final line search alpha, max atom move = 1 4.0444665e-07 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10097 | 0.10097 | 0.10097 | 0.0 | 94.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.9599e-05 | 8.9599e-05 | 8.9599e-05 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0056039 | 0.0056039 | 0.0056039 | 0.0 | 5.25 Other | | 7.756e-05 | | | 0.07 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6020 ave 6020 max 6020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85468 ave 85468 max 85468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85468 Ave neighs/atom = 356.11667 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 199.2 | 199.2 | 199.2 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -20749.881 0 -20749.881 -0.042688965 4335.9607 2 0 -20749.881 0 -20749.881 -0.00028927409 4335.9606 Loop time of 0.108206 on 1 procs for 1 steps with 240 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20749.8809630332 -20749.8809630332 -20749.8809630353 Force two-norm initial, final = 0.0046756083 3.2009635e-05 Force max component initial, final = 0.0027059089 2.1882283e-05 Final line search alpha, max atom move = 0.3695616 8.0868514e-06 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10224 | 0.10224 | 0.10224 | 0.0 | 94.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.5211e-05 | 7.5211e-05 | 7.5211e-05 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0056991 | 0.0056991 | 0.0056991 | 0.0 | 5.27 Other | | 0.0001947 | | | 0.18 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6020 ave 6020 max 6020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85437 ave 85437 max 85437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85437 Ave neighs/atom = 355.9875 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 = 1 18 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) = 199.4 | 199.4 | 199.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20749.881 0 -20749.881 -0.00028927371 Loop time of 1.072e-06 on 1 procs for 0 steps with 240 atoms 279.9% 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 | | 1.072e-06 | | |100.00 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6020 ave 6020 max 6020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85430 ave 85430 max 85430 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 = 85430 Ave neighs/atom = 355.95833 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) = 199.4 | 199.4 | 199.4 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 -899.79999 -20749.881 5.8906021 102.02822 7.2144847 -0.00028927408 -0.00029310696 -0.00026495484 -0.00035063709 -0.00026372895 2.9453011 4.3832525e-16 Loop time of 7.62e-07 on 1 procs for 0 steps with 240 atoms 393.7% 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 | | 7.62e-07 | | |100.00 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6020 ave 6020 max 6020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85430 ave 85430 max 85430 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91200 ave 91200 max 91200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91200 Ave neighs/atom = 380 Neighbor list builds = 0 Dangerous builds = 0 240 -899.799994005993 eV 2.94530105387129 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00