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 -76.804056 0) to (38.402028 76.804056 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8732513 5.8732513 4.1652847 Created 679 atoms using lattice units in orthogonal box = (0 -76.804056 0) to (38.402028 76.804056 4.1652847) create_atoms CPU = 0.001 seconds 679 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8732513 5.8732513 4.1652847 Created 681 atoms using lattice units in orthogonal box = (0 -76.804056 0) to (38.402028 76.804056 4.1652847) create_atoms CPU = 0.000 seconds 681 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-XXXXXXJzLYhe/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 26 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 = 1360 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 26 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) = 582.5 | 582.5 | 582.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -112677.05 0 -112677.05 27005.547 93 0 -117255.48 0 -117255.48 4423.4998 Loop time of 24.459 on 1 procs for 93 steps with 1360 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 = -112677.048416125 -117255.365568174 -117255.482229595 Force two-norm initial, final = 4191.0347 6.0934375 Force max component initial, final = 1073.1974 0.90224691 Final line search alpha, max atom move = 0.072513231 0.065424839 Iterations, force evaluations = 93 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.514 | 19.514 | 19.514 | 0.0 | 79.78 Neigh | 0.15531 | 0.15531 | 0.15531 | 0.0 | 0.63 Comm | 0.012697 | 0.012697 | 0.012697 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 4.7708 | 4.7708 | 4.7708 | 0.0 | 19.51 Other | | 0.006503 | | | 0.03 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15208 ave 15208 max 15208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 461598 ave 461598 max 461598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461598 Ave neighs/atom = 339.41029 Neighbor list builds = 2 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 : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 582.4 | 582.4 | 582.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -117255.48 0 -117255.48 4423.4998 24570.444 97 0 -117260.39 0 -117260.39 74.041548 24647.176 Loop time of 0.772146 on 1 procs for 4 steps with 1360 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 = -117255.482229352 -117260.356858377 -117260.386540143 Force two-norm initial, final = 3344.9542 91.403422 Force max component initial, final = 3031.2565 64.285683 Final line search alpha, max atom move = 4.4872252e-06 0.00028846434 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66907 | 0.66907 | 0.66907 | 0.0 | 86.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033392 | 0.00033392 | 0.00033392 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.10166 | 0.10166 | 0.10166 | 0.0 | 13.17 Other | | 0.001082 | | | 0.14 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15208 ave 15208 max 15208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 461192 ave 461192 max 461192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461192 Ave neighs/atom = 339.11176 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 = 7 26 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) = 579.6 | 579.6 | 579.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -117260.39 0 -117260.39 74.041549 Loop time of 7.31e-07 on 1 procs for 0 steps with 1360 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: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15215 ave 15215 max 15215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 460673 ave 460673 max 460673 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 = 460673 Ave neighs/atom = 338.73015 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) = 579.6 | 579.6 | 579.6 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 -5084.8916 -117260.39 38.383724 154.0719 4.1677018 74.041549 75.022599 181.12599 149.04829 -105.10648 2.6779367 202.48289 Loop time of 7.02e-07 on 1 procs for 0 steps with 1360 atoms 427.4% 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 | | 7.02e-07 | | |100.00 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15215 ave 15215 max 15215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 460673 ave 460673 max 460673 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 517812 ave 517812 max 517812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517812 Ave neighs/atom = 380.74412 Neighbor list builds = 0 Dangerous builds = 0 1360 -5084.89158538016 eV 2.67793665002813 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26