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 -67.163198 0) to (33.581599 67.163198 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6497599 4.6497599 4.1652847 Created 520 atoms using lattice units in orthogonal box = (0 -67.163198 0) to (33.581599 67.163198 4.1652847) create_atoms CPU = 0.000 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6497599 4.6497599 4.1652847 Created 522 atoms using lattice units in orthogonal box = (0 -67.163198 0) to (33.581599 67.163198 4.1652847) create_atoms CPU = 0.000 seconds 522 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-XXXXXXRaBM9u/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 = 6 23 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 6 atoms, new total = 1036 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 = 6 23 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) = 435.2 | 435.2 | 435.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -79370.784 0 -79370.784 38726.925 78 0 -89152.67 0 -89152.67 3663.2179 Loop time of 17.0605 on 1 procs for 78 steps with 1036 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 = -79370.7843222854 -89152.5943107893 -89152.6700086662 Force two-norm initial, final = 15029.544 5.3449459 Force max component initial, final = 4977.1689 0.81353499 Final line search alpha, max atom move = 0.11858751 0.096475085 Iterations, force evaluations = 78 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.556 | 13.556 | 13.556 | 0.0 | 79.46 Neigh | 0.065654 | 0.065654 | 0.065654 | 0.0 | 0.38 Comm | 0.0097412 | 0.0097412 | 0.0097412 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.4238 | 3.4238 | 3.4238 | 0.0 | 20.07 Other | | 0.005012 | | | 0.03 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12536 ave 12536 max 12536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 351715 ave 351715 max 351715 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 351715 Ave neighs/atom = 339.49324 Neighbor list builds = 1 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 435.2 | 435.2 | 435.2 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -89152.67 0 -89152.67 3663.2179 18789.163 80 0 -89154.008 0 -89154.008 0.12365103 18838.937 Loop time of 0.536743 on 1 procs for 2 steps with 1036 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 = -89152.6700085274 -89153.9992375906 -89154.0079969424 Force two-norm initial, final = 1740.4343 6.7571098 Force max component initial, final = 1060.0338 2.9502396 Final line search alpha, max atom move = 1.9684871e-05 5.8075086e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46468 | 0.46468 | 0.46468 | 0.0 | 86.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024028 | 0.00024028 | 0.00024028 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.07108 | 0.07108 | 0.07108 | 0.0 | 13.24 Other | | 0.0007461 | | | 0.14 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12604 ave 12604 max 12604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 352096 ave 352096 max 352096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 352096 Ave neighs/atom = 339.861 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 = 6 23 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) = 435.4 | 435.4 | 435.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -89154.008 0 -89154.008 0.12365149 Loop time of 1.312e-06 on 1 procs for 0 steps with 1036 atoms 228.7% 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 | | 1.312e-06 | | |100.00 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12583 ave 12583 max 12583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 351867 ave 351867 max 351867 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 = 351867 Ave neighs/atom = 339.63996 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) = 435.4 | 435.4 | 435.4 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 -3866.0837 -89154.008 33.618938 134.44736 4.1679273 0.12365157 0.12528996 -10.892416 4.3051506 6.963135 2.7534019 354.39012 Loop time of 1.202e-06 on 1 procs for 0 steps with 1036 atoms 332.8% 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: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12583 ave 12583 max 12583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 351867 ave 351867 max 351867 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 394024 ave 394024 max 394024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 394024 Ave neighs/atom = 380.33205 Neighbor list builds = 0 Dangerous builds = 0 1036 -3866.08366594317 eV 2.75340187472077 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18