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 -46.569299 0) to (9.3138598 46.569299 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5883159 5.5883159 4.1652847 Created 100 atoms using lattice units in orthogonal box = (0 -46.569299 0) to (9.3138598 46.569299 4.1652847) create_atoms CPU = 0.000 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5883159 5.5883159 4.1652847 Created 102 atoms using lattice units in orthogonal box = (0 -46.569299 0) to (9.3138598 46.569299 4.1652847) create_atoms CPU = 0.000 seconds 102 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-XXXXXXII65th/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 = 2 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 = 200 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 = 2 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) = 181.2 | 181.2 | 181.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16495.393 0 -16495.393 27722.364 22 0 -17157.111 0 -17157.111 15667.257 Loop time of 1.39986 on 1 procs for 22 steps with 200 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 = -16495.3934058808 -17157.0961239571 -17157.1106956356 Force two-norm initial, final = 1712.3128 2.4085263 Force max component initial, final = 605.36889 0.42341787 Final line search alpha, max atom move = 0.12824605 0.054301669 Iterations, force evaluations = 22 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2403 | 1.2403 | 1.2403 | 0.0 | 88.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012029 | 0.0012029 | 0.0012029 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.15785 | 0.15785 | 0.15785 | 0.0 | 11.28 Other | | 0.0005533 | | | 0.04 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5489 ave 5489 max 5489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72058 ave 72058 max 72058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72058 Ave neighs/atom = 360.29 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 181.2 | 181.2 | 181.2 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -17157.111 0 -17157.111 15667.257 3613.3006 36 0 -17166.534 0 -17166.534 -80.346711 3653.627 Loop time of 0.57545 on 1 procs for 14 steps with 200 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 = -17157.1106956373 -17166.5285979782 -17166.5338317212 Force two-norm initial, final = 1704.8079 13.502568 Force max component initial, final = 1572.5807 6.9708459 Final line search alpha, max atom move = 4.4425325e-05 0.00030968209 Iterations, force evaluations = 14 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50288 | 0.50288 | 0.50288 | 0.0 | 87.39 Neigh | 0.029837 | 0.029837 | 0.029837 | 0.0 | 5.18 Comm | 0.00043367 | 0.00043367 | 0.00043367 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.041036 | 0.041036 | 0.041036 | 0.0 | 7.13 Other | | 0.001266 | | | 0.22 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5489 ave 5489 max 5489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71323 ave 71323 max 71323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71323 Ave neighs/atom = 356.615 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 = 2 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) = 181.4 | 181.4 | 181.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17166.534 0 -17166.534 -80.346712 Loop time of 9.52e-07 on 1 procs for 0 steps with 200 atoms 210.1% 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 | | 9.52e-07 | | |100.00 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5489 ave 5489 max 5489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71315 ave 71315 max 71315 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 = 71315 Ave neighs/atom = 356.575 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) = 181.4 | 181.4 | 181.4 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 -744.41136 -17166.534 9.311272 94.332701 4.159613 -80.346712 -81.411306 -132.51996 -95.008522 -16.705432 2.7023656 169.25693 Loop time of 6.52e-07 on 1 procs for 0 steps with 200 atoms 613.5% 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 | | 6.52e-07 | | |100.00 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5489 ave 5489 max 5489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71315 ave 71315 max 71315 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75688 ave 75688 max 75688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75688 Ave neighs/atom = 378.44 Neighbor list builds = 0 Dangerous builds = 0 200 -744.411356687425 eV 2.70236563676406 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02