LAMMPS (30 Jul 2021) 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 Lattice spacing in x,y,z = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -53.104678 0.0000000) to (18.775339 53.104678 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8676804 5.9005197 5.1100000 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.104678 0.0000000) to (18.775339 53.104678 5.1100000) create_atoms CPU = 0.004 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8676804 5.9005197 5.1100000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.104678 0.0000000) to (18.775339 53.104678 5.1100000) create_atoms CPU = 0.003 seconds 434 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 38 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 866 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/MO_849011491644_001#item-citation 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:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2934.9837 0 -2934.9837 44126.14 39 0 -3053.7029 0 -3053.7029 10267.94 Loop time of 2.2339 on 1 procs for 39 steps with 866 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2934.98373421587 -3053.70022774462 -3053.70294216718 Force two-norm initial, final = 195.36359 0.15603659 Force max component initial, final = 56.613971 0.040182342 Final line search alpha, max atom move = 1.0000000 0.040182342 Iterations, force evaluations = 39 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2078 | 2.2078 | 2.2078 | 0.0 | 98.83 Neigh | 0.0095296 | 0.0095296 | 0.0095296 | 0.0 | 0.43 Comm | 0.0079808 | 0.0079808 | 0.0079808 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008622 | | | 0.39 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4084.00 ave 4084 max 4084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56456.0 ave 56456 max 56456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56456 Ave neighs/atom = 65.191686 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -3053.7029 0 -3053.7029 10267.94 10189.936 47 0 -3054.1392 0 -3054.1392 -16.836841 10262.914 Loop time of 0.316254 on 1 procs for 8 steps with 866 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 = -3053.70294216718 -3054.13684908619 -3054.13918613628 Force two-norm initial, final = 130.77971 2.1194983 Force max component initial, final = 116.82232 1.5469710 Final line search alpha, max atom move = 0.00020603863 0.00031873579 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3115 | 0.3115 | 0.3115 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095714 | 0.00095714 | 0.00095714 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003795 | | | 1.20 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4096.00 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56264.0 ave 56264 max 56264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56264 Ave neighs/atom = 64.969977 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/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 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.702 | 4.702 | 4.702 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3054.1392 0 -3054.1392 -16.836841 Loop time of 6.796e-06 on 1 procs for 0 steps with 866 atoms 161.9% 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 | | 6.796e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4096.00 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49660.0 ave 49660 max 49660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49660 Ave neighs/atom = 57.344111 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/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 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.702 | 4.702 | 4.702 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 -3054.1392 -3054.1392 18.78444 107.01792 5.1052374 -16.836841 -16.836841 -201.69866 -90.089391 241.27753 2.3267686 456.19353 Loop time of 7.026e-06 on 1 procs for 0 steps with 866 atoms 256.2% 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 | | 7.026e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4096.00 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24830.0 ave 24830 max 24830 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49660.0 ave 49660 max 49660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49660 Ave neighs/atom = 57.344111 Neighbor list builds = 0 Dangerous builds = 0 866 -3054.13918613628 eV 2.32676863997342 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02