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 -73.573597 0) to (42.477736 73.573597 7.2144848) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5350364 6.6027587 7.2144848 Created 1247 atoms using lattice units in orthogonal box = (0 -73.573597 0) to (42.477736 73.573597 7.2144848) create_atoms CPU = 0.001 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5350364 6.6027587 7.2144848 Created 1251 atoms using lattice units in orthogonal box = (0 -73.573597 0) to (42.477736 73.573597 7.2144848) create_atoms CPU = 0.001 seconds 1251 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-XXXXXXe8u58s/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 = 8 25 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 3 atoms, new total = 2495 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 = 8 25 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) = 646 | 646 | 646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -203460.38 0 -203460.38 28250.264 104 0 -214613.61 0 -214613.61 9904.415 Loop time of 39.4614 on 1 procs for 104 steps with 2495 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 = -203460.383135083 -214613.407564084 -214613.612429439 Force two-norm initial, final = 11901.006 8.731042 Force max component initial, final = 3350.102 1.7992975 Final line search alpha, max atom move = 0.10206267 0.1836411 Iterations, force evaluations = 104 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.147 | 29.147 | 29.147 | 0.0 | 73.86 Neigh | 0.31218 | 0.31218 | 0.31218 | 0.0 | 0.79 Comm | 0.016309 | 0.016309 | 0.016309 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 9.9744 | 9.9744 | 9.9744 | 0.0 | 25.28 Other | | 0.01172 | | | 0.03 Nlocal: 2495 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17062 ave 17062 max 17062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 773208 ave 773208 max 773208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773208 Ave neighs/atom = 309.90301 Neighbor list builds = 3 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 : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 645.9 | 645.9 | 645.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -214613.61 0 -214613.61 9904.415 45093.991 112 0 -214655.88 0 -214655.88 -36.7456 45417.561 Loop time of 2.05217 on 1 procs for 8 steps with 2495 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 = -214613.612429087 -214655.871969289 -214655.879096124 Force two-norm initial, final = 13322.633 48.376847 Force max component initial, final = 12142.756 34.365184 Final line search alpha, max atom move = 8.4282739e-06 0.00028963918 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6281 | 1.6281 | 1.6281 | 0.0 | 79.33 Neigh | 0.1023 | 0.1023 | 0.1023 | 0.0 | 4.98 Comm | 0.00087692 | 0.00087692 | 0.00087692 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.31814 | 0.31814 | 0.31814 | 0.0 | 15.50 Other | | 0.002804 | | | 0.14 Nlocal: 2495 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16923 ave 16923 max 16923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 771617 ave 771617 max 771617 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 771617 Ave neighs/atom = 309.26533 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 = 8 25 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) = 644.7 | 644.7 | 644.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -214655.88 0 -214655.88 -36.7456 Loop time of 1.252e-06 on 1 procs for 0 steps with 2495 atoms 239.6% 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 | | 1.252e-06 | | |100.00 Nlocal: 2495 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16909 ave 16909 max 16909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 771623 ave 771623 max 771623 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 = 771623 Ave neighs/atom = 309.26774 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) = 644.7 | 644.7 | 644.7 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 -9308.3598 -214655.88 42.505071 148.16234 7.2118257 -36.7456 -37.23248 -52.603541 -39.226037 -19.867861 2.6701355 1410.2171 Loop time of 9.91e-07 on 1 procs for 0 steps with 2495 atoms 504.5% 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 | | 9.91e-07 | | |100.00 Nlocal: 2495 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16909 ave 16909 max 16909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 771623 ave 771623 max 771623 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 945266 ave 945266 max 945266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 945266 Ave neighs/atom = 378.86413 Neighbor list builds = 0 Dangerous builds = 0 2495 -9308.35984395646 eV 2.67013548094765 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:51