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 -42.477736 0) to (36.786799 42.477736 7.2144848) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6027587 6.5350364 7.2144848 Created 622 atoms using lattice units in orthogonal box = (0 -42.477736 0) to (36.786799 42.477736 7.2144848) create_atoms CPU = 0.001 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6027587 6.5350364 7.2144848 Created 628 atoms using lattice units in orthogonal box = (0 -42.477736 0) to (36.786799 42.477736 7.2144848) create_atoms CPU = 0.001 seconds 628 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-XXXXXX2GIgGZ/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 15 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 0 atoms, new total = 1250 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 15 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) = 370.9 | 370.9 | 370.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -97124.062 0 -97124.062 56388.412 166 0 -107033.38 0 -107033.38 20203.604 Loop time of 31.6707 on 1 procs for 166 steps with 1250 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 = -97124.0621759667 -107033.292923289 -107033.384363813 Force two-norm initial, final = 9016.3038 5.5858992 Force max component initial, final = 2546.5795 1.6119078 Final line search alpha, max atom move = 0.056362857 0.090851732 Iterations, force evaluations = 166 290 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.727 | 23.727 | 23.727 | 0.0 | 74.92 Neigh | 0.5251 | 0.5251 | 0.5251 | 0.0 | 1.66 Comm | 0.015473 | 0.015473 | 0.015473 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 7.3933 | 7.3933 | 7.3933 | 0.0 | 23.34 Other | | 0.01008 | | | 0.03 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10233 ave 10233 max 10233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 393930 ave 393930 max 393930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 393930 Ave neighs/atom = 315.144 Neighbor list builds = 9 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 : 166 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 370.9 | 370.9 | 370.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 166 0 -107033.38 0 -107033.38 20203.604 22546.996 181 0 -107117.74 0 -107117.74 -46.938353 22881.803 Loop time of 1.7263 on 1 procs for 15 steps with 1250 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 = -107033.384363667 -107117.740731754 -107117.744550258 Force two-norm initial, final = 13459.716 41.543728 Force max component initial, final = 12203.373 19.29703 Final line search alpha, max atom move = 1.5664509e-05 0.00030227851 Iterations, force evaluations = 15 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.411 | 1.411 | 1.411 | 0.0 | 81.74 Neigh | 0.058145 | 0.058145 | 0.058145 | 0.0 | 3.37 Comm | 0.00078357 | 0.00078357 | 0.00078357 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.25369 | 0.25369 | 0.25369 | 0.0 | 14.70 Other | | 0.002647 | | | 0.15 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10126 ave 10126 max 10126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 389627 ave 389627 max 389627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389627 Ave neighs/atom = 311.7016 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 = 7 15 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) = 370.9 | 370.9 | 370.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -107117.74 0 -107117.74 -46.938353 Loop time of 9.11e-07 on 1 procs for 0 steps with 1250 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: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10131 ave 10131 max 10131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 389544 ave 389544 max 389544 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 = 389544 Ave neighs/atom = 311.6352 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) = 370.9 | 370.9 | 370.9 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 -4645.065 -107117.74 36.838326 86.126561 7.2119591 -46.938353 -47.560286 -58.029213 -59.400034 -25.25161 2.6390985 1220.5636 Loop time of 8.51e-07 on 1 procs for 0 steps with 1250 atoms 352.5% 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 | | 8.51e-07 | | |100.00 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10131 ave 10131 max 10131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 389544 ave 389544 max 389544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 472988 ave 472988 max 472988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 472988 Ave neighs/atom = 378.3904 Neighbor list builds = 0 Dangerous builds = 0 1250 -4645.0650042893 eV 2.63909846101012 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34