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 -47.124817 0) to (5.8906022 47.124817 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8906022 5.8906022 4.1652847 Created 64 atoms using lattice units in orthogonal box = (0 -47.124817 0) to (5.8906022 47.124817 4.1652847) create_atoms CPU = 0.000 seconds 64 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8906022 5.8906022 4.1652847 Created 66 atoms using lattice units in orthogonal box = (0 -47.124817 0) to (5.8906022 47.124817 4.1652847) create_atoms CPU = 0.000 seconds 66 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-XXXXXXUhGaNk/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 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 = 128 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 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) = 175.3 | 175.3 | 175.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11066.603 0 -11066.603 -0.042698471 1 0 -11066.603 0 -11066.603 -0.042698471 Loop time of 0.0882503 on 1 procs for 1 steps with 128 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 = -11066.6031802743 -11066.6031802743 -11066.6031802741 Force two-norm initial, final = 2.4503265e-06 7.4978417e-07 Force max component initial, final = 1.0980525e-06 3.4298461e-07 Final line search alpha, max atom move = 1 3.4298461e-07 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085132 | 0.085132 | 0.085132 | 0.0 | 96.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.559e-05 | 8.559e-05 | 8.559e-05 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0029603 | 0.0029603 | 0.0029603 | 0.0 | 3.35 Other | | 7.228e-05 | | | 0.08 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378 ave 5378 max 5378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46784 ave 46784 max 46784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46784 Ave neighs/atom = 365.5 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) = 175.3 | 175.3 | 175.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -11066.603 0 -11066.603 -0.042698471 2312.5124 2 0 -11066.603 0 -11066.603 -0.0002892722 2312.5123 Loop time of 0.0885198 on 1 procs for 1 steps with 128 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 = -11066.6031802741 -11066.6031802741 -11066.6031802731 Force two-norm initial, final = 0.002494214 1.7087007e-05 Force max component initial, final = 0.0014437559 1.1716027e-05 Final line search alpha, max atom move = 0.69263785 8.1149639e-06 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085164 | 0.085164 | 0.085164 | 0.0 | 96.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.9851e-05 | 7.9851e-05 | 7.9851e-05 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0030988 | 0.0030988 | 0.0030988 | 0.0 | 3.50 Other | | 0.0001773 | | | 0.20 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378 ave 5378 max 5378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46788 ave 46788 max 46788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46788 Ave neighs/atom = 365.53125 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 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) = 175.5 | 175.5 | 175.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11066.603 0 -11066.603 -0.00028927167 Loop time of 1.202e-06 on 1 procs for 0 steps with 128 atoms 166.4% 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 | | 1.202e-06 | | |100.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378 ave 5378 max 5378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46784 ave 46784 max 46784 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 = 46784 Ave neighs/atom = 365.5 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) = 175.5 | 175.5 | 175.5 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 -479.89333 -11066.603 5.8906021 94.249634 4.1652847 -0.00028927232 -0.00029310518 -0.00025660555 -0.00035200435 -0.00027070564 2.9453011 1.1959102e-16 Loop time of 6.41e-07 on 1 procs for 0 steps with 128 atoms 312.0% 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 | | 6.41e-07 | | |100.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378 ave 5378 max 5378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46784 ave 46784 max 46784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48640 ave 48640 max 48640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48640 Ave neighs/atom = 380 Neighbor list builds = 0 Dangerous builds = 0 128 -479.893330135992 eV 2.94530105417424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00