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 -50.672876 0) to (25.336438 50.672876 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7933801 4.7933801 4.1652847 Created 296 atoms using lattice units in orthogonal box = (0 -50.672876 0) to (25.336438 50.672876 4.1652847) create_atoms CPU = 0.000 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7933801 4.7933801 4.1652847 Created 298 atoms using lattice units in orthogonal box = (0 -50.672876 0) to (25.336438 50.672876 4.1652847) create_atoms CPU = 0.000 seconds 298 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-XXXXXXNSOvtA/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 = 5 17 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 = 588 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 = 5 17 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) = 294.5 | 294.5 | 294.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -47267.461 0 -47267.461 29222.088 66 0 -50497.957 0 -50497.957 4054.5931 Loop time of 9.44486 on 1 procs for 66 steps with 588 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -47267.4607730439 -50497.9085348099 -50497.9566902808 Force two-norm initial, final = 5968.6722 3.6977177 Force max component initial, final = 2028.9019 0.70549614 Final line search alpha, max atom move = 0.12811763 0.090386491 Iterations, force evaluations = 66 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7111 | 7.7111 | 7.7111 | 0.0 | 81.64 Neigh | 0.042342 | 0.042342 | 0.042342 | 0.0 | 0.45 Comm | 0.0063032 | 0.0063032 | 0.0063032 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.6817 | 1.6817 | 1.6817 | 0.0 | 17.81 Other | | 0.00346 | | | 0.04 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8571 ave 8571 max 8571 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 200897 ave 200897 max 200897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200897 Ave neighs/atom = 341.66156 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 294.5 | 294.5 | 294.5 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -50497.957 0 -50497.957 4054.5931 10695.37 68 0 -50498.897 0 -50498.897 -141.03471 10728.052 Loop time of 0.264821 on 1 procs for 2 steps with 588 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -50497.9566902574 -50498.8863721508 -50498.8973495618 Force two-norm initial, final = 1098.13 56.513231 Force max component initial, final = 690.58155 50.534937 Final line search alpha, max atom move = 1.1477849e-05 0.00058003237 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23187 | 0.23187 | 0.23187 | 0.0 | 87.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013867 | 0.00013867 | 0.00013867 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.032366 | 0.032366 | 0.032366 | 0.0 | 12.22 Other | | 0.0004441 | | | 0.17 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8564 ave 8564 max 8564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 201337 ave 201337 max 201337 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201337 Ave neighs/atom = 342.40986 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 = 5 17 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) = 294.7 | 294.7 | 294.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -50498.897 0 -50498.897 -141.03471 Loop time of 1.152e-06 on 1 procs for 0 steps with 588 atoms 260.4% 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 | | 1.152e-06 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8564 ave 8564 max 8564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 201147 ave 201147 max 201147 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 = 201147 Ave neighs/atom = 342.08673 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) = 294.7 | 294.7 | 294.7 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 -2189.8394 -50498.897 25.361799 101.46827 4.1687952 -141.03471 -142.90342 -152.9613 51.800927 -327.54989 2.7634265 337.00305 Loop time of 1.493e-06 on 1 procs for 0 steps with 588 atoms 334.9% 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 | | 1.493e-06 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8564 ave 8564 max 8564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 201147 ave 201147 max 201147 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223256 ave 223256 max 223256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223256 Ave neighs/atom = 379.68707 Neighbor list builds = 0 Dangerous builds = 0 588 -2189.8394315324 eV 2.76342645719811 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10