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 -71.662268 0) to (35.831134 71.662268 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8104542 5.8104542 4.1652847 Created 592 atoms using lattice units in orthogonal box = (0 -71.662268 0) to (35.831134 71.662268 4.1652847) create_atoms CPU = 0.000 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8104542 5.8104542 4.1652847 Created 594 atoms using lattice units in orthogonal box = (0 -71.662268 0) to (35.831134 71.662268 4.1652847) create_atoms CPU = 0.000 seconds 594 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-XXXXXXi4rFQ3/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 24 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 = 1186 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 24 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) = 520 | 520 | 520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -96896.751 0 -96896.751 33248.143 80 0 -102087.73 0 -102087.73 9663.4968 Loop time of 19.7748 on 1 procs for 80 steps with 1186 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -96896.7509357681 -102087.632494348 -102087.73187887 Force two-norm initial, final = 5332.3544 5.9998187 Force max component initial, final = 1011.3369 1.3734626 Final line search alpha, max atom move = 0.086870724 0.11931369 Iterations, force evaluations = 80 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.796 | 15.796 | 15.796 | 0.0 | 79.88 Neigh | 0.163 | 0.163 | 0.163 | 0.0 | 0.82 Comm | 0.011794 | 0.011794 | 0.011794 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.7983 | 3.7983 | 3.7983 | 0.0 | 19.21 Other | | 0.006072 | | | 0.03 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14942 ave 14942 max 14942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 402903 ave 402903 max 402903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402903 Ave neighs/atom = 339.71585 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 520 | 520 | 520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -102087.73 0 -102087.73 9663.4968 21390.739 88 0 -102107.69 0 -102107.69 -201.51757 21540.991 Loop time of 1.40602 on 1 procs for 8 steps with 1186 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 = -102087.731878731 -102107.657115338 -102107.688715196 Force two-norm initial, final = 6285.8018 120.4797 Force max component initial, final = 5719.6464 93.214611 Final line search alpha, max atom move = 7.7032558e-06 0.000718056 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1656 | 1.1656 | 1.1656 | 0.0 | 82.90 Neigh | 0.080335 | 0.080335 | 0.080335 | 0.0 | 5.71 Comm | 0.00075072 | 0.00075072 | 0.00075072 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.15715 | 0.15715 | 0.15715 | 0.0 | 11.18 Other | | 0.002135 | | | 0.15 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14949 ave 14949 max 14949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 401390 ave 401390 max 401390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401390 Ave neighs/atom = 338.44013 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 = 6 25 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) = 520.1 | 520.1 | 520.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -102107.69 0 -102107.69 -201.51757 Loop time of 1.603e-06 on 1 procs for 0 steps with 1186 atoms 187.1% 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 | | 1.603e-06 | | |100.00 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14949 ave 14949 max 14949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 401374 ave 401374 max 401374 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 = 401374 Ave neighs/atom = 338.42664 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) = 520.1 | 520.1 | 520.1 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 -4427.8084 -102107.69 35.809761 144.32722 4.1678876 -201.51757 -204.18768 -79.924118 -231.80253 -300.83638 2.6617393 425.03194 Loop time of 1.583e-06 on 1 procs for 0 steps with 1186 atoms 252.7% 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 | | 1.583e-06 | | |100.00 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14949 ave 14949 max 14949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 401374 ave 401374 max 401374 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 450464 ave 450464 max 450464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450464 Ave neighs/atom = 379.81788 Neighbor list builds = 0 Dangerous builds = 0 1186 -4427.80842248847 eV 2.66173927713238 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22