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 -83.513699 0) to (48.216657 83.513699 7.2144848) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4768643 6.6478567 7.2144848 Created 1608 atoms using lattice units in orthogonal box = (0 -83.513699 0) to (48.216657 83.513699 7.2144848) create_atoms CPU = 0.002 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4768643 6.6478567 7.2144848 Created 1610 atoms using lattice units in orthogonal box = (0 -83.513699 0) to (48.216657 83.513699 7.2144848) create_atoms CPU = 0.001 seconds 1610 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-XXXXXXKWRWFZ/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 = 9 28 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 = 3216 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 = 9 28 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) = 722.8 | 722.8 | 722.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -262862.13 0 -262862.13 25921.134 204 0 -276827.83 0 -276827.83 8749.8647 Loop time of 100.579 on 1 procs for 204 steps with 3216 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 = -262862.132198412 -276827.564777027 -276827.829510666 Force two-norm initial, final = 13041.638 9.6943628 Force max component initial, final = 2570.6032 0.83340754 Final line search alpha, max atom move = 0.082785167 0.068993782 Iterations, force evaluations = 204 395 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 73.405 | 73.405 | 73.405 | 0.0 | 72.98 Neigh | 0.37727 | 0.37727 | 0.37727 | 0.0 | 0.38 Comm | 0.036627 | 0.036627 | 0.036627 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 26.734 | 26.734 | 26.734 | 0.0 | 26.58 Other | | 0.02675 | | | 0.03 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20394 ave 20394 max 20394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 992421 ave 992421 max 992421 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 992421 Ave neighs/atom = 308.58862 Neighbor list builds = 3 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 : 204 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 725 | 725 | 725 Mbytes Step Temp E_pair E_mol TotEng Press Volume 204 0 -276827.83 0 -276827.83 8749.8647 58101.873 211 0 -276870.37 0 -276870.37 63.184986 58463.855 Loop time of 2.1388 on 1 procs for 7 steps with 3216 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -276827.829510417 -276870.351965346 -276870.371833346 Force two-norm initial, final = 15179.957 108.77294 Force max component initial, final = 13828.276 89.835308 Final line search alpha, max atom move = 3.7988318e-06 0.00034126923 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6719 | 1.6719 | 1.6719 | 0.0 | 78.17 Neigh | 0.12575 | 0.12575 | 0.12575 | 0.0 | 5.88 Comm | 0.00088058 | 0.00088058 | 0.00088058 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.33753 | 0.33753 | 0.33753 | 0.0 | 15.78 Other | | 0.002686 | | | 0.13 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20430 ave 20430 max 20430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 991049 ave 991049 max 991049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 991049 Ave neighs/atom = 308.162 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 = 9 29 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) = 724.5 | 724.5 | 724.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -276870.37 0 -276870.37 63.184986 Loop time of 9.11e-07 on 1 procs for 0 steps with 3216 atoms 329.3% 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 | | 9.11e-07 | | |100.00 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20430 ave 20430 max 20430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 991056 ave 991056 max 991056 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 = 991056 Ave neighs/atom = 308.16418 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) = 724.5 | 724.5 | 724.5 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 -12006.236 -276870.37 48.245082 168.03473 7.2116618 63.184986 64.022187 16.963581 107.40182 67.701156 2.6664272 1537.6473 Loop time of 9.22e-07 on 1 procs for 0 steps with 3216 atoms 542.3% 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 | | 9.22e-07 | | |100.00 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20430 ave 20430 max 20430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 991056 ave 991056 max 991056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.21933e+06 ave 1.21933e+06 max 1.21933e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1219328 Ave neighs/atom = 379.14428 Neighbor list builds = 0 Dangerous builds = 0 3216 -12006.2355711432 eV 2.66642723419949 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:44